MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'BMC Medical Genomics' source. Thu, 09 Feb 2012 09:43:29 +0100 http://www.medworm.com/index.php?rid=5642466&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F5%2F6 Conclusion: Gene expression profiling and a supervised method requiring 10-marker classifiers enable the identification of favorable cytogenetic risk acute myeloid leukemia even when samples contain low leukemic blast loads or display poor quality control criterion. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5642466 Mon, 30 Jan 2012 05:00:00 +0100 5642466 http://www.medworm.com/index.php?rid=5633835&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F5%2F5 Conclusions: Our study suggests that hypomethylation is crucial for the onset of and in the progression of liver fibrosis to HCC. The elucidation of this change in methylation status from the onset of fibrosis and subsequent progression to HCC may lead to a new clinical diagnosis. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5633835 Fri, 27 Jan 2012 05:00:00 +0100 5633835 http://www.medworm.com/index.php?rid=5615724&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F5%2F3 Conclusions: This study provides a perspective on the microRNA expression during the development of NPC. It revealed the global trends in miRNA interactome in NPC. It concluded that miRNAs might play important regulatory roles through the target genes and transcription factors in the stepwise development of NPC. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5615724 Thu, 19 Jan 2012 05:00:00 +0100 5615724 http://www.medworm.com/index.php?rid=5615723&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F5%2F4 DiscussionIn this paper, we identify and discuss four disease characteristics - severity, actionability, age of onset, and the somatic/psychiatric nature of disease - and show how these lead to specific ethical issues. By way of illustration, we apply this framework to genetic susceptibility testing for three diseases: type 2 diabetes, age-related macular degeneration and clinical depression. For these three diseases, we point out the ethical issues that are relevant to the question whether it is morally justifiable to offer genetic susceptibility testing to adults or to children or minors, and on what conditions.SummaryWe conclude that the ethical evaluation of personal genome tests is challenging, for the ethical issues differ with the diseases tested for. An understanding of the ethical... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5615723 Thu, 19 Jan 2012 05:00:00 +0100 5615723 http://www.medworm.com/index.php?rid=5590954&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F5%2F2 An new set of 56 gene expression biomarkers could be used to predict early atherosclerosis from leukocytes before the symptoms of heart disease have developed, and this test can be further refined to identify very high risk patients. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5590954 Fri, 13 Jan 2012 05:00:00 +0100 5590954 http://www.medworm.com/index.php?rid=5567126&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F5%2F1 Conclusions: The 'health space' model allows visualization of multiple results and to interpret them. The model presents treatment group effects, subgroups and individual responses. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5567126 Fri, 06 Jan 2012 05:00:00 +0100 5567126 http://www.medworm.com/index.php?rid=5556147&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F86 Conclusions: Our data suggest that the expansion of beta cell mass observed in ob/ob islets is associated with the activation of an immune response that fails to occur in POKO islets. We have also indentified other PPARgamma dependent differentially regulated pathways including cholesterol biosynthesis, apoptosis through TGF-beta signaling and decreased oxidative phosphorylation. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5556147 Fri, 30 Dec 2011 05:00:00 +0100 5556147 http://www.medworm.com/index.php?rid=5531350&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F85 Conclusions: Our data suggest that directional loss and amplification exist in breast cancer. These are highly associated with grade, which may indicate that they are enforced with increasing number of cell divisions. Whether there is selective pressure for some loci to be preferentially amplified or deleted remains to be confirmed. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5531350 Wed, 21 Dec 2011 05:00:00 +0100 5531350 http://www.medworm.com/index.php?rid=5510740&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F84 Conclusion: Genome-wide methylation data from Infinium Methylation BeadChip can be susceptible to batch effects with profound impacts on downstream analyses and conclusions. Normalization can reduce part but not all batch effects. EB correction along with normalization is recommended for effective batch effect removal. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5510740 Fri, 16 Dec 2011 05:00:00 +0100 5510740 http://www.medworm.com/index.php?rid=5481722&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F83 Background: Prediction of left ventricular (LV) remodeling after acute myocardial infarction (MI) is clinically important and would benefit from the discovery of new biomarkers. Methods: Blood samples were obtained upon admission in patients with acute ST-elevation MI who underwent primary percutaneous coronary intervention. Messenger RNA was extracted from whole blood cells. LV function was evaluated by echocardiography at 4-months. Results: In a test cohort of 32 MI patients, integrated analysis of microarrays with a network of protein-protein interactions identified subgroups of genes which predicted LV dysfunction (ejection fraction [less than or equal to]40%) with areas under the receiver operating characteristic curve (AUC) above 0.80. Candidate genes included transforming growth fac... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5481722 Mon, 05 Dec 2011 05:00:00 +0100 5481722 http://www.medworm.com/index.php?rid=5463719&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F82 Conclusions: Our findings will provide valuable data for future analysis of CpG methylation patterns, useful markers for the diagnosis of stomach cancer, as well as a new analysis method for clinical epigenomics investigations. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5463719 Fri, 02 Dec 2011 03:28:26 +0100 5463719 http://www.medworm.com/index.php?rid=5453140&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F81 Conclusions: We conclude that relative to array variance , pool-construction variance is of less importance in reducing the variance in allele frequency estimation from DNA pools; however, it may be more important than previously thought. We have prepared a simple online tool, PoolingPlanner (available at http://www.kchew.ca/PoolingPlanner/), which calculates the effective sample size (ESS) of a DNA pool given a range of replicate array values and variance estimates. ESS can be used in a power calculator to perform pool-adjusted calculations. This allows one to quickly calculate the loss of power associated with a pooling experiment to make an informed decision on whether a pool-based GWAS is worth pursuing. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5453140 Mon, 28 Nov 2011 05:00:00 +0100 5453140 http://www.medworm.com/index.php?rid=5446435&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F80 Conclusions: All in all, we show that BMP signaling has a remarkable effect on gene transcription in breast cancer cells and that the functions affected follow a logical temporal pattern. Our results also uncover components of the common cellular transcriptional response to BMP4 and BMP7. Most importantly, this study provides a list of potential novel BMP target genes relevant in breast cancer. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5446435 Fri, 25 Nov 2011 05:00:00 +0100 5446435 http://www.medworm.com/index.php?rid=5446436&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F79 Background: Identification of patients who likely will or will not benefit from cytotoxic chemotherapy through the use of biomarkers could greatly improve clinical management by better defining appropriate treatment options for patients. microRNAs may be potentially useful biomarkers that help guide individualized therapy for cancer because microRNA expression is dysregulated in cancer. In order to identify miRNA signatures for gastric cancer and for predicting clinical resistance to cisplatin/fluorouracil (CF) chemotherapy, a comprehensive miRNA microarray analysis was performed using endoscopic biopsy samples. Methods: Biopsy samples were collected prior to chemotherapy from 90 gastric cancer patients treated with CF and from 34 healthy volunteers. At the time of disease progression, pos... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5446436 Wed, 23 Nov 2011 05:00:00 +0100 5446436 http://www.medworm.com/index.php?rid=5372287&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F78 Conclusions: EC miRNA expression levels are generally consistent across EC types. Three microRNAs were variable within the dataset indicating potential regulatory changes that could impact on EC phenotypic differences. MiRNA expression in endothelial, epithelial and hematologic cells differentiate these cell types. This data establishes a valuable resource characterizing the diverse miRNA signature of ECs. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5372287 Wed, 02 Nov 2011 04:00:00 +0100 5372287 http://www.medworm.com/index.php?rid=5372288&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F77 Conclusion: This is the first study to explore the variability of gene expression patterns in whole biopsies from normal breasts and identified distinct subtypes of normal breast tissue. Further studies are needed to determine the specific cell contribution to the variation in the biology of normal breasts, how the clusters identified relate to breast cancer risk and their possible link to the origin of the different molecular subtypes of breast cancer. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5372288 Tue, 01 Nov 2011 04:00:00 +0100 5372288 http://www.medworm.com/index.php?rid=5372290&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F75 Conclusions: In this study, we used both single-end and paired-end sequencing strategies to discover gene fusions in breast cancer transcriptomes with BRCA1 mutations. We found that the use of paired-end reads is an effective tool for transcriptome profiling of gene fusions. Our findings suggest that while gene fusions are present in some BRCA1-mutated breast cancers, they are infrequent and not recurrent. However, private fusions may still be valuable as potential patient-specific biomarkers for diagnosis and treatment. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5372290 Thu, 27 Oct 2011 04:00:00 +0100 5372290 http://www.medworm.com/index.php?rid=5372289&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F76 Conclusions: Our findings, derived from a different type of analysis of microarray data, highlight the importance of analyzing coordinated gene expression to find molecular pathways involved in melanoma progression. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5372289 Thu, 27 Oct 2011 04:00:00 +0100 5372289 http://www.medworm.com/index.php?rid=5353750&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F74 Conclusions: Our study indicates that PBLs from sALS patients are strong responders to systemic signals or local signals acquired by cell trafficking, representing changes in gene expression similar to those present in brain and spinal cord of sALS patients. PBLs may provide a useful means to study ALS pathogenesis. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5353750 Tue, 25 Oct 2011 04:00:00 +0100 5353750 http://www.medworm.com/index.php?rid=5320185&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F73 Conclusions: The IR presents a quantitative metric to estimate the information content of gene expression data with respect to particular phenotypes. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5320185 Fri, 14 Oct 2011 04:00:00 +0100 5320185 http://www.medworm.com/index.php?rid=5353751&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F72 DiscussionThe human microbiome is the entire complement of microorganisms that exists in and on every human body. Currently most biobanks focus primarily on human tissues and/or associated data (e.g. health records). Accordingly, most discussions in the social sciences and humanities on these issues are focused (appropriately so) on the implications of biobanks and sharing data derived from human tissues. However, rapid advances in human microbiome research involve collecting large amounts of data on microorganisms that exist in symbiotic relationships with the human body. Currently it is not clear whether these microorganisms should be considered part of or separate from the human body. Arguments can be made for both, but ultimately it seems that the dichotomy of human versus non-human an... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5353751 Fri, 07 Oct 2011 04:00:00 +0100 5353751 http://www.medworm.com/index.php?rid=5300916&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F72 DiscussionThe human microbiome is the entire complement of microorganisms that exists in and on every human body. Currently most biobanks focus primarily on human tissues and/or associated data (e.g. health records). Accordingly, most discussions in the social sciences and humanities on these issues are focused (appropriately so) on the implications of biobanks and sharing data derived from human tissues. However, rapid advances in human microbiome research involve collecting large amounts of data on microorganisms that exist in symbiotic relationships with the human body. Currently it is not clear whether these microorganisms should be considered part of or separate from the human body. Arguments can be made for both, but ultimately it seems that the dichotomy of human versus non-human an... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5300916 Fri, 07 Oct 2011 04:00:00 +0100 5300916 http://www.medworm.com/index.php?rid=5291489&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F70 Conclusions: This study represents the first use of BPR on whole lung tissue; previously, BPR was primarily used to develop predictive models for cancer. This also represents the first report of an independently validated IPF gene expression signature. In summary, BPR is a promising tool for the development of gene expression signatures from non-neoplastic lung tissue. In the future, BPR might be used to develop definitive diagnostic gene signatures for IPF, prognostic gene signatures for IPF or gene signatures for other non-neoplastic lung disorders such as bronchiolitis obliterans. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5291489 Wed, 05 Oct 2011 04:00:00 +0100 5291489 http://www.medworm.com/index.php?rid=5291490&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F69 DiscussionEthical and legal frameworks governing consent dissuade cross-domain data sharing. Paradoxically, analysis of consent models for disease-specific and population-based research reveals such a high degree of similarity that bridging consent could be possible if additional information regarding bridging was incorporated into consent forms. We submit that bridging of consent could be supported if current trends endorsing a new interpretation of consent are adopted. To illustrate this we sketch potential bridging consent scenarios.SummaryA bridging consent, respectful of the spirit of initial consent, is feasible and would require only small changes to the content of consents currently being used. Under a bridging consent approach, the initial data and samples collection can serve an ... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5291490 Tue, 04 Oct 2011 04:00:00 +0100 5291490 http://www.medworm.com/index.php?rid=5266920&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F68 Conclusions: The application of high throughput sequencing technologies in cancer genomics opens up a new dimension for the identification of disease mechanisms. In particular the ability to use small amounts of FFPE samples available from surgical tumor resections and histopathological examinations facilitates the collection of precious tissue materials. However, care needs to be taken in regard to the locations of the biopsies, which can have an influence on the prediction of copy number variations. Bearing these technological challenges in mind will significantly improve many large-scale sequencing studies and will - in the long term - result in a more reliable prediction of individual cancer therapies. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5266920 Thu, 29 Sep 2011 04:00:00 +0100 5266920 http://www.medworm.com/index.php?rid=5266921&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F67 Background: Facioscapulohumeral muscular dystrophy (FSHD) is a dominant disease linked to contraction of an array of tandem 3.3-kb repeats (D4Z4) at 4q35. Within each repeat unit is a gene, DUX4, that can encode a protein containing two homeodomains. A DUX4 transcript derived from the last repeat unit in a contracted array is associated with pathogenesis but it is unclear how. Methods: Using exon-based microarrays, the expression profiles of myogenic precursor cells were determined. Both undifferentiated myoblasts and myoblasts differentiated to myotubes derived from FSHD patients and controls were studied after immunocytochemical verification of the quality of the cultures. To further our understanding of FSHD and normal myogenesis, the expression profiles obtained were compared to those ... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5266921 Tue, 27 Sep 2011 04:00:00 +0100 5266921 http://www.medworm.com/index.php?rid=5244784&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F66 Conclusions: Based on the preservation of mRNA expression profiles that are characteristic for the histological subtype we propose that these model systems are representative for the primary tumor from which they are derived. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5244784 Tue, 20 Sep 2011 04:00:00 +0100 5244784 http://www.medworm.com/index.php?rid=5231394&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F65 Conclusions: Our data suggest a critical role of miRNAs in MSC neuronal differentiation, and miR-34a contributes in neuronal precursor motility, which may be crucial for stem cells to home to the target sites they should be. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5231394 Mon, 19 Sep 2011 04:00:00 +0100 5231394 http://www.medworm.com/index.php?rid=5115649&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F64 ${item.shortDescription} (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5115649 Tue, 09 Aug 2011 23:00:00 +0100 5115649 http://www.medworm.com/index.php?rid=5115650&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F63 ${item.shortDescription} (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5115650 Mon, 08 Aug 2011 23:00:00 +0100 5115650 http://www.medworm.com/index.php?rid=5115651&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F62 ${item.shortDescription} (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5115651 Sun, 07 Aug 2011 23:00:00 +0100 5115651 http://www.medworm.com/index.php?rid=5056609&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F61 A human breast cancer predictor generated from transcriptome patterns in transgenic mouse tumor model peripheral blood samples serves as a proof-of-concept for using animal models to develop genomic biomarkers. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5056609 Thu, 21 Jul 2011 23:00:00 +0100 5056609 http://www.medworm.com/index.php?rid=5046619&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F60 ${item.shortDescription} (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5046619 Mon, 18 Jul 2011 23:00:00 +0100 5046619 http://www.medworm.com/index.php?rid=5025780&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F59 Conclusion: This study enhances understanding of the interaction network that executes inflammatory responses in human MI. Network-encoded information can be translated into knowledge with potential prognostic application. Independent evaluations are required to further estimate the clinical relevance of the new prognostic genes. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5025780 Wed, 13 Jul 2011 23:00:00 +0100 5025780 http://www.medworm.com/index.php?rid=5016052&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F57 Conclusions: These results suggest specific transcriptional pathways that may operate to create the unique molecular phenotype of PA and thus opportunities for corresponding targeted therapeutic intervention. Moreover, this study also demonstrates how integration of gene expression data with TF-gene and TF-TF interaction data is a powerful approach to generating testable hypotheses to better understand cell-type specific genetic programs relevant to cancer. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5016052 Sun, 10 Jul 2011 23:00:00 +0100 5016052 http://www.medworm.com/index.php?rid=5016051&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F58 Conclusions: Reliable and consistent predictions of oncogenic pathway activities can be obtained from FFPE tumor tissue samples. The ability to reliably utilize FFPE patient tumor tissue samples for genomic analyses will lead to a better understanding of the biology of disease progression and, in the clinical setting, will provide tools to guide the choice of therapeutics to those most likely to be effective in treating a patient's disease. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5016051 Sun, 10 Jul 2011 23:00:00 +0100 5016051 http://www.medworm.com/index.php?rid=5004742&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F56 Conclusions: We have modified a previously published meta-analysis method and identified a common metastatic signature by comparing primary tumors versus metastases in various tumor types. This approach, as well as the gene signature identified, provides important insights to the common metastatic process and a foundation for future discoveries that could have broad application, such as drug discovery, metastasis prediction, and mechanistic studies. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5004742 Wed, 06 Jul 2011 23:00:00 +0100 5004742 http://www.medworm.com/index.php?rid=5004743&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F55 Conclusions: The identification of three gene signatures showing a relevant overlap of pathways and ontologies,increases the likelihood of finding potential marker genes for AD. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=5004743 Mon, 04 Jul 2011 23:00:00 +0100 5004743 http://www.medworm.com/index.php?rid=4990386&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F53 Conclusion: The functional cancer map provides a systematic view on molecular similarities across different cancers by comparing tumors on the level of pathway activity. This work resulted in identification of novel superimposed functional pathways potentially linked to cancer biology. Therefore, our work may serve as a starting point for rationalizing combination of tumor therapeutics as well as for expanding the application of well-established targeted tumor therapies. