-
1
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
10.1038/75556 10802651
-
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 Gene Ontology: Tool for the unification of biology Nature Genetics 2000, 25:25-29. 10.1038/75556 10802651
-
(2000)
Nature Genetics
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
3
-
-
0030925920
-
Pfam: A comprehensive database of protein domain families based on seed alignments
-
10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L 9223186
-
Sonnhammer EL Eddy SR R D Pfam: A comprehensive database of protein domain families based on seed alignments Proteins 1997, 28:405-420. 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L 9223186
-
(1997)
Proteins
, vol.28
, pp. 405-420
-
-
Sonnhammer, E.L.1
Eddy, S.R.2
Durbin, R.3
-
4
-
-
25444502609
-
PAGE: Parametric Analysis of Gene Set Enrichment
-
1183189 15941488 10.1186/1471-2105-6-144
-
Kim S Volsky DJ PAGE: Parametric Analysis of Gene Set Enrichment BMC Bioinformatics 2005, 6:144. 1183189 15941488 10.1186/1471-2105-6-144
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 144
-
-
Kim, S.1
Volsky, D.J.2
-
5
-
-
0347513219
-
Characterizing gene sets with FuncAssociate
-
10.1093/bioinformatics/btg363 14668247
-
Berriz GF King OD Bryant B Sander C P RF Characterizing gene sets with FuncAssociate Bioinformatics 2003, 19:2502-2504. 10.1093/bioinformatics/ btg363 14668247
-
(2003)
Bioinformatics
, vol.19
, pp. 2502-2504
-
-
Berriz, G.F.1
King, O.D.2
Bryant, B.3
Sander, C.4
Roth, F.P.5
-
7
-
-
0037263812
-
MAPPFinder: Using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data
-
151291 12540299 10.1186/gb-2003-4-1-r7
-
Doniger SW Salomonis N Dahlquist KD Vranizan K Lawlor SC Conklin BR MAPPFinder: Using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data Genome Biology 2003, 4:R7. 151291 12540299 10.1186/gb-2003-4-1-r7
-
(2003)
Genome Biology
, vol.4
-
-
Doniger, S.W.1
Salomonis, N.2
Dahlquist, K.D.3
Vranizan, K.4
Lawlor, S.C.5
Conklin, B.R.6
-
8
-
-
0642340507
-
Significance analysis of lexical bias in microarray data
-
10.1186/gb-2003-4-2-r12
-
Kim CC Falkow S Significance analysis of lexical bias in microarray data Genome Biology 2003, 4:12. 10.1186/gb-2003-4-2-r12
-
(2003)
Genome Biology
, vol.4
, pp. 12
-
-
Kim, C.C.1
Falkow, S.2
-
10
-
-
1542399989
-
FatiGo: A web tool for finding significant associations of Gene Ontology terms with groups of genes
-
10.1093/bioinformatics/btg455 14990455
-
Al-Shahrour F Díaz-Uriarte R Dopazo J FatiGo: A web tool for finding significant associations of Gene Ontology terms with groups of genes Bioinformatics 2004, 20:578-580. 10.1093/bioinformatics/btg455 14990455
-
(2004)
Bioinformatics
, vol.20
, pp. 578-580
-
-
Al-Shahrour, F.1
Díaz-Uriarte, R.2
Dopazo, J.3
-
11
-
-
3142665525
-
GOstat: Find statistically overrepresented Gene Ontologies within a group of genes
-
10.1093/bioinformatics/bth088 14962934
-
Beißbarth T Speed TP GOstat: Find statistically overrepresented Gene Ontologies within a group of genes Bioinformatics 2004, 20:1464-1465. 10.1093/bioinformatics/bth088 14962934
-
(2004)
Bioinformatics
, vol.20
, pp. 1464-1465
-
-
Beißbarth, T.1
Speed, T.P.2
-
12
-
-
24644470505
-
Ontologcal analysis of gene expression data: Current tools, limitations and open problems
-
2435250 15994189 10.1093/bioinformatics/bti565
-
Khatri P Drǎghici S Ontologcal analysis of gene expression data: current tools, limitations and open problems Bioinformatics 2005, 21:3587-3595. 2435250 15994189 10.1093/bioinformatics/bti565
-
(2005)
Bioinformatics
, vol.21
, pp. 3587-3595
-
-
Khatri, P.1
Drǎghici, S.2
-
13
-
-
0038054341
-
PGC-1α-responsive genes involved in oxidative phosphorylaton are coordinately downregulated in human diabetes
-
10.1038/ng1180 12808457
-
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 PGC-1α-responsive genes involved in oxidative phosphorylaton are coordinately downregulated in human diabetes Nature Genetics 2003, 34:267-273. 10.1038/ng1180 12808457
-
(2003)
Nature Genetics
, vol.34
, pp. 267-273
-
-
Mootha, V.K.1
Lindgren, C.M.2
Eriksson, K.F.3
Subramanian, A.4
Sihag, S.5
Lehar, J.6
Puigserver, P.7
Carlsson, E.8
Ridderstråle, M.9
Laurila, E.10
Houstis, N.11
Daly, M.J.12
Patterson, N.13
Mesirov, J.P.14
Golub, T.R.15
Tamayo, P.16
Spiegelman, B.17
Lander, E.S.18
Hirschhorn, J.N.19
Altshuler, D.20
Groop, L.C.21
more..
