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Tag gene_sets [33 articles]

Recent papers classified by the tag gene_sets.
  • An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis
    Nature Genetics, Vol. 37, No. 1. (19 December 2004), 48.
    by Alejandro Sweet-Cordero, Sayan Mukherjee, Aravind Subramanian, Han You, Jeffrey J Roix, Christine Ladd-Acosta, Jill Mesirov, Todd R Golub, Tyler Jacks
    posted to gene_sets microarray somatic_mutations by srp33 on 2008-07-21 23:33:16 as ** along with 2 people and 1 group jfr ealloza BioinfoCIPF
  • Large-scale integration of cancer microarray data identifies a robust common cancer signature
    BMC Bioinformatics, Vol. 8 (30 July 2007), 275.
    by Lei Xu, Donald Geman, Raimond L Winslow
    posted to gene_sets microarray signatures by srp33 on 2008-07-28 18:16:13 as ** along with 2 people jfr shigepong
  • Discovering statistically significant pathways in expression profiling studies.
    Proc Natl Acad Sci U S A, Vol. 102, No. 38. (20 September 2005), pp. 13544-13549.
    by L Tian, SA Greenberg, SW Kong, J Altschuler, IS Kohane, PJ Park
    posted to gene_sets microarray pathway_analysis by srp33 on 2008-04-28 15:19:41 as ** along with 7 people and 1 group dragonrez maryee ealloza frohike justescaped giovenko heliopais BioinfoCIPF
  • Testing association of a pathway with survival using gene expression data
    Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1950-1957.
    by Jelle J Goeman, Jan Oosting, Anne-Marie Cleton-Jansen, Jakob K Anninga, Hans C van Houwelingen
    posted to gene_sets microarray pathway_analysis by srp33 on 2008-04-24 22:34:57 as **
  • Application of a priori established gene sets to discover biologically important differential expression in microarray data
    PNAS, Vol. 102, No. 43. (25 October 2005), pp. 15278-15279.
    by Andrea Bild, Phillip G Febbo
    posted to gene_sets microarray by srp33 on 2008-05-08 22:47:39 as ** along with 3 people and 1 group maryee ealloza jdiggans BioinfoCIPF
  • Probabilistic discovery of overlapping cellular processes and their regulation.
    J Comput Biol, Vol. 12, No. 7. (September 2005), pp. 909-927.
    by A Battle, E Segal, D Koller
    posted to gene_sets microarray pathway_analysis by srp33 on 2008-07-31 22:59:20 as ** along with 3 people ptrobajo nirfriedman roys
  • From the Cover: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    PNAS, Vol. 102, No. 43. (25 October 2005), pp. 15545-15550.
    by Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander, Jill P Mesirov
    posted to gene_sets microarray pathway_analysis by srp33 on 2008-05-14 04:29:25 as ** along with 23 people and 4 groups ihpark chrisamiller dragonrez jfr balajis maryee xwbcn hpiwowar aviad_work ealloza jdiggans jeremymiller frohike hawkeyehammer schuylrp natstreet heliopais shikin waghsk roys ellakat sgoetz AbnerCYH Bioinformatics BioinfoCIPF GeschwindLab Indigene
  • Molecular concepts analysis links tumors, pathways, mechanisms, and drugs.
    Neoplasia, Vol. 9, No. 5. (May 2007), pp. 443-454.
    by DR Rhodes, S Kalyana-Sundaram, SA Tomlins, V Mahavisno, N Kasper, R Varambally, TR Barrette, D Ghosh, S Varambally, AM Chinnaiyan
    posted to gene_sets pathway_analysis by srp33 on 2008-05-21 19:54:13 as ** along with 2 people jfr waghsk
  • A gene sets approach for identifying prognostic gene signatures for outcome prediction
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Seon Y Kim, Yong S Kim
    posted to gene_sets microarray prognosis by srp33 on 2008-04-24 22:50:59 as ** along with 4 people Zephyrus jfr barriot ptrobajo
  • PAGE: parametric analysis of gene set enrichment.
    BMC Bioinformatics, Vol. 6 (2005)
    by SY Kim, DJ Volsky
    posted to gene_sets by srp33 on 2008-04-25 05:01:02 as ** along with 6 people and 1 group pradeep2005s ealloza jdiggans waghsk heliopais giovenko BioinfoCIPF
  • Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by E Edelman, A Porrello, J Guinney, B Balakumaran, A Bild, PG Febbo, S Mukherjee
    posted to gene_sets microarray by srp33 on 2008-04-28 15:23:04 as ** along with 5 people and 1 group dragonrez jfr frohike heliopais barriot Bioinformatics
  • Peeling off the hidden genetic heterogeneities of cancers based on disease-relevant functional modules.
