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Accurate molecular classification of cancer using simple rulesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: BMC Medical Genomics - October 30, 2009 Category: Genetics & Stem Cells Authors: Xiaosheng WangOsamu Gotoh Source Type: journals

Exon expression in lymphoblastoid cell lines from subjects with schizophrenia before and after glucose deprivationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: BMC Medical Genomics - September 21, 2009 Category: Genetics & Stem Cells Authors: Maureen MartinBrandi RollinsP. Adolpho SequeiraAndrea MesenWilliam ByerleyRichard SteinEmily MoonHuda AkilEdward JonesStanley WatsonJack BarchasLynn DeLisiRichard MyersAlan SchatzbergWilliam BunneyMarquis Vawter Source Type: journals

Transcriptional profiling differences for articular cartilage and repair tissue in equine joint surface lesionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: BMC Medical Genomics - September 13, 2009 Category: Genetics & Stem Cells Authors: Michael MienaltowskiLiping HuangDavid FrisbieC. Wayne McIlwraithArnold StrombergArne BathkeJames MacLeod Source Type: journals

Glucocorticoids with different chemical structures but similar glucocorticoid receptor potency regulate subsets of common and unique genes in human trabecular meshwork cells.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: BMC Medical Genomics - September 9, 2009 Category: Genetics & Stem Cells Authors: Alissar NehmeEdward LobenhoferW StamerJeffrey Edelman Source Type: journals

Evaluation of a new high-dimensional miRNA profiling platformEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: BMC Medical Genomics - August 26, 2009 Category: Genetics & Stem Cells Authors: Julie CunninghamAnn ObergPedro BorralhoBetsy KrenAmy FrenchLiang WangBrian BotBruce MorlanKevin SilversteinRod StaggsYan ZengAnne-Francoise LamblinChristopher HilkerJian-Bing FanClifford SteerStephen Thibodeau Source Type: journals

Induction of the interleukin 6/ signal transducer and activator of transcription pathway in the lungs of mice sub-chronically exposed to mainstream tobacco smoke.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: BMC Medical Genomics - August 20, 2009 Category: Genetics & Stem Cells Authors: Sabina HalappanavarMarsha RussellMartin StampfliAndrew WilliamsCarole Yauk Source Type: journals

Anti-oncogenic and pro-differentiation effects of clorgyline, a monoamine oxidase A inhibitor, on high grade prostate cancer cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: BMC Medical Genomics - August 19, 2009 Category: Genetics & Stem Cells Authors: Hongjuan ZhaoVincent FlamandDonna Peehl Source Type: journals

MicroRNA-125a is over-expressed in insulin target tissues in a spontaneous rat model of Type 2 DiabetesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 rat...
Source: BMC Medical Genomics - August 17, 2009 Category: Genetics & Stem Cells Authors: Blanca HerreraHelen LockstoneJennifer TaylorQuin WillsPamela KaisakiAmy BarrettCarme CampsCristina FernandezJiannis RagoussisDominique GauguierMark McCarthyCecilia Lindgren Source Type: journals

A gene expression profile for detection of sufficient tumour cells in breast tumour tissue: microarray diagnosis eligibilityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The developed 13-gene profile provides an objective tool for assessment whether a breast cancer sample contains sufficient tumour cells for microarray diagnostics. It will improve the efficiency and throughput for diagnostic gene expression profiling as it no longer requires histopathological analysis for initial tumour percentage scoring. Such profile will also be very use useful for assessment of tumour cell percentage in biopsies where conventional histopathology is difficult, such as fine needle aspirates. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - August 11, 2009 Category: Genetics & Stem Cells Authors: Paul RoepmanArenda SchuurmanLeonie DelahayeAnke WitteveenArno FlooreAnnuska Glas Source Type: journals

Integrated microarray and multiplex cytokine analyses of Kaposi's Sarcoma Associated Herpesvirus viral FLICE Inhibitory Protein K13 affected genes and cytokines in human blood vascular endothelial cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: While K13 may account for change in the expression of a majority of genes observed following KSHV infection, it is not sufficient for inducing lymphatic reprogramming of blood vascular endothelial cells. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - August 5, 2009 Category: Genetics & Stem Cells Authors: Vasu PunjHittu MattaSandra SchamusPreet Chaudhary Source Type: journals