-
14
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
1239896 16199517 10.1073/pnas.0506580102
-
Subramanian A Tamayo P Mootha VK Mukherjee S Ebert BL Gillette MA Paulovich A Pomeroy SL Golub TR Lander ES Mesirov JP Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles Proceedings of the National Academy of Sciences of the United States of America 2005, 102:15545-15550. 1239896 16199517 10.1073/pnas.0506580102
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
Mesirov, J.P.11
-
16
-
-
34249663294
-
Analyzing gene expression data in terms of gene sets: Methodological issues
-
10.1093/bioinformatics/btm051 17303618
-
Goeman JJ Bühlmann P Analyzing gene expression data in terms of gene sets: Methodological issues Bioinformatics 2007, 23:980-987. 10.1093/bioinformatics/btm051 17303618
-
(2007)
Bioinformatics
, vol.23
, pp. 980-987
-
-
Goeman, J.J.1
Bühlmann, P.2
-
17
-
-
35348890683
-
On testing the significance of sets of genes
-
10.1214/07-AOAS101
-
Efron B Tibshirani R On testing the significance of sets of genes The Annals of Applied Statistics 2007, 1:107-129. 10.1214/07-AOAS101
-
(2007)
The Annals of Applied Statistics
, vol.1
, pp. 107-129
-
-
Efron, B.1
Tibshirani, R.2
-
18
-
-
3142673366
-
Using the Gene Ontology for Microarray Data Mining: A Comparison of MEthods and Application to Age Effects in Human Prefrontal Cortex
-
10.1023/B:NERE.0000023608.29741.45 15176478
-
Pavlidis P Qin J Arango V Mann JJ Sibille E Using the Gene Ontology for Microarray Data Mining: A Comparison of MEthods and Application to Age Effects in Human Prefrontal Cortex Neurochemical Research 2004, 29:1213-1222. 10.1023/B:NERE.0000023608.29741.45 15176478
-
(2004)
Neurochemical Research
, vol.29
, pp. 1213-1222
-
-
Pavlidis, P.1
Qin, J.2
Arango, V.3
Mann, J.J.4
Sibille, E.5
-
19
-
-
33847324900
-
Extensions to gene set enrichment
-
10.1093/bioinformatics/btl599 17127676
-
Jiang Z Gentleman R Extensions to gene set enrichment Bioinformatics 2007, 23:306-313. 10.1093/bioinformatics/btl599 17127676
-
(2007)
Bioinformatics
, vol.23
, pp. 306-313
-
-
Jiang, Z.1
Gentleman, R.2
-
21
-
-
18744389489
-
Significance analysis of functional categories in gene expression studies: A structured permutation approach
-
10.1093/bioinformatics/bti260 15647293
-
Barry WT Nobel AB Wright FA Significance analysis of functional categories in gene expression studies: A structured permutation approach Bioinformatics 2005, 21:1943-1949. 10.1093/bioinformatics/bti260 15647293
-
(2005)
Bioinformatics
, vol.21
, pp. 1943-1949
-
-
Barry, W.T.1
Nobel, A.B.2
Wright, F.A.3
-
22
-
-
25444472585
-
Pathway level analysis of gene expression using singular value decomposition
-
1261155 16156896 10.1186/1471-2105-6-225
-
Tomfohr J Lu J Kepler TB Pathway level analysis of gene expression using singular value decomposition BMC Bioinformatics 2005, 6:225. 1261155 16156896 10.1186/1471-2105-6-225
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 225
-
-
Tomfohr, J.1
Lu, J.2
Kepler, T.B.3
-
23
-
-
0345832338
-
A global test for groups of genes: Testing association with a clinical outcome
-
10.1093/bioinformatics/btg382 14693814
-