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4990386 Wed, 29 Jun 2011 23:00:00 +0100 4990386 http://www.medworm.com/index.php?rid=4990385&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F54 Conclusions: Normal tissue sampled concurrently with tumor is an important source of bias in breast genomic predictors. All genomic predictors show some sensitivity to normal tissue contamination and ideal strategies for mitigating this bias vary depending upon the particular genes and computational methods used in the predictor. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4990385 Wed, 29 Jun 2011 23:00:00 +0100 4990385 http://www.medworm.com/index.php?rid=4973938&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F51 Background: Recent genome-wide association (GWA) analyses have identified common single nucleotide polymorphisms (SNPs) that are associated with obesity. However, the reported genetic variation in obesity explains only a minor fraction of the total genetic variation expected to be present in the population. Thus many genetic variants controlling obesity remain to be identified. The aim of this study was to use GWA followed by multiple stepwise validations to identify additional genes associated with obesity. Methods: We performed a GWA analysis in 164 morbidly obese subjects (BMI:body mass index >40 kg/m2) and 163 Swedish subjects (>45 years) who had always been lean. The 700 SNPs displaying the strongest association with obesity in the GWA were analyzed in a second cohort comprising 460 m... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4973938 Mon, 27 Jun 2011 23:00:00 +0100 4973938 http://www.medworm.com/index.php?rid=4966390&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F50 Conclusion: Our genome-wide methylation study in CRC clearly supports most of the previous findings; additionally we found a large number of novel DML in CRC tissue. If confirmed in future studies, these findings may lead to identification of genomic markers for potential clinical application. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4966390 Wed, 22 Jun 2011 23:00:00 +0100 4966390 http://www.medworm.com/index.php?rid=4909398&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F49 Conclusions: Known biomarkers of glioblastoma survival were confirmed, and new general and clinical-dependent gene profiles were uncovered. The comparison of biomarkers across glioblastoma phases and functional analyses offered insights into the role of genes. These findings support the development of more accurate and personalized prognostic tools and gene-based therapies that improve the survival and quality of life of individuals afflicted by glioblastoma multiforme. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4909398 Mon, 06 Jun 2011 23:00:00 +0100 4909398 http://www.medworm.com/index.php?rid=4890390&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F48 Background: Gastric cancer samples obtained by histologic macrodissection contain a relatively high stromal content that may significantly influence gene expression profiles. Differences between the gene expression signature derived from macrodissected gastric cancer samples and the signature obtained from isolated gastric cancer epithelial cells from the same biopsies using laser-capture microdissection (LCM) were evaluated for their potential experimental biases. Methods: RNA was isolated from frozen tissue samples of gastric cancer biopsies from 20 patients using both histologic macrodissection and LCM techniques. RNA from LCM was subject to an additional round of T7 RNA amplification. Expression profiling was performed using Affymetrix HG-U133A arrays. Genes identified in the expressio... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4890390 Wed, 01 Jun 2011 23:00:00 +0100 4890390 http://www.medworm.com/index.php?rid=4860026&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F47 Conclusions: We provide a package that outperforms the existing ones in terms of modelling flexibility, power, convergence rate, ease of covariate adjustment, and requirements for sample size and signal quality. Therefore, we offer CNVassoc as a method for routine use in CNV association studies. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4860026 Mon, 23 May 2011 23:00:00 +0100 4860026 http://www.medworm.com/index.php?rid=4851688&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F46 Conclusions: Non-luminal-like types are all representatives of aggressive disease, and this could be attributed to the similarity in overall gene expression to stem and progenitor cell types. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4851688 Sun, 22 May 2011 23:00:00 +0100 4851688 http://www.medworm.com/index.php?rid=4846543&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F45 In this study, we compared the DNA methylation profile of multiple tumor suppressor genes (APC, DAPK, E-cadherin, hMLH1, IRF8, p14, p15, RASSF1A, SFRP1 and SOCS-1) in bladder cancer patients from different Chinese sub-populations including Taiwan (104 cases), Hong Kong (82 cases) and China (24 cases) by MSP. Two normal human urothelium were also included as control. To investigate the diagnostic potential of using DNA methylation in non-invasive detection of bladder cancer, degree of methylation of DAPK, IRF8, p14, RASSF1A and SFRP1 was also accessed by quantitative MSP in urine samples from thirty bladder cancer patients and nineteen non-cancer controls. Results: There were distinct DNA methylation epigenotypes among the different sub-populations. Further, samples from Taiwan and China de... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4846543 Thu, 19 May 2011 23:00:00 +0100 4846543 http://www.medworm.com/index.php?rid=4846544&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F44 Conclusion: We have identified an alternative bioinformatics approach for predicting miRNA targets in human colon cancer and for reverse engineering the miRNA:mRNA network using inversely related mRNA and miRNA joint expression profiles. We demonstrated the superiority of our predictive method compared to the correlation based target prediction algorithm through a simulation study. We anticipate that the unique miRNA targets predicted by the proposed method will advance the understanding the molecular mechanism of colon cancer and will suggest novel therapeutic targets after further experimental validations. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4846544 Wed, 18 May 2011 23:00:00 +0100 4846544 http://www.medworm.com/index.php?rid=4838169&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F43 Conclusion: The interfaces of the presented database enable the user to search and view mutations in an intuitive and straight-forward manner. The database is freely accessible at http://rcgdb.bioinf.uni-sb.de/MutomeWeb/. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4838169 Mon, 16 May 2011 23:00:00 +0100 4838169 http://www.medworm.com/index.php?rid=4838170&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F42 Conclusion: Our microarray analysis identified novel antisense transcripts with expression profiles specific to cancer tissue, some of which might play a role in the regulatory networks underlying oncogenesis and thus are potential targets for further experimental validation. Our microarray data are available at http://www.brc.riken.go.jp/ncrna2007/viewer-Saito-01/index.html. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4838170 Sun, 15 May 2011 23:00:00 +0100 4838170 http://www.medworm.com/index.php?rid=4826983&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F41 Conclusion: The findings demonstrate the use of zebrafish for characterizing estrogen-like environmental carcinogens and anti-estrogen drug screening. From an evolutionary perspective, our findings suggest that estrogen regulation of cell cycle is perhaps one of the earliest forms of steroidal-receptor controlled cellular processes. Our study provides first evidence of molecular conservation of estrogen-responsiveness between zebrafish and human cancer cell lines, hence demonstrating the potential of zebrafish for estrogen-related cancer research. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4826983 Sun, 15 May 2011 23:00:00 +0100 4826983 http://www.medworm.com/index.php?rid=4826984&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F40 Conclusions: These results provide the first genome-wide examination of the effects of insulin therapy on retinal gene expression changes with diabetes. While insulin clearly normalizes the majority of genes dysregulated in response to diabetes, a number of genes related to inflammatory processes, microvascular integrity, and neuronal function are still altered in expression in euglycemic diabetic rats. Gene expression changes not rescued or prevented by insulin treatment may be critical to the pathogenesis of diabetic retinopathy, as it occurs in diabetic patients receiving insulin replacement, and are prototypical of metabolic memory. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4826984 Sat, 14 May 2011 23:00:00 +0100 4826984 http://www.medworm.com/index.php?rid=4810946&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F38 Conclusions: PHY906 together with CPT-11 triggers unique changes not activated by each one alone suggesting that the combination creates a unique tissue-specific response. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4810946 Tue, 10 May 2011 23:00:00 +0100 4810946 http://www.medworm.com/index.php?rid=4793508&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F37 Conclusions: The presented results indicate promising clinical and therapeutic implications. Our findings also directly point out to the necessity of adopting a function-centric, rather a gene-centric, view in the understanding of phenotypes or diseases harboring CNAs. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4793508 Thu, 05 May 2011 23:00:00 +0100 4793508 http://www.medworm.com/index.php?rid=4740624&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F36 Conclusions: We conclude that two AONs can be used to target two different genes, MSTN and DMD, in a straightforward manner. Targeting multiple ligands of TGF-beta family will be more promising as adjuvant therapies for DMD. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4740624 Tue, 19 Apr 2011 23:00:00 +0100 4740624 http://www.medworm.com/index.php?rid=4730850&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F35 Conclusions: Our results demonstrated a significant role of alternative splicing in high stage neuroblastoma, and suggested a MYCN-associated splicing regulation pathway in stage 4+ tumors. The identification of differentially spliced genes and pathways in neuroblastoma tumors of different stages and molecular subtypes may be important to the understanding of cancer biology and the discovery of diagnostic markers or therapeutic targets in neuroblastoma. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4730850 Sun, 17 Apr 2011 23:00:00 +0100 4730850 http://www.medworm.com/index.php?rid=4708232&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F34 Conclusions: We have developed a sensitive, simple, and fast method for automatically detecting functional modules in tumors based solely on patterns of recurrent genomic aberration. Due to its ability to analyze very large amounts of diverse data, we expect it to be increasingly useful when applied to the many comprehensive tumor sets scheduled to be analysed in the near future. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4708232 Wed, 13 Apr 2011 23:00:00 +0100 4708232 http://www.medworm.com/index.php?rid=4708233&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F33 Conclusions: The repression of modules that contain cell survival genes in N0 tumors reinforces the important role that apoptosis plays in the regulation of metastasis. In addition, because tumor samples used here were not microdissected, tumor gene expression data are represented together with the stroma, which may reveal signaling between the microenvironment and tumor cells. For instance, in non-recurrent tumors, extracellular region module was repressed, indicating that the stroma and tumor cells may have fewer interactions, which disable metastasis development. Finally, the genes highlighted in our analysis can be implicated in more than one pathway or characteristic, suggesting that therapeutic approaches to prevent tumor progression should target more than one gene or pathway, speci... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4708233 Tue, 12 Apr 2011 23:00:00 +0100 4708233 http://www.medworm.com/index.php?rid=4702529&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F32 Background: Comparative Genomic Hybridization (CGH) is a molecular approach for detecting DNA Copy Number Alterations (CNAs) in tumor, which are among the key causes of tumorigenesis. However in the post-genomic era, most studies in cancer biology have been focusing on Gene Expression Profiling (GEP) but not CGH, and as a result, an enormous amount of GEP data had been accumulated in public databases for a wide variety of tumor types. We exploited this resource of GEP data to define possible recurrent CNAs in tumor. In addition, the CNAs identified by GEP would be more functionally relevant CNAs in the disease pathogenesis since the functional effects of CNAs can be reflected by altered gene expression. Methods: We proposed a novel computational approach, coined virtual CGH (vCGH), which e... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4702529 Mon, 11 Apr 2011 23:00:00 +0100 4702529 http://www.medworm.com/index.php?rid=4691566&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F31 Conclusions: By applying these approaches to a number of synthetic and real microarray datasets we show that for linear classifiers the optimal proportion depends on the overall number of samples available and the degree of differential expression between the classes. The optimal proportion was found to depend on the full dataset size (n) and classification accuracy -- with higher accuracy and smaller $n$ resulting in more assigned to the training set. The commonly used strategy of allocating 2/3rd of cases for training was close to optimal for reasonable sized datasets ($n \ge 100$) with strong signals (i.e. $85\%$ or greater full dataset accuracy). In general, we recommend use of our nonparametric resampling approach for determing the optimal split.This approach can be applied to any dat... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4691566 Thu, 07 Apr 2011 23:00:00 +0100 4691566 http://www.medworm.com/index.php?rid=4681701&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F30 Conclusions: We show that valuable new information can be gained from meta analysis of existing microarray data deposited in public repositories. While single microarray studies rarely exhibit a sample number which allows robust feature selection, this can be achieved by combining published data using DWD. This approach is not only efficient, but also very cost-effective. Independent validation shows the validity of the results from this meta analysis and confirms SERPINA1 as a potent mRNA marker for PTC in a total (meta analysis plus validation) of 181 samples. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4681701 Tue, 05 Apr 2011 23:00:00 +0100 4681701 http://www.medworm.com/index.php?rid=4662623&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F27 Conclusions: This study highlights the ability of gene expression profiling to distinguish lymphoma from reactive conditions and classify the major subtypes of lymphoma in a diagnostic setting. A cost-effective single platform "mini-chip" assay could, in principle, be developed to aid the quick diagnosis of lymph node biopsies with the potential to incorporate other pathological entities into such an assay. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4662623 Wed, 30 Mar 2011 23:00:00 +0100 4662623 http://www.medworm.com/index.php?rid=4662622&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F28 Conclusions: The assignment of a ranked immunological relevance score to all human genes extends the content of existing immune gene resources and enriches our understanding of immune involvement in complex biological networks. The application of this approach to tumor immunity represents an automated systems strategy that quantifies the immunological component in complex disease. In so doing, it stratifies patients according to their immune profiles, which may lead to effective computational prognostic and clinical guides. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4662622 Wed, 30 Mar 2011 23:00:00 +0100 4662622 http://www.medworm.com/index.php?rid=4662621&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F29 Conclusions: Distinct gene expression patterns associated with sex hormones are detectable in a random group of postmenopausal women, as demonstrated by the finding of a novel oestrogen signature. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4662621 Wed, 30 Mar 2011 23:00:00 +0100 4662621 http://www.medworm.com/index.php?rid=4651087&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F26 Background: Alterations in gene expression in peripheral blood cells have been shown to be sensitive to the presence and extent of coronary artery disease (CAD). A non-invasive blood test that could reliably assess obstructive CAD likelihood would have diagnostic utility. Results: Microarray analysis of RNA samples from a 195 patient Duke CATHGEN registry case:control cohort yielded 2,438 genes with significant CAD association (p (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4651087 Sun, 27 Mar 2011 23:00:00 +0100 4651087 http://www.medworm.com/index.php?rid=4635257&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F24 Conclusions: Identification of significantly changed proteins in biofluids and blood cells using a non-targeted approach, together with the outcome of targeted analysis revealed both known and novel markers for a 36h fasting period, including the cellular proteins RhoGDI2 and CLIC1, and plasma proteins ApoA4, leptin and MMP-3. The PBMC proteome exhibited the lowest between-subject variability and therefore these cells appear to represent the best biosamples for biomarker discovery in human nutrigenomics. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4635257 Fri, 25 Mar 2011 00:00:00 +0100 4635257 http://www.medworm.com/index.php?rid=4635256&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F25 Conclusions: Our findings demonstrate that different results are obtained with different platforms and illustrate the trade-off that exists between sensitivity and specificity. The large number of apparently false positive CNV calls on each of the platforms supports the need for validating clinically important findings with a different technology. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4635256 Fri, 25 Mar 2011 00:00:00 +0100 4635256 http://www.medworm.com/index.php?rid=4630262&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F23 Conclusions: This study is expected to identify targets for chemoresistant issues and highlights the interconnectivity of chemoresistant mechanisms. The experimental results not only offer insights into the mode of biological action of drug resistance but also provide information on potential key targets (new biological hypothesis) for further drug-development efforts. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4630262 Thu, 24 Mar 2011 00:00:00 +0100 4630262 http://www.medworm.com/index.php?rid=4548652&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F22 Conclusions: The potential role of P. catoniae and N. flavescens oral health markers should be assessed in large-scale clinical studies. The combination of both, open-ended and targeted molecular approaches provides us with information that will increase our understanding of the interplay between the human host and its microbiome. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4548652 Fri, 04 Mar 2011 00:00:00 +0100 4548652 http://www.medworm.com/index.php?rid=4543907&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F21 Conclusions: We have developed a method to detect associations of regional copy number abnormalities in cancer data. Along with finding statistically relevant CNA co-occurrences, our algorithm points towards a generally low specificity for co-occurrence of regional imbalances in CNA rich samples, which may have negative impact on pathway modeling approaches relying on frequent CNA events. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4543907 Thu, 03 Mar 2011 00:00:00 +0100 4543907 http://www.medworm.com/index.php?rid=4530808&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F20 Conclusions: In a study of patients undergoing bare metallic stent implantation, we have identified and replicated differential gene expression in peripheral blood mononuclear cells, studied across a time series of blood samples. The genes identified suggest alterations in cellular growth and metabolism pathways, and these results provide the basis for further specific functional hypothesis generation and testing of the mechanisms of ISR. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4530808 Mon, 28 Feb 2011 00:00:00 +0100 4530808 http://www.medworm.com/index.php?rid=4511048&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F19 DiscussionThe presented results provide novel findings that build a basis of further investigations of diagnostic biomarkers, targeted therapies and studies on MDS pathogenesis. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4511048 Wed, 23 Feb 2011 00:00:00 +0100 4511048 http://www.medworm.com/index.php?rid=4463386&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F18 Background: Paclitaxel is a microtubule-stabilizing drug that has been commonly used in treating cancer. Due to genetic heterogeneity within patient populations, therapeutic response rates often vary. Here we used the NCI60 panel to identify SNPs associated with paclitaxel sensitivity. Using the panel's GI50 response data available from Developmental Therapeutics Program, cell lines were categorized as either sensitive or resistant. PLINK software was used to perform a genome-wide association analysis of the cellular response to paclitaxel with the panel's SNP-genotype data on the Affymetrix 125k SNP array. FastSNP software helped predict each SNP's potential impact on their gene product. mRNA expression differences between sensitive and resistant cell lines was examined using data from Bi... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4463386 Fri, 11 Feb 2011 00:00:00 +0100 4463386 http://www.medworm.com/index.php?rid=4435794&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F17 Conclusions: The most strongly associated locus for SUAL in EA populations was also the most strongly associated locus in this AA sample. This finding provides evidence for the role of SLC2A9 in uric acid metabolism across human populations. Additionally, our findings demonstrate the utility of following-up EA populations GWAS signals in African-ancestry populations with weaker linkage disequilibrium. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4435794 Fri, 04 Feb 2011 00:00:00 +0100 4435794 http://www.medworm.com/index.php?rid=4410508&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F16 Conclusions: This is a first report using 1M array CGH for the discovery of cancer genes and biomarkers. We show the remarkable capacity of this technology to discover CNVs, micro-copy number alterations and even gene fusions. However, these platforms require excellent genomic DNA quality and do not tolerate relatively small imperfections related to the whole genome amplification. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4410508 Thu, 27 Jan 2011 00:00:00 +0100 4410508 http://www.medworm.com/index.php?rid=4404355&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F15 Conclusions: : Importantly, this modular ASD database provides a platform from which data mining, bioinformatics, and/or computational biology strategies may be adopted to develop predictive disease models that may offer further insights into the molecular underpinnings of this disorder. It also serves as a general model for disease-driven databases curating phenotypic characteristics of corresponding animal models. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4404355 Thu, 27 Jan 2011 00:00:00 +0100 4404355 http://www.medworm.com/index.php?rid=4404356&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F14 Conclusions: We developed and validated an algorithm to provide a virtual normal reference signal directly from tumor samples and minimize noise in the derivation of the raw CN signal. The algorithm reduces the variability of assays performed across different reagent and array batches, methods of sample preservation, multiple personnel, and among different laboratories. This approach may be valuable when matched normal samples are unavailable or the paired normal specimens have been subjected to variations in methods of preservation. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4404356 Wed, 26 Jan 2011 00:00:00 +0100 4404356 http://www.medworm.com/index.php?rid=4398212&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F12 Conclusions: The proposed method addresses the weakness of conventional methods by adding a redundancy reduction stage and utilizing Gene Ontology information. It predicts marker genes for colon, DLBCL and prostate cancer with a high accuracy. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help in the search for a cure for cancers. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4398212 Wed, 26 Jan 2011 00:00:00 +0100 4398212 http://www.medworm.com/index.php?rid=4398211&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F13 IntroductionThe eMERGE (electronic MEdical Records and GEnomics) Network is an NHGRI-supported consortium of five institutions to explore the utility of DNA repositories coupled to Electronic Medical Record (EMR) systems for advancing discovery in genome science. eMERGE also includes a special emphasis on the ethical, legal and social issues related to these endeavors.Organization: The five sites are supported by an Administrative Coordinating Center. Setting of network goals is initiated by working groups: (1) Genomics, (2) Informatics, and (3) Consent & Community Consultation, which also includes active participation by investigators outside the eMERGE funded sites, and (4) Return of Results Oversight Committee. The Steering Committee, comprised of site PIs and representatives and NHGRI ... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4398211 Wed, 26 Jan 2011 00:00:00 +0100 4398211 http://www.medworm.com/index.php?rid=4393001&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F10 Conclusions: Patients that were predicted confidently by the classifiers as cancer can receive immediate and appropriate treatment whilst patients that were predicted confidently as healthy will be spared from unnecessary treatment. We believe that our method can be a useful tool to translate the gene expression signatures into clinical practice for personalized medicine. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4393001 Mon, 24 Jan 2011 00:00:00 +0100 4393001 http://www.medworm.com/index.php?rid=4376443&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F9 Conclusions: These data demonstrate that the biology underpinning the native, molecular classification of human colon cancer--previously thought to be highly heterogeneous-- was clarified through the lens of comprehensive transcriptome analysis. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4376443 Thu, 20 Jan 2011 00:00:00 +0100 4376443 http://www.medworm.com/index.php?rid=4359737&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F8 Conclusions: We present a comprehensive overview of the molecular networks perturbed in ILDs, discuss several potential key molecular regulatory circuits, and identify microRNA species that may play central roles in facilitating the progression of ILDs. These findings advance our understanding of these diseases at the molecular level, provide new molecular signatures in defining the specific characteristics of the diseases, suggest new hypotheses, and reveal new potential targets for therapeutic intervention. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4359737 Mon, 17 Jan 2011 00:00:00 +0100 4359737 http://www.medworm.com/index.php?rid=4341800&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F7 Background: Infection with H. pylori is important in the etiology of gastric cancer. Gastric cancer is infrequent in Africa, despite high frequencies of H. pylori infection, referred to as the African enigma. Variation in environmental and host factors influencing gastric cancer risk between different populations have been reported but little is known about the biological differences between gastric cancers from different geographic locations. We aim to study genomic instability patterns of gastric cancers obtained from patients from United Kingdom (UK) and South Africa (SA), in an attempt to support the African enigma hypothesis at the biological level. Methods: DNA was isolated from 67 gastric adenocarcinomas, 33 UK patients, 9 Caucasian SA patients and 25 native SA patients. Microsatell... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4341800 Thu, 13 Jan 2011 00:00:00 +0100 4341800 http://www.medworm.com/index.php?rid=4336132&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F5 Conclusions: This study introduces multiple ways of defining the representative features and effective thresholding regularized estimation approaches. It provides convincing evidence that the higher-order representative features may have important implications for the prediction of cancer prognosis. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4336132 Wed, 12 Jan 2011 00:00:00 +0100 4336132 http://www.medworm.com/index.php?rid=4336131&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F6 Conclusions: Because of the importance of IFNbeta in cancer, our results suggest that creQTL may provide a finer picture of gene regulation and may reveal additional molecular targets for intervention. An open source R implementation of the method is available at http://sites.google.com/site/kenkompass/. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4336131 Wed, 12 Jan 2011 00:00:00 +0100 4336131 http://www.medworm.com/index.php?rid=4336133&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F4 Conclusions: The regions we discovered are candidates for future studies on cardiovascular outcomes, particularly in African Americans. The methods we employed can also provide an outline for genetic researchers interested in jointly testing SNP and CNV effects and/or applying mixed model procedures on a genome-wide scale. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4336133 Tue, 11 Jan 2011 00:00:00 +0100 4336133 http://www.medworm.com/index.php?rid=4317237&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F2 Conclusions: A network-based biomarker using constructed protein association networks is a useful tool to highlight the pathways and mechanisms of the lung carcinogenic process and, more importantly, provides potential therapeutic targets to combat cancer. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4317237 Thu, 06 Jan 2011 00:00:00 +0100 4317237 http://www.medworm.com/index.php?rid=4312841&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F4%2F1 Conclusions: The suppression of developmental networks may represent a remnant of a broad malfunction of regulatory pathways leading to inaccurate boundary formation and improper structural development in the embryonic heart. We suggest that small tissue specific genomic and/or epigenetic fluctuations could be cumulative, leading to regulatory network disruption and failure of proper cardiac development. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4312841 Wed, 05 Jan 2011 00:00:00 +0100 4312841 http://www.medworm.com/index.php?rid=4284049&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F61 Conclusions: Our microarray gene profiling study revealed that the expression of genes involved in adipogenesis is profoundly altered in the subcutaneous adipose tissue of morbidly obese subjects. This expression pattern is consistent with an immature adipocyte phenotype that could reflect the expansion of the adipose tissue during obesity. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4284049 Thu, 23 Dec 2010 00:00:00 +0100 4284049 http://www.medworm.com/index.php?rid=4274440&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F60 Conclusions: The relative RNA abundance obtained from two highly differing density gene panels are correlated with eight common genes differentiating HER2+ and HER2- breast tumors. Network analyses demonstrated biological consistency between the 1.5K and 24K gene panels. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4274440 Mon, 20 Dec 2010 00:00:00 +0100 4274440 http://www.medworm.com/index.php?rid=4263132&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F59 Conclusions: Our results support a genetic distinction between BHDS-associated tumors and other renal neoplasias. In addition, deregulation of the PGC-1alpha-TFAM signaling axis is most pronounced in renal tumors that harbor FLCN mutations and in tumors from other organs that have relatively low expression of FLCN. These results are consistent with the recently discovered interaction between FLCN and AMPK and support a model in which FLCN is a regulator of mitochondrial function. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4263132 Thu, 16 Dec 2010 00:00:00 +0100 4263132 http://www.medworm.com/index.php?rid=4248081&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F57 Conclusions: Alleles associated with genetic disease differ from randomly selected HapMap alleles and neutral expectations. The evolutionary history of alleles (frequency and ancestral vs. derived state) influences whether they are implicated in genome-wide assocation studies. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4248081 Fri, 10 Dec 2010 00:00:00 +0100 4248081 http://www.medworm.com/index.php?rid=4218320&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F56 Conclusion: This study provides a comprehensive characterization of the whole blood transcriptome in obesity and demonstrates that the investigation of gene expression profiles from whole blood can inform and illustrate the biological processes related to regulation of body mass. Additionally, the ability of pathway-related gene expression to predict class membership suggests the feasibility of a similar approach for identifying clinically useful blood-based predictors of weight loss success following dietary or surgical interventions. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4218320 Wed, 01 Dec 2010 00:00:00 +0100 4218320 http://www.medworm.com/index.php?rid=4202261&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F55 Conclusions: We developed an empirical Bayes model to study the association between DNA methylation in the promoter region and gene expression. Our approach generates both global (across all genes) and local (individual gene) views of the interplay. It provides important insight on future effort to develop therapeutic agent to re-sensitize breast cancer cells to treatment. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4202261 Thu, 25 Nov 2010 00:00:00 +0100 4202261 http://www.medworm.com/index.php?rid=4195425&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F54 Conclusions: We propose that these elements may be interpreted as hallmarks for dose-sensitive genes, particularly for those genes whose gain or loss may be directly implied in neurodevelopmental disorders. Therefore, their presence in genomic imbalances of unknown effect might be suggestive of a clinically relevant condition. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4195425 Tue, 23 Nov 2010 00:00:00 +0100 4195425 http://www.medworm.com/index.php?rid=4148749&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F53 Conclusion: The molecular defects in the silencing of RELB involve an increase in H3K9- but not CpG-island methylation in the promoter regions. Increase in acetyl-H3 in resistant female but not male CLL samples as well as a decrease of total cellular level of RelB after an inhibition of histone deacetylase (HDAC) by trichostatin A (TSA), further emphasize the role of epigenetic modifications which could discriminate two CLL subsets. Together, these results highlighted the epigenetic RELB silencing as a new marker of the progressive disease in males. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4148749 Wed, 10 Nov 2010 00:00:00 +0100 4148749 http://www.medworm.com/index.php?rid=4131265&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F51 Conclusions: Therefore, these results can be used for developing high specificity biomarkers sensing cancer invasion and predicting response to neoadjuvant therapy, as well as potential multi-cancer metastasis inhibiting therapeutics targeting the corresponding biological mechanism. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4131265 Wed, 03 Nov 2010 00:00:00 +0100 4131265 http://www.medworm.com/index.php?rid=4115323&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F50 Conclusions: As a meta-query engine, Genotator provides high coverage of both historical genetic research as well as recent advances in the genetic understanding of specific diseases. As such, Genotator provides a real-time aggregation of ranked data that remains current with the pace of research in the disease fields. Genotator's algorithm appropriately transforms query terms to match the input requirements of each targeted databases and accurately resolves named synonyms to ensure full coverage of the genetic results with official nomenclature. Genotator generates an excel-style output that is consistent across disease queries and readily importable to other applications. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4115323 Thu, 28 Oct 2010 23:00:00 +0100 4115323 http://www.medworm.com/index.php?rid=4115324&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F49 Conclusions: Literature mining compiled ROS-diabetes related targets from the biomedical literature and led us to evaluate the biological relevance of selected targets in the pathogenesis of diabetic neuropathy. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4115324 Tue, 26 Oct 2010 23:00:00 +0100 4115324 http://www.medworm.com/index.php?rid=4094519&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F48 Conclusions: The hepatic miRNA expression pattern that exists in CHC patients before combination therapy is associated with their therapeutic outcome. This information can be utilized as a novel biomarker to predict drug response and can also be applied to developing novel anti-viral therapy for CHC patients. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4094519 Thu, 21 Oct 2010 23:00:00 +0100 4094519 http://www.medworm.com/index.php?rid=4076409&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F47 Conclusions: A multi-step admixture mapping analysis of AA ESKD patients replicated the finding of a candidate risk locus on chromosome 22, contributing to the heightened susceptibility of African Americans to develop non-diabetic ESKD, and underscores the importance of using mutual information and multiple ancestry inference approaches to achieve a robust analysis, using relatively small datasets of "affected" only individuals. The current study suggests solutions to some limitations of existing admixture mapping methodologies, such as considerations regarding the distribution of ancestry information along the genome and its effects on power calculations and sample size. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4076409 Sun, 17 Oct 2010 23:00:00 +0100 4076409 http://www.medworm.com/index.php?rid=4064015&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F45 Conclusion: The findings provide a novel comprehensive approach for understanding the pathogenesis of various co-associated chronic inflammatory diseases by combining the power of pathway analysis with gene regulatory network evaluation. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4064015 Tue, 12 Oct 2010 23:00:00 +0100 4064015 http://www.medworm.com/index.php?rid=4064014&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F46 Conclusions: Our microarray analysis represents the first ex vivo study comparing gene expression profiles of CD8 T cells isolated from distinct sites after immunization with an adenoviral vector by different routes. It confirms earlier phenotypic data indicating that lung i.n. cells are more activated than lung i.d. CD8 T cells. The sustained expression of chemokines and activation genes enables pulmonary CD8 T cells to remain in the lungs for extended periods after i.n. immunization. This may account for the early inhibition of M. tuberculosis growth observed in Ad85A i.n. immunized mice and explain the effectiveness of i.n. compared to parenteral immunization with this viral vector. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4064014 Tue, 12 Oct 2010 23:00:00 +0100 4064014 http://www.medworm.com/index.php?rid=4029948&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F44 Conclusions: Our study shows that global mRNA expression analysis is a useful strategy to examine molecular effects of drugs, which allowed us the discovery of new biomarkers of 17AAG activity and provided more insights into the complex mechanism of 17AAG resistance. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=4029948 Sun, 03 Oct 2010 23:00:00 +0100 4029948 http://www.medworm.com/index.php?rid=3997049&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F42 Conclusions: Overall, the study suggests a link between polymorphisms in folate metabolic genes and DS risk in Italian women. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3997049 Thu, 23 Sep 2010 23:00:00 +0100 3997049 http://www.medworm.com/index.php?rid=3997048&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F43 Conclusions: The in vivo gene expression atlas for LNCaP was sequenced and support a role for the androgen receptor in CRPC. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3997048 Thu, 23 Sep 2010 23:00:00 +0100 3997048 http://www.medworm.com/index.php?rid=3964428&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F40 Conclusions: Our data provide evidences for a reduced number and altered morphology of endothelial progenitor cells in Down syndrome, also showing the higher susceptibility to oxidative stress and to pathogen infection compared to euploid cells, thereby confirming the angiogenesis and immune response deficit observed in Down syndrome individuals. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3964428 Sun, 12 Sep 2010 23:00:00 +0100 3964428 http://www.medworm.com/index.php?rid=3956860&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F39 Conclusion: We applied an intelligent pattern recognition method for analyzing the regulation of metabolism and elucidated substantial regulation of human breast cancer at the interplay of cholesterol biosynthesis and bile acid metabolism pointing to specific breast cancer treatment. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3956860 Thu, 09 Sep 2010 23:00:00 +0100 3956860 http://www.medworm.com/index.php?rid=3887991&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F38 Conclusions: Our proposed approach to the analysis of GAW16 data for rheumatoid arthritis was based on an underlying biological similarities-based method applied to candidate and known disease genes. Application of our method could identify likely causal candidate disease genes of rheumatoid arthritis, and could yield biological insights that not detected when focusing only on genes that give the strongest evidence by multiple testing. We hope that our proposed method complements the "most significant SNPs/genes" model, and provides additional insights into the pathogenesis of rheumatoid arthritis and other diseases, when searching datasets for hundreds of genetic variances. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3887991 Thu, 19 Aug 2010 23:00:00 +0100 3887991 http://www.medworm.com/index.php?rid=3847884&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F36 Conclusions: Degraded RNA from tumor samples (RIN > 5) can still be used to perform gene expression analysis. A much higher biological variance between patients is observed compared to the effect that is imposed by degradation of RNA. Nevertheless there are genes, very short ones and those with the probe binding side close to the 5' end that should be excluded from gene expression analysis when working with degraded RNA. These results are limited to the Agilent 44k microarray platform and should be carefully interpreted when transferring to other settings. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3847884 Sun, 08 Aug 2010 23:00:00 +0100 3847884 http://www.medworm.com/index.php?rid=3830430&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F35 Conclusions: Our Y chromosome analysis suggests that the same is protected from the effects of arsenic by some unknown mechanisms maintaining its structural and functional integrities. Thus, arsenic effects on the human body seem to be different compared to that on the cultured cells. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3830430 Thu, 05 Aug 2010 23:00:00 +0100 3830430 http://www.medworm.com/index.php?rid=3825984&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F33 Conclusion: This novel high throughput platform was able to successfully interrogate the methylation state of individual cytosines and identified 19 prospective CpG sites associated with risk of diabetic nephropathy. These differences in DNA methylation are worthy of further follow-up in replication studies using larger cohorts of diabetic patients with and without nephropathy. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3825984 Wed, 04 Aug 2010 23:00:00 +0100 3825984 http://www.medworm.com/index.php?rid=3825983&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F34 Background: Excessive accumulation of body fat, in particular in the visceral fat depot, is a major risk factor to develop a variety of diseases such as type 2 diabetes. The mechanisms underlying the increased risk of obese individuals to develop co-morbid diseases are largely unclear.We aimed to identify genes expressed in subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) that are related to blood parameters involved in obesity co-morbidity, such as plasma lipid and glucose levels, and to compare gene expression between the fat depots. Methods: Whole-transcriptome SAT and VAT gene expression levels were determined in 75 individuals with a BMI >35 kg/m2. Modules of co-expressed genes likely to be functionally related were identfied and correlated with BMI, plasma levels o... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3825983 Wed, 04 Aug 2010 23:00:00 +0100 3825983 http://www.medworm.com/index.php?rid=3815340&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F32 Conclusions: Our analyses found NDUFA1, RPL19, RAB5C, and RPS18 to occupy the top ranking positions among 15 suitable reference genes optimal for normalization of lung tissue expression data. Significantly, the approach used in this study can be applied to data generated using new generation sequencing platforms for the identification of reference genes optimal within diverse contexts. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3815340 Mon, 02 Aug 2010 23:00:00 +0100 3815340 http://www.medworm.com/index.php?rid=3801390&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F31 Conclusions: These results are the first to show that the radiation induced bystander signal induces a widespread gene expression response at 30 minutes after treatment and these changes are accompanied by modification of signaling proteins in the PI3K-AKT-GSK3betapathway. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3801390 Wed, 28 Jul 2010 23:00:00 +0100 3801390 http://www.medworm.com/index.php?rid=3756858&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F29 Conclusions: Our results indicate that not only individual genes but entire networks of gene interaction are influenced by cigarette smoking. This is the largest in vivo transcriptomic epidemiological study of smoking to date and reveals the significant and comprehensive influence of cigarette smoke, as an environmental variable, on the expression of genes. The central importance of this manuscript is to provide a summary of the relationships between gene expression and smoking in this exceptionally large cross-sectional data set. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3756858 Wed, 14 Jul 2010 23:00:00 +0100 3756858 http://www.medworm.com/index.php?rid=3728944&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F28 Conclusions: Our data support the hypothesis of a primary role for altered gene expression in ATRX syndrome and suggest that the GRAF1/OPHN-1-L gene might be involved in the pathogenesis of the mental retardation. Moreover a novel alternative splicing transcript of such gene, predominantly expressed in brain tissues, was identified. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3728944 Mon, 05 Jul 2010 23:00:00 +0100 3728944 http://www.medworm.com/index.php?rid=3717402&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F27 Conclusions: Our results support that MB could be a valuable intervention and should be investigated as a therapeutic agent against neural damage associated with I/R injury induced by cardiac arrest. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3717402 Wed, 30 Jun 2010 23:00:00 +0100 3717402 http://www.medworm.com/index.php?rid=3713159&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F26 Conclusions: These data demonstrate that the RAS pathway signature is superior to KRAS mutation status for the prediction of dependence on RAS signaling, can predict response to PI3K and RAS pathway inhibitors, and is likely to have the most clinical utility in lung and breast tumors. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3713159 Tue, 29 Jun 2010 23:00:00 +0100 3713159 http://www.medworm.com/index.php?rid=3705733&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F25 Conclusions: Our results highlight the need to apply powerful gene score methods prior to pathway enrichment tests, and that controlling for genes that attain genome wide significance enable further biological insight. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3705733 Sun, 27 Jun 2010 23:00:00 +0100 3705733 http://www.medworm.com/index.php?rid=3694324&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F24 Conclusions: Our results suggest that despite a high degree of degradation, RNA from buccal cells from cheek mucosa could be used to detect differential gene expression between smokers and nonsmokers. However the RNA degradation, increase in sample variability and microarray failure rate show that buccal samples should be used with caution as source material in expression studies. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3694324 Wed, 23 Jun 2010 23:00:00 +0100 3694324 http://www.medworm.com/index.php?rid=3686092&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F23 Conclusions: We developed an algorithm for cancer classification based on genome-wide patterns of copy number aberrations and demonstrated its superiority to existing clustering methods. The algorithm was applied to define genomic subgroups of three cancer types and identify cell lines representative of these subgroups. Our data enabled the assembly of representative cell line panels for testing drug candidates. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3686092 Mon, 21 Jun 2010 23:00:00 +0100 3686092 http://www.medworm.com/index.php?rid=3639823&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F22 Conclusions: Our study supports the hypothesis that platelet phenotypes in response to ASA likely have genetic control and the combined approach of linkage and association offers an alternative approach to prioritizing regions of interest for subsequent follow-up. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3639823 Sun, 06 Jun 2010 23:00:00 +0100 3639823 http://www.medworm.com/index.php?rid=3602394&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F20 DiscussionWe caution that imprecision of language when conveying research conclusions, compounded by the potential distortion of findings by the media, can lead to the stigmatization of racial and ethnic groups.SummaryIt is essential that the scientific community and with those reporting and disseminating research findings continue to foster a socially responsible dialogue about genetic variation and human difference. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3602394 Tue, 25 May 2010 23:00:00 +0100 3602394 http://www.medworm.com/index.php?rid=3559123&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F18 Conclusions: This study provides evidence that eEPCs are haematopoietic cells with a molecular phenotype linked to monocytes; whereas OECs exhibit commitment to the endothelial lineage. These findings indicate that OECs might be an attractive cell candidate for inducing therapeutic angiogenesis, while eEPC should be used with caution because of their monocytic nature. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3559123 Wed, 12 May 2010 23:00:00 +0100 3559123 http://www.medworm.com/index.php?rid=3541358&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F17 Conclusions: We have developed a scalable and statistical method to identify possible environmental associations with disease using publicly available data and have validated some of the associations in the literature. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3541358 Wed, 05 May 2010 23:00:00 +0100 3541358 http://www.medworm.com/index.php?rid=3537014&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F15 Conclusions: These findings and the identification of five universal markers of chronic inflammation suggest that these diseases have a common background in pathomechanism, but still can be separated by peripheral blood gene expression. Importantly, the identified genes can be associated with overlapping biological processes including changed inflammatory response. Gene panels based on such markers can play a major role in the development of personalized medicine, in monitoring disease progression and can lead to the identification of new potential drug targets in chronic inflammation. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3537014 Tue, 04 May 2010 23:00:00 +0100 3537014 http://www.medworm.com/index.php?rid=3528886&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F14 Conclusions: A significant and common denominator in the results was the potential induction of signaling changes associated with immune or inflammatory response in the absence of a specific protein. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3528886 Mon, 03 May 2010 23:00:00 +0100 3528886 http://www.medworm.com/index.php?rid=3514302&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F13 Conclusions: This pathway network analysis demonstrated that mitochondrial dysfunction, oxidative stress, cell-cycle dysregulation, and the MAPK-signaling abnormality are significantly associated with a pituitary adenoma. These pathway-network data provide new insights into the molecular mechanisms of human pituitary adenoma pathogenesis, and new clues for an in-depth investigation of pituitary adenoma and biomarker discovery. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3514302 Tue, 27 Apr 2010 23:00:00 +0100 3514302 http://www.medworm.com/index.php?rid=3510479&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F12 Conclusions: Given their occult nature, opportunities to study premalignant stem/progenitor cells in human have been few. The ability to propagate and direct the differentiation of aneuploid hESCs provides a powerful in vitro system for investigating biological properties of human cells exhibiting features of premalignant stem cells. This in vitro culture system can be used to elucidate changes in gene expression occurring enroute to malignant transformation and to identify molecular markers of cancer stem/progenitor cells. These markers are invaluable for diagnostic purposes and may be novel targets for therapeutic intervention. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3510479 Mon, 26 Apr 2010 23:00:00 +0100 3510479 http://www.medworm.com/index.php?rid=3447697&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F10 Conclusions: Our report of another ASD patient carrying the splice site mutation IVS5+2T>C, in ASMT further supports an involvement of this gene in autism. Moreover, our results also suggest that other melatonin related genes might be interesting candidates for further investigation in the search for genes involved in autism spectrum disorders and related neurobehavioral phenotypes. However, further studies of the novel variants identified in this study are warranted to shed light on their potential role in the pathophysiology of these disorders. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3447697 Wed, 07 Apr 2010 23:00:00 +0100 3447697 http://www.medworm.com/index.php?rid=3353262&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F7 Conclusions: Although mspecLINE applies an information retrieval technique to theMEDLINE database, it is distinct from previous MEDLINE query tools inthat it combines the knowledge expressed in scientific literature withempirical proteomics data. The tool provides valuable informationabout candidate protein targets to researchers studying human diseaseand is freely available on a public web server. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3353262 Wed, 10 Mar 2010 00:00:00 +0100 3353262 http://www.medworm.com/index.php?rid=3341730&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F6 Conclusions: This study demonstrates, for the first time, that the expression profiles of childhood leukemia are largely unique, with limited similarities to transcriptional programs active in normal hematopoietic cells, non-hematopoietic normal tissues or the most common forms of human cancer. In addition to providing important pathogenetic insights, these findings should facilitate the identification of candidate genes or transcriptional programs that can be used as unique targets in leukemia. