-
2
-
-
0037941585
-
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
-
10.1038/ng1165, 12740579
-
Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 2003, 34:166-176. 10.1038/ng1165, 12740579.
-
(2003)
Nat Genet
, vol.34
, pp. 166-176
-
-
Segal, E.1
Shapira, M.2
Regev, A.3
Pe'er, D.4
Botstein, D.5
Koller, D.6
Friedman, N.7
-
3
-
-
33751222851
-
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle
-
10.1186/1471-2105-7-421, 1637117, 17010188
-
Wu WS, Li WH, Chen BS. Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 2006, 7:421. 10.1186/1471-2105-7-421, 1637117, 17010188.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 421
-
-
Wu, W.S.1
Li, W.H.2
Chen, B.S.3
-
4
-
-
77957903560
-
The spatial distribution of cis-regulatory elements in yeast promoters and its implications for transcription regulation
-
10.1186/1471-2164-11-581, 3091728, 20958978
-
Lin Z, Wu WS, Liang H, Yoo Y, Li WH. The spatial distribution of cis-regulatory elements in yeast promoters and its implications for transcription regulation. BMC Genomics 2010, 11:581. 10.1186/1471-2164-11-581, 3091728, 20958978.
-
(2010)
BMC Genomics
, vol.11
, pp. 581
-
-
Lin, Z.1
Wu, W.S.2
Liang, H.3
Yoo, Y.4
Li, W.H.5
-
5
-
-
55049118189
-
Identifying gene regulatory modules of heat shock response in yeast
-
10.1186/1471-2164-9-439, 2575218, 18811975
-
Wu WS, Li WH. Identifying gene regulatory modules of heat shock response in yeast. BMC Genomics 2008, 9:439. 10.1186/1471-2164-9-439, 2575218, 18811975.
-
(2008)
BMC Genomics
, vol.9
, pp. 439
-
-
Wu, W.S.1
Li, W.H.2
-
6
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
10.1126/science.1075090, 12399584
-
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-804. 10.1126/science.1075090, 12399584.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
Zeitlinger, J.11
Jennings, E.G.12
Murray, H.L.13
Gordon, D.B.14
Ren, B.15
Wyrick, J.J.16
Tagne, J.B.17
Volkert, T.L.18
Fraenkel, E.19
Gifford, D.K.20
Young, R.A.21
more..
-
7
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
10.1038/nature02800, 3006441, 15343339
-
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA. Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431:99-104. 10.1038/nature02800, 3006441, 15343339.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
Danford, T.W.6
Hannett, N.M.7
Tagne, J.B.8
Reynolds, D.B.9
Yoo, J.10
Jennings, E.G.11
Zeitlinger, J.12
Pokholok, D.K.13
Kellis, M.14
Rolfe, P.A.15
Takusagawa, K.T.16
Lander, E.S.17
Gifford, D.K.18
Fraenkel, E.19
Young, R.A.20
more..
-
8
-
-
34247629588
-
Genetic reconstruction of a functional transcriptional regulatory network
-
10.1038/ng2012, 17417638
-
Hu Z, Killion PJ, Iyer VR. Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet 2007, 39:683-687. 10.1038/ng2012, 17417638.
-
(2007)
Nat Genet
, vol.39
, pp. 683-687
-
-
Hu, Z.1
Killion, P.J.2
Iyer, V.R.3
-
9
-
-
0035999977
-
A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
-
10.1093/bioinformatics/18.4.546, 12016052
-
Pan W. A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 2002, 18(4):546-554. 10.1093/bioinformatics/18.4.546, 12016052.
-
(2002)
Bioinformatics
, vol.18
, Issue.4
, pp. 546-554
-
-
Pan, W.1
-
10
-
-
33747344944
-
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
-
10.1186/1471-2105-7-359, 1544358, 16872483
-
Jeffrey IB, Higgins DG, Culhane AC. Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics 2006, 7:359. 10.1186/1471-2105-7-359, 1544358, 16872483.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 359
-
-
Jeffrey, I.B.1
Higgins, D.G.2
Culhane, A.C.3
-
11
-
-
77955817629
-
Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets
-
10.1093/nar/gkq232, 2919724, 20385592
-
Reimand J, Vaquerizas JM, Todd AE, Vilo J, Luscombe NM. Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets. Nucleic Acids Res 2010, 38(14):4768-4777. 10.1093/nar/gkq232, 2919724, 20385592.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.14
, pp. 4768-4777
-
-
Reimand, J.1
Vaquerizas, J.M.2
Todd, A.E.3
Vilo, J.4
Luscombe, N.M.5
-
12
-
-
4544341015
-
Linear models and empirical Bayes methods for accessing differential expression in microarray experiments
-
Smyth GK. Linear models and empirical Bayes methods for accessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:3.