Goeman JJ Geer van de SA Kort FD van Houwelingen HC A global test for groups of genes: Testing association with a clinical outcome Bioinformatics 2004, 20:93-99. 10.1093/bioinformatics/btg382 14693814
-
(2004)
Bioinformatics
, vol.20
, pp. 93-99
-
-
Goeman, J.J.1
Geer, S.A.2
Kort, F.D.3
van Houwelingen, H.C.4
-
25
-
-
33846669543
-
Discovering tightly regulated and differeitially expressed gene sets in whole genome expression data
-
10.1093/bioinformatics/btl315
-
Ye C Eskin E Discovering tightly regulated and differeitially expressed gene sets in whole genome expression data Bioinformaitcs 2006, 23:e84-e90. 10.1093/bioinformatics/btl315
-
(2006)
Bioinformaitcs
, vol.23
-
-
Ye, C.1
Eskin, E.2
-
26
-
-
34147120136
-
Nonparametric pathway-based regression models for analysis of genomic data
-
10.1093/biostatistics/kxl007 16772399
-
Wei Z Li H Nonparametric pathway-based regression models for analysis of genomic data Biostatistics 2007, 8:265-284. 10.1093/biostatistics/kxl007 16772399
-
(2007)
Biostatistics
, vol.8
, pp. 265-284
-
-
Wei, Z.1
Li, H.2
-
28
-
-
34547844074
-
A Markov random field model for network-based analysis of genomic data
-
10.1093/bioinformatics/btm129 17483504
-
Wei Z Li H A Markov random field model for network-based analysis of genomic data Bioinformatics 2007, 23:1537-1544. 10.1093/bioinformatics/ btm129 17483504
-
(2007)
Bioinformatics
, vol.23
, pp. 1537-1544
-
-
Wei, Z.1
Li, H.2
-
29
-
-
34347326247
-
Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models
-
1904360 17571924 10.1371/journal.pgen.0030096
-
Liu M Liberzon A Kong SW Lai WR Park PJ Kohane IS Kasif S Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models PLoS Genetics 2007, 3:e96. 1904360 17571924 10.1371/journal.pgen.0030096
-
(2007)
PLoS Genetics
, vol.3
-
-
Liu, M.1
Liberzon, A.2
Kong, S.W.3
Lai, W.R.4
Park, P.J.5
Kohane, I.S.6
Kasif, S.7
-
31
-
-
34248593385
-
Gene expression network analysis and applications to immunology
-
10.1093/bioinformatics/btm019 17267429
-
Nacu c Critchley-Thorne R Lee P Holmes S Gene expression network analysis and applications to immunology Bioinformatics 2007, 23:850-858. 10.1093/bioinformatics/btm019 17267429
-
(2007)
Bioinformatics
, vol.23
, pp. 850-858
-
-
Nacu, C.1
Critchley-Thorne, R.2
Lee, P.3
Holmes, S.4
-
32
-
-
0035214299
-
Trimming, weighting, and grouping SNPs in human case-control association studies
-
311222 11731502 10.1101/gr.204001
-
Hoh J Wille A Ott J Trimming, weighting, and grouping SNPs in human case-control association studies Genome Research 2001, 11:2115-2119. 311222 11731502 10.1101/gr.204001
-
(2001)
Genome Research
, vol.11
, pp. 2115-2119
-
-
Hoh, J.1
Wille, A.2
Ott, J.3
-
33
-
-
0041530047
-
Resampling-based multiple testing for microarray data analysis
-
10.1007/BF02595811
-
Ge Y Dudoit S P ST Resampling-based multiple testing for microarray data analysis Test 2003, 12:1-77. 10.1007/BF02595811
-
(2003)
Test
, vol.12
, pp. 1-77
-
-
Ge, Y.1
Dudoit, S.2
Speed, T.P.3
-
34
-
-
0036020892
-
A direct approach to false discovery rates
-
10.1111/1467-9868.00346
-
Storey JD A direct approach to false discovery rates Journal of the Royal Statistical Society, Series B 2002, 64:479-498. 10.1111/ 1467-9868.00346
-
(2002)
Journal of the Royal Statistical Society, Series B
, vol.64