Identification and Validation of Suitable Endogenous Reference Genes for Gene Expression Studies in Human Peripheral BloodEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The reference genes identified in this study are stably expressed in whole blood of humans of both genders with multiple disease conditions and ages 2 to 78. Importantly, they also have different functions within cells and thus should be expressed independently of each other. These genes should be useful as normalization genes for microarray and RT-PCR whole blood studies of human physiology, metabolism and disease. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - August 4, 2009 Category: Genetics & Stem Cells Authors: Boryana StamovaMichelle AppersonWynn WalkerYingfang TianHuichun XuPeter AdamczykXinhua ZhanDa-Zhi LiuBradley AnderIsaac LiaoJeffrey GreggRenee TurnerGlen JicklingLisa LitFrank Sharp Source Type: journals

Candidate pathways and genes for prostate cancer: a meta-analysis of gene expression dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The results of this study suggest that prostate tumor progression is associated with the suppression of integrin-based cell adhesion. Suppression of integrin expression driven by integrin-mediated cell death may lead to increased cell proliferation and motility and increase tumor malignancy. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - August 3, 2009 Category: Genetics & Stem Cells Authors: Ivan GorlovJinyoung ByunOlga GorlovaAna AparicioEleni EfstathiouChristopher Logothetis Source Type: journals

Host sequence motifs shared by HIV predict response to antiretroviral therapyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: HIV sequence mutates in a way that preserves peptide sequence motifs that are also found in the human proteome. The presence and absence of such motifs at specific regions of the HIV sequence is highly predictive of response to therapy. These motifs are well established in bioinformatics databases and do not require identification via in-vitro mutation experiments. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - July 22, 2009 Category: Genetics & Stem Cells Authors: William DampierPerry EvansLyle UngarAydin Tozeren Source Type: journals

An assessment of the portability of ancestry informative markers between human populationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: We find that BritAIMs are generally not useful to distinguish between continental groups or within continental groups distantly related to Britain. Moreover, our analyses suggest that the portability of AIMs across geographical scales (e.g. between Europe and Britain) can be limited and should therefore be taken into consideration in the design and interpretation of genetic association studies. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - July 19, 2009 Category: Genetics & Stem Cells Authors: Sean MylesMark StonekingNic Timpson Source Type: journals

Novel transcriptional profile in wrist muscles from cerebral palsy patientsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This is the first transcriptional profile performed on spastic muscle of CP patients and these adaptations were not characteristic of those observed in other disease states such as Duchenne muscular dystrophy and immobilization-induced muscle atrophy. Further research is required to understand the mechanism of muscle adaptation to this upper motor neuron lesion that could lead to the development of innovative therapies. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - July 13, 2009 Category: Genetics & Stem Cells Authors: Lucas SmithEva PontenYvette HedstromSamuel WardHenry ChambersShankar SubramaniamRichard Lieber Source Type: journals

Finding exclusively deleted or amplified genomic areas in lung adenocarcinomas using a novel chromosomal pattern analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Analyzing jointly deletions and amplifications through our latent class model analysis allows highlighting specific genomic areas with exclusively amplified or deleted recurrent CNAs which are good candidate for harboring oncogenes or tumor suppressor genes. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - July 13, 2009 Category: Genetics & Stem Cells Authors: Philippe BroetPatrick TanMarco AlifanoSophie Camilleri-BroetSylvia Richardson Source Type: journals

Genomic profiling distinguishes familial multiple and sporadic multiple meningiomasEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Genomic profiling can provide an unbiased adjunct to traditional meningioma classification and provides a basis for exploring the different genetic underpinnings of tumor initiation and progression. Most importantly, the striking difference observed between sporadic and familial multiple meningiomas indicates that genomic profiling can provide valuable information for differential diagnosis of subjects with multiple meningiomas and for considering the risk for tumor occurrence in their family members. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - July 8, 2009 Category: Genetics & Stem Cells Authors: Yiping ShenFabio NunesAnat Stemmer-RachamimovMarianne JamesGayatry MohapatraScott PlotkinRebecca BetenskyDavid EnglerJennifer RoyVijaya RameshJames Gusella Source Type: journals