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3341730 Mon, 08 Mar 2010 00:00:00 +0100 3341730 http://www.medworm.com/index.php?rid=3257796&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F4 Conclusions: Clinically, elucidating the patterns of action of decitabine could aid in predicting the likelihood of up-regulating epigenetically silenced tumor suppressor genes and others from pathways involved with tumor biology. As a first step toward an eventual translational application, we build a classifier to predict gene up-regulation based on promoter methylation and CpG content, which achieves a performance of 0.74 AUC. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3257796 Tue, 09 Feb 2010 00:00:00 +0100 3257796 http://www.medworm.com/index.php?rid=3215425&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F3 Background: Prevalence of obesity is increasing to pandemic proportions. However, obese subjects differ in insulin resistance, adipokine production and co-morbidities. Based on fasting plasma analysis, obese subjects were grouped as Low Acylation Stimulating protein (ASP) and Triglyceride (TG) (LAT) vs High ASP and TG (HAT). Subcutaneous (SC) and omental (OM) adipose tissues (n=21) were analysed by microarray, and biologic pathways in lipid metabolism and inflammation were specifically examined. Methods: LAT and HAT groups were matched in age, obesity, insulin, and glucose, and had similar expression of insulin-related genes (InsR, IRS-1). ASP related genes tended to be increased in the HAT group and were correlated (factor B, adipsin, complement C3, p (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3215425 Wed, 27 Jan 2010 00:00:00 +0100 3215425 http://www.medworm.com/index.php?rid=3207495&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F3%2F2 Conclusions: Taken as a whole, the data obtained from this global gene profiling experiment have provided a detailed characterization of Graffi virus induced erythro- and megakaryoblastic leukaemias with many genes reported specific to the transcriptome of these leukaemias for the first time. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3207495 Tue, 26 Jan 2010 00:00:00 +0100 3207495 http://www.medworm.com/index.php?rid=3135010&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F72 Conclusions: Utilizing of gene expression profiling data from different tissues of individuals with or without T2DM or animal models thereof is a powerful tool for prioritizing SNPs from WGAS for further replication studies. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3135010 Thu, 31 Dec 2009 00:00:00 +0100 3135010 http://www.medworm.com/index.php?rid=3107877&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F70 Conclusions: We provide a computational framework to reconstruct the genetic regulatory network from the microarray data using biological knowledge and constraint-based inferences. Our method is helpful in verifying possible interaction relations in gene regulatory networks and filtering out incorrect relations inferred by imperfect methods. We predicted not only individual gene related to cancer but also discovered significant gene regulation networks. Our method is also validated in several enriched published papers and databases and the significant gene regulatory networks perform critical biological functions and processes including cell adhesion molecules, androgen and estrogen metabolism, smooth muscle contraction, and GO-annotated processes. Those significant gene regulations and th... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3107877 Mon, 21 Dec 2009 00:00:00 +0100 3107877 http://www.medworm.com/index.php?rid=3099480&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F69 Conclusion: Our molecular taxonomy of epithelial human cancer indicates surprising correlations over tissues. This may have a significant impact on the classification of many cancer sites and may guide pathologists, both in research and daily practice. Moreover, these results based on unsupervised analysis yielded a signature predictive of clinical outcome in breast cancer. Additionally, we hypothesize that metastases from gastrointestinal origin either remember their tissue of origin or adapt to the tissue of destination. More specifically, colon metastases in the liver show strong evidence for such a bimodal tissue specific profile. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3099480 Thu, 17 Dec 2009 00:00:00 +0100 3099480 http://www.medworm.com/index.php?rid=3091747&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F68 Conclusions: Present results provide novel evidence on the molecular basis of tumor growth inhibition mediated by mastic oil and set a rational basis for application of genomics and bioinformatic methodologies in the screening of natural compounds with potential cancer chemopreventive activities. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3091747 Tue, 15 Dec 2009 00:00:00 +0100 3091747 http://www.medworm.com/index.php?rid=3043436&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F67 Conclusions: This study identified HDACi-induced alterations in critical genes involved in nucleotide metabolism, angiogenesis, mitosis and cell survival which may represent potential intervention points for novel therapeutic combinations in colon cancer. This information will assist in the identification of novel pathways and targets that are modulated by HDACi, providing much-needed information on HDACi mechanism of action and providing rationale for novel drug combination partners. We identified a core signature of 11 genes which were modulated by both vorinostat and LBH589 in a similar manner in both cell lines. These core genes will assist in the development and validation of a common gene set which may represent a molecular signature of HDAC inhibition in colon cancer. (Source: BMC ... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3043436 Mon, 30 Nov 2009 00:00:00 +0100 3043436 http://www.medworm.com/index.php?rid=3038959&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F66 Conclusions: We describe a metadata approach for managing similarities and differences in clinical datasets in a standardized way that uses Common Data Elements (CDEs). We apply and evaluate the approach by integrating the five different clinical datasets of METABRIC. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=3038959 Mon, 30 Nov 2009 00:00:00 +0100 3038959 http://www.medworm.com/index.php?rid=2942463&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F64 Conclusions: In cancerous gene expression datasets, a small number of genes, even one or two if selected correctly, is capable of achieving an ideal cancer classification effect. This finding also means that very simple rules may perform well for cancerous class prediction. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=2942463 Fri, 30 Oct 2009 00:00:00 +0100 2942463 http://www.medworm.com/index.php?rid=2823003&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F62 Conclusion: Experimental manipulation of cells lines from subjects with schizophrenia may be a useful approach to explore stress related gene expression alterations in schizophrenia and to identify SNP variants associated with gene expression. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=2823003 Mon, 21 Sep 2009 23:00:00 +0100 2823003 http://www.medworm.com/index.php?rid=2792444&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F60 Conclusions: The magnitude of divergence in transcriptional profiles between normal chondrocytes and the cells that populate repair tissue reveal substantial functional differences between these two cell populations. At the four-month postoperative time point, the relative deficiency within repair tissue of gene transcripts which typically define articular cartilage indicate that while cells occupying the lesion might be of mesenchymal origin, they have not recapitulated differentiation to the chondrogenic phenotype of normal articular chondrocytes. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=2792444 Sun, 13 Sep 2009 23:00:00 +0100 2792444 http://www.medworm.com/index.php?rid=2781031&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F58 Conclusions: Human trabecular meshwork cells in culture express all known GRalpha and GRbeta translational isoforms, and GCs with similar potency but subtly different chemical structure are capable of regulating common and unique gene subsets and presumably biologic responses in these cells. These GC structure-dependent effects appear to be TM cell-lineage dependent. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=2781031 Wed, 09 Sep 2009 23:00:00 +0100 2781031 http://www.medworm.com/index.php?rid=2740399&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F57 Conclusions: These results indicate that very small amounts of starting material are sufficient to allow sensitive miRNA profiling using the Illumina miRNA high-dimensional platform. Nonlinear biases were observed between replicates, indicating the need for abundance-dependent normalization. Overall, the performance characteristics of the Illumina miRNA profiling system were excellent. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=2740399 Wed, 26 Aug 2009 23:00:00 +0100 2740399 http://www.medworm.com/index.php?rid=2722634&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F56 Conclusion: Global transcriptional analysis identified a set of genes responding to MTS exposure in mouse lung. These genes returned to basal levels following smoking cessation, providing evidence to support the benefits of smoking cessation. Detailed analyses were undertaken for IL-6 and its associated pathways. Our results provide further insight into the role of these pathways in lung injury and inflammation induced by MTS. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=2722634 Thu, 20 Aug 2009 23:00:00 +0100 2722634 http://www.medworm.com/index.php?rid=2715060&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F55 Conclusions: Our results suggest that inhibitors of MAO-A, already in clinical use to treat depression, may have potential application as therapeutic PCa drugs by inhibiting oncogenic pathway activity and promoting differentiation. (Source: BMC Medical Genomics) BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=2715060 Wed, 19 Aug 2009 23:00:00 +0100 2715060 http://www.medworm.com/index.php?rid=2707963&cid=s_36936_50_f&fid=36936&url=http%3A%2F%2Fwww.biomedcentral.com%2F1755-8794%2F2%2F54 Background: MicroRNAs (miRNAs) are non-coding RNA molecules involved in post-transcriptional control of gene expression of a wide number of genes, including those involved in glucose homeostasis. Type 2 diabetes (T2D) is characterized by hyperglycaemia and defects in insulin secretion and action at target tissues. We sought to establish differences in global miRNA expression in two insulin-target tissues from inbred rats of spontaneously diabetic and normoglycaemic strains. Methods: We used a miRNA microarray platform to measure global miRNA expression in two insulin-target tissues: liver and adipose tissue from inbred rats of spontaneously diabetic (Goto-Kakizaki [GK]) and normoglycaemic (Brown-Norway [BN]) strains which are extensively used in genetic studies of T2D. MiRNA data were inte... BMC Medical Genomics journals http://www.medworm.com/rss/comments.php?id=2707963 Mon, 17 Aug 2009 23:00:00 +0100 2707963