-
(2004)
Stat Appl Genet Mol Biol
, vol.3
, pp. 3
-
-
Smyth, G.K.1
-
13
-
-
12344269924
-
GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
-
10.1093/bioinformatics/bth456, 3037731, 15297299
-
Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G. GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 2004, 20(18):3710-3715. 10.1093/bioinformatics/bth456, 3037731, 15297299.
-
(2004)
Bioinformatics
, vol.20
, Issue.18
, pp. 3710-3715
-
-
Boyle, E.I.1
Weng, S.2
Gollub, J.3
Jin, H.4
Botstein, D.5
Cherry, J.M.6
Sherlock, G.7
-
14
-
-
84859699831
-
The Gene Ontology: enhancements for 2011
-
3245151, 22102568, The Gene Ontology Consortium
-
The Gene Ontology Consortium The Gene Ontology: enhancements for 2011. Nucleic Acids Res 2012, 40(Database issue):D559-D564. 3245151, 22102568, The Gene Ontology Consortium.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
-
-
-
15
-
-
0036699526
-
Revealing modular organization in the yeast transcriptional network
-
Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N. Revealing modular organization in the yeast transcriptional network. Nat Genet 2002, 31(4):370-377.
-
(2002)
Nat Genet
, vol.31
, Issue.4
, pp. 370-377
-
-
Ihmels, J.1
Friedlander, G.2
Bergmann, S.3
Sarig, O.4
Ziv, Y.5
Barkai, N.6
-
16
-
-
0001884644
-
Individual comparison by ranking methods
-
Wilcoxon F. Individual comparison by ranking methods. Biom Bull 1945, 1:80-83.
-
(1945)
Biom Bull
, vol.1
, pp. 80-83
-
-
Wilcoxon, F.1
-
17
-
-
0035733690
-
Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae
-
10.1038/ng776, 11694880
-
Ge H, Liu Z, Church GM, Vidal M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 2001, 29:482-486. 10.1038/ng776, 11694880.
-
(2001)
Nat Genet
, vol.29
, pp. 482-486
-
-
Ge, H.1
Liu, Z.2
Church, G.M.3
Vidal, M.4
-
18
-
-
78651328883
-
The BioGRID Interaction Database: 2011 update
-
3013707, 21071413
-
Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 2011, 39(Database issue):D698-D704. 3013707, 21071413.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.DATABASE ISSUE
-
-
Stark, C.1
Breitkreutz, B.J.2
Chatr-Aryamontri, A.3
Boucher, L.4
Oughtred, R.5
Livstone, M.S.6
Nixon, J.7
Van Auken, K.8
Wang, X.9
Shi, X.10
Reguly, T.11
Rust, J.M.12
Winter, A.13
Dolinski, K.14
Tyers, M.15
-
19
-
-
58149333393
-
Systematic identification of yeast cell cycle transcription factors using multiple data sources
-
10.1186/1471-2105-9-522, 2613934, 19061501
-
Wu WS, Li WH. Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics 2008, 9:522. 10.1186/1471-2105-9-522, 2613934, 19061501.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 522
-
-
Wu, W.S.1
Li, W.H.2
-
20
-
-
84858588614
-
Saccharomyces Genome Database: the genomics resource of budding yeast
-
3245034, 22110037
-
Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED. Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res 2012, 40(Database issue):D700-D705. 3245034, 22110037.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
-
-
Cherry, J.M.1
Hong, E.L.2
Amundsen, C.3
Balakrishnan, R.4
Binkley, G.5
Chan, E.T.6
Christie, K.R.7
Costanzo, M.C.8
Dwight, S.S.9
Engel, S.R.10
Fisk, D.G.11
Hirschman, J.E.12
Hitz, B.C.13
Karra, K.14
Krieger, C.J.15
Miyasato, S.R.16
Nash, R.S.17
Park, J.18
Skrzypek, M.S.19
Simison, M.20
Weng, S.21
Wong, E.D.22
more..