Functional annotations of diabetes nephropathy susceptibility loci through analysis of genome-wide renal gene expression in rat models of diabetes mellitusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Combining transcriptomics in animal models and comparative genomics provides important information to improve functional annotations of disease susceptibility loci in humans and experimental support for testing candidate genes in human genetics. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - July 8, 2009 Category: Genetics & Stem Cells Authors: Yaomin HuPamela KaisakiKarene ArgoudSteven WilderKarin WallacePeng WoonChristine BlancherLise TarnowPer-Henrik GroopSamy HadjadjMichel MarreHans-Henrik ParvingMartin FarrallRoger CoxMark LathropNathalie VionnetMarie-Therese BihoreauDominique Gauguier Source Type: journals

The Gene expression Grade Index: a potential predictor of relapse for endocrine-treated breast cancer patients in the BIG 1-98 trialEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This analysis supports the GGI as a good predictor of relapse for ER-positive patients, even among patients who receive L. Validation of these results, in a larger series from BIG 1-98, is planned using the simplified GGI represented by a smaller set of genes and tested by qRT-PCR on paraffin-embedded tissues. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - July 1, 2009 Category: Genetics & Stem Cells Authors: Christine DesmedtAnita Giobbie-HurderPatrick NevenRobert ParidaensMarie-Rose ChristiaensAnn SmeetsFrancoise LallemandBenjamin Haibe-KainsGiuseppe VialeRichard GelberMartine PiccartChristos Sotiriou Source Type: journals

NMD inhibition fails to identify tumour suppressor genes in microsatellite stable gastric cancer cell linesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Although UPF1 was substantially repressed, thus resulting in the inhibition of the NMD system, we did not find genes inactivated by nonsense mutations. Our results show that the GINI strategy leads to a high number of false positives. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - June 28, 2009 Category: Genetics & Stem Cells Authors: Tineke BuffartMarianne TijssenJamila El-BchiriAlex DuvalMark van de WielBauke YlstraGerrit MeijerBeatriz Carvalho Source Type: journals

A Gene Signature for Post-Infectious Chronic Fatigue SyndromeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Differential expression of key genes identified in this study offer an insight into the possible mechanism of chronic fatigue following infection. The representative biomarkers identified in this research appear promising as potential biomarkers for differential diagnosis and treatment. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - June 24, 2009 Category: Genetics & Stem Cells Authors: John GowSuzanne HaganPawel HerzykCelia CannonPeter BehanAbhijit Chaudhuri Source Type: journals

Gene expression profiling identifies activated growth factor signaling in poor prognosis (Luminal-B) estrogen receptor positive breast cancerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These data demonstrate that activation of GF signaling pathways, independent of HER2 over-expression, could be contributing to the poor prognosis of the luminal-B ER+ BC subtype. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - June 23, 2009 Category: Genetics & Stem Cells Authors: Sherene LoiChristos SotiriouBenjamin Haibe-KainsFrancoise LallemandNelly ConusMartine PiccartTerence SpeedGrant McArthur Source Type: journals

MLL rearrangements in pediatric acute lymphoblastic and myeloblastic leukemias: MLL specific and lineage specific signaturesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our study demonstrated that a small subset of genes identifies MLL-specific rearrangements and clearly separates acute leukemia samples according to lineage origin. The subset included well-known genes and newly discovered markers that identified ALL and AML subgroups, with and without MLL rearrangements. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - June 22, 2009 Category: Genetics & Stem Cells Authors: Andrea ZangrandoMarta Campo Dell'OrtoGeertruy KronnieGiuseppe Basso Source Type: journals

Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Pyrosequencing of small RNAs, together with a computational pipeline, can be used to identify miRNAs in tumor and other tissues. Measures of miRNA end variability may in the future be incorporated into the discovery pipeline as a discriminatory feature. Breast cancer samples show a distinct miRNA expression profile compared to normal adjacent breast. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - June 9, 2009 Category: Genetics & Stem Cells Authors: Sanne NygaardAnders JacobsenMorten LindowJens EriksenEva BalslevHenrik FlygerNiels TolstrupSoren MollerAnders KroghThomas Litman Source Type: journals

Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Selective epigenetic disruption of distinct biological pathways was observed during development of platinum resistance in ovarian cancer. Integrated analysis of DNA methylation and gene expression may allow for the identification of new therapeutic targets and/or biomarkers prognostic of disease response. Finally, our results suggest that epigenetic therapies may facilitate the prevention or reversal of transcriptional repression responsible for chemoresistance and the restoration of sensitivity to platinum-based chemotherapeutics. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - June 8, 2009 Category: Genetics & Stem Cells Authors: Meng LiCurt BalchJohn MontgomeryMikyoung JeongJae Hoon ChungPearlly YanTim HuangSun KimKenneth Nephew Source Type: journals

A longitudinal study of gene expression in healthy individualsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This study defines the range and variability of gene expression in healthy men and women over a six-month period. These parameters can be used to estimate the number of subjects needed to observe significant differences from normal gene expression in clinical studies. A set of genes that varied by gender was also identified as were a set of genes with elevated expression in a subject with iron deficiency anemia and another subject being treated for lung cancer. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - June 7, 2009 Category: Genetics & Stem Cells Authors: Chris KarlovichGuillemette Duchateau-NguyenAndrea JohnsonPatricia McLoughlinMercidita NavarroCarole FleurbaeyLori SteinerMichel TessierTracy NguyenMonika Wilhelm-SeilerJohn Caulfield Source Type: journals

Genomic profiling identifies common HPV-associated chromosomal alterations in squamous cell carcinomas of cervix and head and neckEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: In this study hrHPV-specific, organ-specific, and pan-SCC chromosomal alterations were identified. The existence of hrHPV-specific alterations in SCCs of different anatomical origin suggests that these alterations are crucial for hrHPV-mediated carcinogenesis. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - June 1, 2009 Category: Genetics & Stem Cells Authors: Saskia WiltingSerge SmeetsPeter SnijdersWessel van WieringenMark van de WielGerrit MeijerBauke YlstraC Rene LeemansChris MeijerRuud BrakenhoffBoudewijn BraakhuisRenske Steenbergen Source Type: journals

Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart diseaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: We identified patterns comprised of putative cis-regulatory motifs enriched in the upstream promoter sequence of genes that undergo similar changes in expression secondary to cardiomyopathies of various etiologies. Our analysis is a first step towards understanding transcription factor networks that are active in regulating gene expression during degenerative heart disease. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - May 28, 2009 Category: Genetics & Stem Cells Authors: Charles DankoArkady Pertsov Source Type: journals

Hypermethylation of genomic 3.3-kb repeats is frequent event in HPV-positive cervical cancerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Our results demonstrate that hypermethylation rather than hypomethylation of 3.3-kb repeats is the predominant event in HPV-associated cervical cancer and provide new insight into the epigenetic changes of repetitive DNA elements in carcinogenesis. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - May 27, 2009 Category: Genetics & Stem Cells Authors: Alexey KatarginLarissa PavlovaFjodor KisseljovNatalia Kisseljova Source Type: journals

The A's, G's, C's, and T's of Health DisparitiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In order to eliminate health disparities in the United States, more efforts are needed to address the breadth of social issues directly contributing to the healthy divide observed across racial and ethnic groups. Socioeconomic status, education, and, very generally, the environment are intimately linked to health outcomes. However, with the tremendous advances in technology and increased investigation into human genetic variation, genomics is poised to play a valuable role in bolstering efforts to find new treatments and preventions for chronic conditions and diseases that disparately affect certain groups. Promising studi...
Source: BMC Medical Genomics - May 22, 2009 Category: Genetics & Stem Cells Authors: Edward RamosCharles Rotimi Source Type: journals

Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: A list of host proteins highly enriched with those targeted by HIV-1 proteins can be obtained by searching for host protein motifs along virus protein sequences. The resulting set of host proteins predicted to be targeted by virus proteins will become more accurate with better annotations of motifs and domains. Nevertheless, our study validates the role of linear binding motifs shared by virus and host proteins as an important part of the crosstalk between virus and host. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - May 18, 2009 Category: Genetics & Stem Cells Authors: Perry Evans, Will Dampier, Lyle Ungar and Aydin Tozeren Source Type: journals

