Molecular signatures database (MSigDB) 3.0

被引:4244
作者
Liberzon, Arthur [1 ]
Subramanian, Aravind [1 ]
Pinchback, Reid [1 ]
Thorvaldsdottir, Helga [1 ]
Tamayo, Pablo [1 ]
Mesirov, Jill P. [1 ]
机构
[1] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA
关键词
GENES;
D O I
10.1093/bioinformatics/btr260
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets. Results: We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site.
引用
收藏
页码:1739 / 1740
页数:2
相关论文
共 13 条
  • [1] Gene Ontology: tool for the unification of biology
    Ashburner, M
    Ball, CA
    Blake, JA
    Botstein, D
    Butler, H
    Cherry, JM
    Davis, AP
    Dolinski, K
    Dwight, SS
    Eppig, JT
    Harris, MA
    Hill, DP
    Issel-Tarver, L
    Kasarskis, A
    Lewis, S
    Matese, JC
    Richardson, JE
    Ringwald, M
    Rubin, GM
    Sherlock, G
    [J]. NATURE GENETICS, 2000, 25 (01) : 25 - 29
  • [2] Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization
    Cahan, Patrick
    Rovegno, Felicia
    Mooney, Denise
    Newman, John C.
    St. Laurent, Georges, III
    McCaffrey, Timothy A.
    [J]. GENE, 2007, 401 (1-2) : 12 - 18
  • [3] GeneSigDB-a curated database of gene expression signatures
    Culhane, Aedin C.
    Schwarzl, Thomas
    Sultana, Razvan
    Picard, Kermshlise C.
    Picard, Shaita C.
    Lu, Tim H.
    Franklin, Katherine R.
    French, Simon J.
    Papenhausen, Gerald
    Correll, Mick
    Quackenbush, John
    [J]. NUCLEIC ACIDS RESEARCH, 2010, 38 : D716 - D725
  • [4] CCancer: a bird's eye view on gene lists reported in cancer- related studies
    Dietmann, Sabine
    Lee, Wanseon
    Wong, Philip
    Rodchenkov, Igor
    Antonov, Alexey V.
    [J]. NUCLEIC ACIDS RESEARCH, 2010, 38 : W118 - W123
  • [5] Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    Huang, Da Wei
    Sherman, Brad T.
    Lempicki, Richard A.
    [J]. NUCLEIC ACIDS RESEARCH, 2009, 37 (01) : 1 - 13
  • [6] KEGG: Kyoto Encyclopedia of Genes and Genomes
    Kanehisa, M
    Goto, S
    [J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 27 - 30
  • [7] Reactome knowledgebase of human biological pathways and processes
    Matthews, Lisa
    Gopinath, Gopal
    Gillespie, Marc
    Caudy, Michael
    Croft, David
    de Bono, Bernard
    Garapati, Phani
    Hemish, Jill
    Hermjakob, Henning
    Jassal, Bijay
    Kanapin, Alex
    Lewis, Suzanna
    Mahajan, Shahana
    May, Bruce
    Schmidt, Esther
    Vastrik, Imre
    Wu, Guanming
    Birney, Ewan
    Stein, Lincoln
    D'Eustachio, Peter
    [J]. NUCLEIC ACIDS RESEARCH, 2009, 37 : D619 - D622
  • [8] TRANSFAC® and its module TRANSCompel®:: transcriptional gene regulation in eukaryotes
    Matys, V.
    Kel-Margoulis, O. V.
    Fricke, E.
    Liebich, I.
    Land, S.
    Barre-Dirrie, A.
    Reuter, I.
    Chekmenev, D.
    Krull, M.
    Hornischer, K.
    Voss, N.
    Stegmaier, P.
    Lewicki-Potapov, B.
    Saxel, H.
    Kel, A. E.
    Wingender, E.
    [J]. NUCLEIC ACIDS RESEARCH, 2006, 34 : D108 - D110
  • [9] PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    Mootha, VK
    Lindgren, CM
    Eriksson, KF
    Subramanian, A
    Sihag, S
    Lehar, J
    Puigserver, P
    Carlsson, E
    Ridderstråle, M
    Laurila, E
    Houstis, N
    Daly, MJ
    Patterson, N
    Mesirov, JP
    Golub, TR
    Tamayo, P
    Spiegelman, B
    Lander, ES
    Hirschhorn, JN
    Altshuler, D
    Groop, LC
    [J]. NATURE GENETICS, 2003, 34 (03) : 267 - 273
  • [10] ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression
    Parkinson, Helen
    Kapushesky, Misha
    Kolesnikov, Nikolay
    Rustici, Gabriella
    Shojatalab, Mohammad
    Abeygunawardena, Niran
    Berube, Hugo
    Dylag, Miroslaw
    Emam, Ibrahim
    Farne, Anna
    Holloway, Ele
    Lukk, Margus
    Malone, James
    Mani, Roby
    Pilicheva, Ekaterina
    Rayner, Tim F.
    Rezwan, Faisal
    Sharma, Anjan
    Williams, Eleanor
    Bradley, Xiangqun Zheng
    Adamusiak, Tomasz
    Brandizi, Marco
    Burdett, Tony
    Coulson, Richard
    Krestyaninova, Maria
    Kurnosov, Pavel
    Maguire, Eamonn
    Neogi, Sudeshna Guha
    Rocca-Serra, Philippe
    Sansone, Susanna-Assunta
    Sklyar, Nataliya
    Zhao, Mengyao
    Sarkans, Ugis
    Brazma, Alvis
    [J]. NUCLEIC ACIDS RESEARCH, 2009, 37 : D868 - D872