    Molecular medicine (Cambridge, Mass.), Vol. 12, No. 1-3. (r 2006), pp. 25-33.
    by JZ Xu, Z Guo, M Zhang, X Li, YJ Li, SQ Rao
    posted to gene_sets by srp33 on 2008-05-28 17:04:16 as **
  • Computation of significance scores of unweighted Gene Set Enrichment Analyses
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Andreas Keller, Christina Backes, Hans P Lenhof
    posted to gene_sets by heliopais on 2008-05-16 15:48:02 as ** along with 4 people and 1 group jfr ealloza shigepong GeeSharpMinor BioinfoCIPF
  • GSEA-P: A desktop application for Gene Set Enrichment Analysis
    Bioinformatics (20 July 2007), btm369.
    by Aravind Subramanian, Heidi Kuehn, Joshua Gould, Pablo Tamayo, Jill P Mesirov
    posted to gene_sets gsea tools by heliopais on 2008-02-29 13:53:41 as read along with 8 people and 1 group jyuh cassj ealloza schuylrp barriot waszak dmontaner Eugene BioinfoCIPF
  • Gene-set approach for expression pattern analysis
    Brief Bioinform (17 January 2008), bbn001.
    by Dougu Nam, Seon-Young Kim
    posted to gene_sets by heliopais on 2008-05-14 13:56:44 as ** along with 10 people jyuh seemu thomaskelder lp2 giovenko AlexanderPico tmmurali yas beete klo
  • Circumventing the cut-off for enrichment analysis
    Brief Bioinform, Vol. 7, No. 2. (1 June 2006), pp. 202-203.
    by Eitan Rubin
    posted to gene_sets by heliopais on 2008-05-15 12:21:22 as **
  • Individual mRNA expression profiles reveal the effects of specific microRNAs
    Genome Biology, Vol. 9 (16 May 2008), R82.
    by Amit Arora, David AC Simpson
    posted to microrna_microarray microrna gene_sets by heliopais on 2008-06-11 14:54:50 as ***** along with 4 people and 1 group giovenko jfr imtechnology daforerog microRNA
  • Statistical concerns about the GSEA procedure.
    Nat Genet, Vol. 36, No. 7. (July 2004)
    by D Damian, M Gorfine
    posted to commentary gene_sets by heliopais on 2008-05-15 11:45:59 as ** along with 2 people and 1 group ealloza schuylrp BioinfoCIPF
  • Identification of Differentially Expressed Gene Categories in Microarray Studies Using Nonparametric Multivariate Analysis.
    Bioinformatics (27 November 2007)
    by Dan Nettleton, Justin Recknor, James M Reecy
    edited by John Quackenbush
    posted to gene_sets by heliopais on 2008-02-19 11:27:59 as read along with 3 people jyuh jfr shigepong
  • Pathway Analysis of Microarray Data via Regression
    Journal of Computational Biology, Vol. 0, No. 0. (0), pp. 1-9.
    by AJ Adewale, I Dinu, JD Potter, Q Liu, Y Yasui
    posted to gene_sets by heliopais on 2008-04-24 10:01:49 as ** along with 6 people tmmurali csgillespie huali jyuh jfr AlexanderPico
  • Improving gene set analysis of microarray data by SAM-GS
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Irina Dinu, John Potter, Thomas Mueller, Qi Liu, Adeniyi Adewale, Gian Jhangri, Gunilla Einecke, Konrad Famulski, Philip Halloran, Yutaka Yasui
    posted to gene_sets by heliopais on 2008-04-24 09:37:59 as **** along with 8 people and 1 group jfr ealloza shigepong ghattem GeeSharpMinor waghsk LuigiAugugliaro renatomilani BioinfoCIPF
  • Detecting multivariate differentially expressed genes
    BMC Bioinformatics, Vol. 8 (09 May 2007), 150.
    by Roland Nilsson, Jose M Pena, Johan Bjorkegren, Jesper Tegner
    posted to gene_sets by heliopais on 2008-01-07 11:50:16 as ** along with 4 people shigepong GeeSharpMinor fmenolascina lassefolkersen
  • Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis
    BMC Bioinformatics, Vol. 8 (17 November 2007), 453.
    by Tae-Min Kim, Yeun-Jun Chung, Mun-Gan Rhyu, Myeong H Jung
    posted to gene_sets by heliopais on 2008-05-14 13:45:26 as ** along with 2 people jfr ealloza
  • PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.