Similar gene expression profiles of sporadic, PGL2-, and SDHD-linked paragangliomas suggest a common pathway to tumorigenesisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The similarity in gene-expression profiles suggests that PGL2, like SDHD, is involved in the functionality of the SDH complex, and that tumor formation in these subgroups involves the same pathways as in SDH linked paragangliomas. We were not able to clarify the exact identity of PGL2 on 11q13. The lack of differential gene-expression of chromosome 11 genes might indicate that chromosome 11 loss, as demonstrated in SDHD-linked paragangliomas, is an important feature in the formation of paragangliomas regardless of their genetic background. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - May 11, 2009 Category: Genetics & Stem Cells Authors: Erik F Hensen, Jelle J Goeman, Jan Oosting, Andel GL van der Mey, Pancras CW Hogendoorn, Cor WRJ Cremers, Peter Devilee and Cees J Cornelisse Source Type: journals

Data integration from two microarray platforms identifies bi-allelic genetic inactivation of RIC8A in a breast cancer cell lineEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We demonstrate a data integration strategy leading to the identification of RIC8A as a gene undergoing a classical double-hit genetic inactivation in a breast cancer cell line, as well as in vivo evidence of loss of RIC8A expression in a subgroup of aggressive TP53 mutant breast cancers. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - May 11, 2009 Category: Genetics & Stem Cells Authors: Aslaug Aamodt Muggerud, Henrik Edgren, Maija Wolf, Kristine Kleivi, Emelyne Dejeux, Jorg Tost, Therese Sorlie and Olli Kallioniemi Source Type: journals

Identification of microbial DNA in human cancerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: DK-MICROBE can identify previously unknown infectious agents in human tumors, and is now available for further applications for the identification of pathogen DNA in human cancer and other diseases. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - May 8, 2009 Category: Genetics & Stem Cells Authors: Christopher G Duncan, Rebecca J Leary, Jimmy Cheng-Ho Lin, Jordan Cummins, Chunhui Di, Carl F Schaefer, Tian-Li Wang, Gregory J Riggins, Jennifer Edwards, Darell Bigner, Levy Kopelovich, Bert Vogelstein, Kenneth W Kinzler, Victor E Velculescu and Hai Yan Source Type: journals

High-resolution analysis of copy number alterations and associated expression changes in ovarian tumorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These analyses provide detailed views of ovarian cancer genomic changes and highlight the benefits of using multiple reference sample types for the evaluation of CNA-specific expression changes. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - May 6, 2009 Category: Genetics & Stem Cells Authors: Peter M Haverty, Lawrence S Hon, Joshua S Kaminker, John Chant and Zemin Zhang Source Type: journals

Development of a fingerprinting panel using medically relevant polymorphismsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The polymorphisms in this panel are currently represented on a number of common genotyping platforms making QA/QC flexible enough to accommodate a large number of studies. In addition, this panel can serve as a resource for investigators who are interested in the effects of disease in a population, particularly for common diseases. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - April 20, 2009 Category: Genetics & Stem Cells Authors: Deanna S Cross, Lynn C Ivacic and Catherine A McCarty Source Type: journals

Complexity in the Genetic Architecture of Leukoaraiosis in Hypertensive Sibships from the GENOA StudyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These results indicate that the genetic architecture of leukoaraiosis is complex, yet predictive, when the contributions of SNP main effects are considered in combination with effects of SNP interactions with other genes and covariates. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - April 7, 2009 Category: Genetics & Stem Cells Authors: Jennifer A Smith, Stephen T Turner, Yan V Sun, Myriam Fornage, Reagan J Kelly, Thomas H Mosley, Clifford R Jack, Iftikhar J Kullo and Sharon LR Kardia Source Type: journals

Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Target prediction programs and expression profiling techniques do not yet adequately represent the complexity of miRNA-mediated gene repression, and new methods may be required to better elucidate these pathways. Our data suggest the physiologic impact of miRNAs on cellular transcription results from a multifaceted network of miRNA and mRNA relationships, working together in an interconnected system and in context of hundreds of RNA species. The methods described here for comparative analysis of cellular miRNA and mRNA will be useful for understanding genome wide regulatory responsiveness and refining miRNA pr...
Source: BMC Medical Genomics - March 25, 2009 Category: Genetics & Stem Cells Authors: Jennifer S. Guimbellot, Stephen W. Erickson, Tapan Mehta, Hui Wen, Grier P. Page, Eric J. Sorscher and Jeong S. Hong Source Type: journals

