Identifying biological themes within lists of genes with EASE

被引:1391
作者
Hosack, DA
Dennis, G
Sherman, BT
Lane, HC
Lempicki, RA
机构
[1] SAIC Frederick Inc, Lab Immunopathogenesis & Bioinformat, Frederick, MD 21702 USA
[2] NIAID, Clin & Mol Retrovirol Sect, NIH, Bethesda, MD 20892 USA
关键词
D O I
10.1186/gb-2003-4-10-r70
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
EASE is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE and other high-throughput genomic data. The biological themes returned by EASE recapitulate manually determined themes in previously published gene lists and are robust to varying methods of normalization, intensity calculation and statistical selection of genes. EASE is a powerful tool for rapidly converting the results of functional genomics studies from 'genes' to 'themes'.
引用
收藏
页数:8
相关论文
共 30 条
[1]   Gene Ontology: tool for the unification of biology [J].
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 .
NATURE GENETICS, 2000, 25 (01) :25-29
[2]   THE SWISS-PROT PROTEIN-SEQUENCE DATA-BANK [J].
BAIROCH, A ;
BOECKMANN, B .
NUCLEIC ACIDS RESEARCH, 1991, 19 :2247-2248
[3]  
Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkh121, 10.1093/nar/gkr1065]
[4]   BBID: the biological biochemical image database [J].
Becker, KG ;
White, SL ;
Muller, J ;
Engel, J .
BIOINFORMATICS, 2000, 16 (08) :745-746
[5]   MGD: the Mouse Genome Database [J].
Blake, JA ;
Richardson, JE ;
Bult, RJ ;
Kadin, JA ;
Eppig, JT .
NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :193-195
[6]   Gene expression and viral prodution in latently infected, resting CD4+ T cells in viremic versus aviremic HIV-infected individuals [J].
Chun, TW ;
Justement, JS ;
Lempicki, RA ;
Yang, J ;
Dennis, G ;
Hallahan, CW ;
Sanford, C ;
Pandya, P ;
Liu, SY ;
McLaughlin, M ;
Ehler, LA ;
Moir, S ;
Fauci, AS .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (04) :1908-1913
[7]   HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication [J].
Cicala, C ;
Arthos, J ;
Selig, SM ;
Dennis, G ;
Hosack, DA ;
Van Ryk, D ;
Spangler, ML ;
Steenbeke, TD ;
Khazanie, P ;
Gupta, N ;
Yang, J ;
Daucher, M ;
Lempicki, RA ;
Fauci, AS .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (14) :9380-9385
[8]   Statistical tests for differential expression in cDNA microarray experiments [J].
Cui, XQ ;
Churchill, GA .
GENOME BIOLOGY, 2003, 4 (04)
[9]   GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways [J].
Dahlquist, KD ;
Salomonis, N ;
Vranizan, K ;
Lawlor, SC ;
Conklin, BR .
NATURE GENETICS, 2002, 31 (01) :19-20
[10]   DAVID: Database for annotation, visualization, and integrated discovery [J].
Dennis, G ;
Sherman, BT ;
Hosack, DA ;
Yang, J ;
Gao, W ;
Lane, HC ;
Lempicki, RA .
GENOME BIOLOGY, 2003, 4 (09)