    Nat Genet, Vol. 34, No. 3. (July 2003), pp. 267-273.
    by VK Mootha, CM Lindgren, KF Eriksson, A Subramanian, S Sihag, J Lehar, P Puigserver, E Carlsson, M Ridderstråle, E Laurila, N Houstis, MJ Daly, N Patterson, JP Mesirov, TR Golub, P Tamayo, B Spiegelman, ES Lander, JN Hirschhorn, D Altshuler, LC Groop
    posted to gene_sets by heliopais on 2008-05-15 12:02:42 as ** along with 6 people and 2 groups dragonrez maryee ealloza giovanni shikin magusina BioinfoCIPF GeschwindLab
  • A multivariate extension of the gene set enrichment analysis.
    J Bioinform Comput Biol, Vol. 5, No. 5. (October 2007), pp. 1139-1153.
    by L Klebanov, G Glazko, P Salzman, A Yakovlev, Y Xiao
    posted to gene_sets by heliopais on 2008-04-24 15:23:31 as *** along with 2 people ealloza waghsk
  • Analyzing gene expression data in terms of gene sets: methodological issues.
    Bioinformatics (15 February 2007)
    by Jelle J J Goeman, Peter Bühlmann
    posted to gene_sets by heliopais on 2008-04-24 10:12:19 as ** along with 5 people and 2 groups jfr ealloza shigepong jyuh diging_data BioinfoCIPF BTS-PT-AS-CS
  • GlobalANCOVA: exploration and assessment of gene group effects
    Bioinformatics, Vol. 24, No. 1. (17 November 2007), pp. 78-85.
    by Manuela Hummel, Reinhard Meister, Ulrich Mansmann
    edited by John Quackenbush
    posted to gene_sets by heliopais on 2008-05-27 16:54:02 as ** along with 2 people jyuh ealloza
  • Gene expression network analysis and applications to immunology
    Bioinformatics, Vol. 23, No. 7. (1 April 2007), pp. 850-858.
    by Nacu, Serban, Critchley-Thorne, Rebecca, Lee, Peter, Holmes, Susan
    posted to gene_sets by heliopais on 2008-05-16 14:52:36 as ****
  • SEGS: Search for enriched gene sets in microarray data.
    Journal of Biomedical Informatics, Vol. 41, No. 4. (15 December 2007), pp. 588-601.
    by Igor Trajkovski, Nada Lavrač, Jakub Tolar
    posted to gene_sets by heliopais on 2008-09-22 16:52:28 as ** along with 3 people jyuh jfr GeeSharpMinor
  • Comparative evaluation of gene-set analysis methods
    BMC Bioinformatics, Vol. 8 (07 November 2007), 431.
    by Qi Liu, Irina Dinu, Adeniyi J Adewale, John D Potter, Yutaka Yasui
    posted to gene_sets by heliopais on 2008-04-24 12:00:12 as ** along with 5 people ptrobajo jfr ealloza shigepong idonaldson
  • Extensions to gene set enrichment
    Bioinformatics, Vol. 23, No. 3. (1 February 2007), pp. 306-313.
    by Zhen Jiang, Robert Gentleman
    posted to gene_sets by heliopais on 2008-04-24 13:46:39 as ** along with 5 people and 1 group ealloza djkt waghsk giovenko magusina BioinfoCIPF
  • GeneTrail--advanced gene set enrichment analysis.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by C Backes, A Keller, J Kuentzer, B Kneissl, N Comtesse, YA Elnakady, R Müller, E Meese, HP Lenhof
    posted to gene_sets by heliopais on 2008-05-15 09:55:14 as ** along with 2 people jyuh jfr
  • Genome-Wide Expression Profiling Reveals EBV-Associated Inhibition of MHC Class I Expression in Nasopharyngeal Carcinoma
    Cancer Res, Vol. 66, No. 16. (15 August 2006), pp. 7999-8006.
    by Srikumar Sengupta, Johan A den Boon, I-How Chen, Michael A Newton, David B Dahl, Meng Chen, Yu-Juen Cheng, William H Westra, Chien-Jen Chen, Allan Hildesheim, Bill Sugden, Paul Ahlquist
    posted to gene_sets by heliopais on 2008-02-29 14:37:08 as ***
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