, pp. 479-498
-
-
Storey, J.D.1
-
35
-
-
0034676455
-
Surfing the p53 network
-
10.1038/35042675
-
Vogelstein B Lane D Levine AJ Surfing the p53 network Nature 2002, 408:307-310. 10.1038/35042675
-
(2002)
Nature
, vol.408
, pp. 307-310
-
-
Vogelstein, B.1
Lane, D.2
Levine, A.J.3
-
36
-
-
33748275681
-
The p53 Tumor Suppressor Participates in Multiple Cell Cycle Checkpoints
-
10.1002/jcp.20689 16741928
-
Giono LE Manfredi JJ The p53 Tumor Suppressor Participates in Multiple Cell Cycle Checkpoints Journal of Cellular Physiology 2006, 209:13-20. 10.1002/jcp.20689 16741928
-
(2006)
Journal of Cellular Physiology
, vol.209
, pp. 13-20
-
-
Giono, L.E.1
Manfredi, J.J.2
-
37
-
-
0032528176
-
p53-dependent Ceramide Response to Genotoxic Stress
-
508891 9664074 10.1172/JCI1180
-
Dbaibo GS Pushkareva MY Rachid RA Alter N Smyth MJ Obeid LM Hannun YA p53-dependent Ceramide Response to Genotoxic Stress The Journal of Clinical Investigation 1998, 102:329-339. 508891 9664074 10.1172/JCI1180
-
(1998)
The Journal of Clinical Investigation
, vol.102
, pp. 329-339
-
-
Dbaibo, G.S.1
Pushkareva, M.Y.2
Rachid, R.A.3
Alter, N.4
Smyth, M.J.5
Obeid, L.M.6
Hannun, Y.A.7
-
38
-
-
0037379914
-
Fas-Mediated Apoptosis Is Dependent on Wild-Type p53 Status in Human Cancer Cells Expressing a Temperature-Sensitive p53 Mutant Alanine-143
-
12670900
-
Li Y Raffo AJ Drew L Mao Y Tran A Petrylak DP Fine RL Fas-Mediated Apoptosis Is Dependent on Wild-Type p53 Status in Human Cancer Cells Expressing a Temperature-Sensitive p53 Mutant Alanine-143 Cancer Research 2003, 63:1527-1533. 12670900
-
(2003)
Cancer Research
, vol.63
, pp. 1527-1533
-
-
Li, Y.1
Raffo, A.J.2
Drew, L.3
Mao, Y.4
Tran, A.5
Petrylak, D.P.6
Fine, R.L.7
-
39
-
-
0032517786
-
P53 Is Essential For Developmental Neuron Death as Regulated by the TrkA and p75 Neurotrophin Receptors
-
2132983 9852160 10.1083/jcb.143.6.1691
-
Aloyz RS Bamji SX Pozniak CD Toma JG Atwal J Kaplan DR Miller FD P53 Is Essential For Developmental Neuron Death as Regulated by the TrkA and p75 Neurotrophin Receptors The Journal of Cell Biology 1998, 143:1691-1703. 2132983 9852160 10.1083/jcb.143.6.1691
-
(1998)
The Journal of Cell Biology
, vol.143
, pp. 1691-1703
-
-
Aloyz, R.S.1
Bamji, S.X.2
Pozniak, C.D.3
Toma, J.G.4
Atwal, J.5
Kaplan, D.R.6
Miller, F.D.7
-
40
-
-
27844554840
-
Pitx2a binds to human papillomavirus type 18 E6 protein and inhibits E6-mediated P53 degradation in HeLa cells
-
1479768 16129685 10.1074/jbc.M502974200
-
Wei Q Pitx2a binds to human papillomavirus type 18 E6 protein and inhibits E6-mediated P53 degradation in HeLa cells The Journal of Biological Chemistry 2005, 280:37790-37797. 1479768 16129685 10.1074/ jbc.M502974200
-
(2005)
The Journal of Biological Chemistry
, vol.280
, pp. 37790-37797
-
-
Wei, Q.1
-
41
-
-
4544387440
-
A Powerful Strategy to Account for Multiple Testing in the Context of Haplotype Analysis
-
1182044 15290652 10.1086/424390
-
Becker T Knapp M A Powerful Strategy to Account for Multiple Testing in the Context of Haplotype Analysis American Journal of Human Genetics 2004, 75:561-570. 1182044 15290652 10.1086/424390
-
(2004)
American Journal of Human Genetics
, vol.75
, pp. 561-570
-
-
Becker, T.1
Knapp, M.2
|