Distinct gene subsets in pterygia formation and recurrence: dissecting complex biological phenomenon using genome wide expression dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Aberrant wound healing is therefore a key process in this disease, and strategies in wound remodeling may be appropriate in halting pterygium or its recurrence. For patients demonstrating a profile of 'recurrence', it may be necessary to manage as a poorer prognostic case and perhaps, more adjunctive treatment after resection of the primary lesion. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - March 10, 2009 Category: Genetics & Stem Cells Authors: Louis Tong, Jamie Chew, Henry Yang, Leonnard PK Ang, Donald TH Tan and Roger W Beuerman Source Type: journals

Impact of sample acquisition and linear amplification on gene expression profiling of lung adenocarcinoma: laser capture micro-dissection cell-sampling versus bulk tissue-samplingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: LCM-coupled microarray expression profiling was shown to uniquely identify a large number of differentially expressed probesets not otherwise found using bulk tissue sampling. The information gain realized from the LCM sampling was limited to differential analysis, as the absolute expression values obtained for some probesets using this study's protocol were biased during the second round of amplification. Consequently, LCM may enable investigators to obtain additional information in microarray studies not easily found using bulk tissue samples, but it is of critical importance that potential amplification bia...
Source: BMC Medical Genomics - March 9, 2009 Category: Genetics & Stem Cells Authors: Eric W Klee, Sibel Erdogan, Lori Tillmans, Farhad Kosari, Zhifu Sun, Dennis A Wigle, Ping Yang, Marie C Aubry and George Vasmatzis Source Type: journals

Impaired immune function in Gulf War Illness.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: GWI patients demonstrated impaired immune function as demonstrated by decreased NK cytotoxicity and altered gene expression associated with NK cell function. Pro-inflammatory cytokines, T-cell ratios, and dysregulated mediators of the stress response (including salivary cortisol) were also altered in GWI cases compared to control subjects. An interesting and potentially important observation was that the exercise challenge augments these differences, with the most significant effects observed immediately after the stressor, possibly implicating some block in the NK and CD8 T-cells ability to respond to "stress...
Source: BMC Medical Genomics - March 5, 2009 Category: Genetics & Stem Cells Authors: Toni Whistler, Mary Ann Fletcher, William Lonergan, Xiao R Zeng, Jin-Mann S Lin, Arthur LaPerriere, Suzanne D Vernon and Nancy G Klimas Source Type: journals

Promoter methylation correlates with reduced NDRG2 expression in advanced colon tumourEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The findings highlight the usefulness of combining gene expression patterns and epigenetic data to identify tumour biomarkers, and suggest that NDRG2 silencing might bear influence on tumour invasiveness, being associated with a more advanced stage. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - March 3, 2009 Category: Genetics & Stem Cells Authors: Ada Piepoli, Rosa Cotugno, Giuseppe Merla, Annamaria Gentile, Bartolomeo Augello, Michele Quitadamo, Antonio Merla, Anna Panza, Massimo Carella, Rosalia Maglietta, Annarita D'Addabbo, Nicola Ancona, Saverio Fusilli, Francesco Perri and Angelo Andriulli Source Type: journals

Disease-associated pathophysiologic structures in pediatric rheumatic diseases show characteristics of scale-free networks seen in physiologic systems: implications for pathogenesis and treatmentEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Genome-level transcriptional profiling from childhood onset rheumatic diseases suggested complex interactions in two arms of the immune system in both diseases. The disease associated networks showed scale-free network patterns similar to those reported in normal physiology. We postulate that these features have important implications for therapy as such networks are relatively resistant to perturbation. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - February 23, 2009 Category: Genetics & Stem Cells Authors: Mark Barton Frank, Shirley Wang, Amita Aggarwal, Nicholas Knowlton, Kaiyu Jiang, Yanmin Chen, Ryan McKee, Brad Chaser, Timothy McGhee, Jeanette Osban and James N Jarvis Source Type: journals

Disease-Associated Pathophysiologic Structures in Pediatric Rheumatic diseases show characteristics of scale-free networks seen in physiologic systems: implications for pathogenesis and treatmentEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Genome-level transcriptional profiling from childhood onset rheumatic diseases suggested complex interactions in two arms of the immune system in both diseases. The disease associated networks showed scale-free network patterns similar to those reported in normal physiology. We postulate that these features have important implications for therapy as such networks are relatively resistant to perturbation. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - February 23, 2009 Category: Genetics & Stem Cells Authors: Mark Barton Frank, Shirley Wang, Amita Aggarwal, Nicholas Knowlton, Kaiyu Jiang, Yanmin Chen, Ryan McKee, Brad Chaser, Timothy McGhee, Jeanette Osban and James N Jarvis Source Type: journals

High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarraysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - February 19, 2009 Category: Genetics & Stem Cells Authors: Yuker Wang, Victoria E.H. Carlton, George Karlin-Neumann, Ronald Sapolsky, Li Zhang, Martin Moorhead, Zhigang C Wang, Andrea L Richardson, Robert Warren, Axel Walther, Melissa Bondy, Aysegul Sahin, Ralf Krahe, Musaffe Tuna, Patricia A Thompson, Paul T Spe Source Type: journals

Diurnal variation of the human adipose transcriptome and the link to metabolic diseaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Diurnal rhythm plays an important role in the physiology and regulation of energy metabolism in the adipose tissue and should be considered in the selection of novel targets for the treatment of obesity and other metabolic disorders. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - February 9, 2009 Category: Genetics & Stem Cells Authors: Andrey Loboda, Walter K Kraft, Bernard Fine, Jeffrey Joseph, Michael Nebozhyn, Chunsheng Zhang, Yudong He, Xia Yang, Christopher Wright, Mark Morris, Ira Chalikonda, Mark Ferguson, Valur Emilsson, Amy Leonardson, John Lamb, Hongyue Dai, Eric Schadt, Howar Source Type: journals

Muscle Research and Gene Ontology: New standards for improved data integration.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The revised GO structure should improve the interpretation of data from high-throughput (e.g. microarray and proteomic) experiments in the area of muscle science and muscle disease. We actively encourage community feedback on, and gene product annotation with these new terms. Please visit the Muscle Community Annotation Wiki (http://wiki.geneontology.org/index.php/Muscle_Biology). (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - January 29, 2009 Category: Genetics & Stem Cells Authors: Erika Feltrin, Stefano Campanaro, Alexander D. Diehl, Elisabeth Ehler, Georgine Faulkner, Jennifer Fordham, Chiara Gardin, Midori Harris, David Hill, Ralph Knoell, Paolo Laveder, Lorenza Mittempergher, Alessandra Nori, Carlo Reggiani, Vincenzo Sorrentino, Source Type: journals

Validation of previously identified serum biomarkers for breast cancer with SELDI-TOF MS: a case control studyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study's aim is to validate three proteins previously reported to be discriminative between breast cancer cases and healthy controls. These proteins had been identified as a fragment of inter-alpha trypsin inhibitor H4 (4.3 kDa), C-terminal-truncated form of C3a des arginine anaphylatoxin (8.1 kDa) and C3a des arginine anaphylatoxin (8.9 kDa). Methods: Serum protein profiles of 48 breast cancer patients and 48 healthy controls were analyzed with surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). Differences in protein intensity between breast cancer cases and controls were me...
Source: BMC Medical Genomics - January 19, 2009 Category: Genetics & Stem Cells Authors: Annemieke W.J. van Winden, Marie-Christine W. Gast, Jos H. Beijnen, Emiel J.TH. Rutgers, Diederick E. Grobbee, Petra H.M. Peeters and Carla H. van Gils Source Type: journals

Iron behaving badly: inappropriate Iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseasesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Overall we argue, by synthesising a widely dispersed literature, that the role of poorly liganded iron has been rather underappreciated in the past, and that in combination with peroxide and superoxide its activity underpins the behaviour of a great many physiological processes that degrade over time. Understanding these requires an integrative, systems-level approach. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - January 8, 2009 Category: Genetics & Stem Cells Authors: Douglas B Kell Source Type: journals

Genomic selection of reference genes for real-time PCR in human myocardiumEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This study used publicly available gene array data to identify a strategy for normalization involving two reference genes in combination that may have broad application for accurate and reliable normalization of RT-qPCR data in failed and non-failed human myocardium. (Source: BMC Medical Genomics)
Source: BMC Medical Genomics - December 29, 2008 Category: Genetics & Stem Cells Authors: Anna P Pilbrow, Leigh J Ellmers, Michael A Black, Christine S Moravec, Wendy E Sweet, Richard W Troughton, A MARK Richards, Chris M Frampton and Vicky A Cameron Source Type: journals