-
21
-
-
1242294502
-
Activation of the Saccharomyces cerevisiae heat shock transcription factor under glucose starvation conditions by Snf1 protein kinase
-
Hahn JS, Thiele DJ. Activation of the Saccharomyces cerevisiae heat shock transcription factor under glucose starvation conditions by Snf1 protein kinase. J Biol Chem 2004, 279(7):5169-5176.
-
(2004)
J Biol Chem
, vol.279
, Issue.7
, pp. 5169-5176
-
-
Hahn, J.S.1
Thiele, D.J.2
-
22
-
-
33644843117
-
A stress regulatory network for co-ordinated activation of proteasome expression mediated by yeast heat shock transcription factor
-
10.1111/j.1365-2958.2006.05097.x, 16556235
-
Hahn JS, Neef DW, Thiele DJ. A stress regulatory network for co-ordinated activation of proteasome expression mediated by yeast heat shock transcription factor. Mol Microbiol 2006, 60(1):240-251. 10.1111/j.1365-2958.2006.05097.x, 16556235.
-
(2006)
Mol Microbiol
, vol.60
, Issue.1
, pp. 240-251
-
-
Hahn, J.S.1
Neef, D.W.2
Thiele, D.J.3
-
23
-
-
33646748283
-
A systems approach to mapping DNA damage response pathways
-
10.1126/science.1122088, 2811083, 16709784
-
Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. A systems approach to mapping DNA damage response pathways. Science 2006, 312(5776):1054-1059. 10.1126/science.1122088, 2811083, 16709784.
-
(2006)
Science
, vol.312
, Issue.5776
, pp. 1054-1059
-
-
Workman, C.T.1
Mak, H.C.2
McCuine, S.3
Tagne, J.B.4
Agarwal, M.5
Ozier, O.6
Begley, T.J.7
Samson, L.D.8
Ideker, T.9
-
24
-
-
47049121708
-
Regulation of thermotolerance by stress-induced transcription factors in Saccharomyces cerevisiae
-
10.1128/EC.00029-08, 2394977, 18359875
-
Yamamoto N, Maeda Y, Ikeda A, Sakurai H. Regulation of thermotolerance by stress-induced transcription factors in Saccharomyces cerevisiae. Eukaryotic Cell 2008, 7(5):783-790. 10.1128/EC.00029-08, 2394977, 18359875.
-
(2008)
Eukaryotic Cell
, vol.7
, Issue.5
, pp. 783-790
-
-
Yamamoto, N.1
Maeda, Y.2
Ikeda, A.3
Sakurai, H.4
-
25
-
-
0033004441
-
Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast
-
Mannhaupt G, Schnall R, Karpov V, Vetter I, Feldmann H. Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast. FEBS Lett 1999, 450(1-2):27-34.
-
(1999)
FEBS Lett
, vol.450
, Issue.1-2
, pp. 27-34
-
-
Mannhaupt, G.1
Schnall, R.2
Karpov, V.3
Vetter, I.4
Feldmann, H.5
-
26
-
-
49249094963
-
Structure and properties of transcriptional networks driving selenite stress response in yeasts
-
10.1186/1471-2164-9-333, 2515152, 18627600
-
Salin H, Fardeau V, Piccini E, Lelandais G, Tanty V, Lemoine S, Jacq C, Devaux F. Structure and properties of transcriptional networks driving selenite stress response in yeasts. BMC Genomics 2008, 9:333. 10.1186/1471-2164-9-333, 2515152, 18627600.
-
(2008)
BMC Genomics
, vol.9
, pp. 333
-
-
Salin, H.1
Fardeau, V.2
Piccini, E.3
Lelandais, G.4
Tanty, V.5
Lemoine, S.6
Jacq, C.7
Devaux, F.8
-
27
-
-
3042725387
-
Transcriptional profiling of extracellular amino acid sensing in Saccharomyces cerevisiae and the role of Stp1p and Stp2p
-
10.1002/yea.1120, 15197729
-
Eckert-Boulet N, Nielsen PS, Friis C, dos Santos MM, Nielsen J, Kielland-Brandt MC, Regenberg B. Transcriptional profiling of extracellular amino acid sensing in Saccharomyces cerevisiae and the role of Stp1p and Stp2p. Yeast 2004, 21(8):635-648. 10.1002/yea.1120, 15197729.
-
(2004)
Yeast
, vol.21
, Issue.8
, pp. 635-648
-
-
Eckert-Boulet, N.1
Nielsen, P.S.2
Friis, C.3
dos Santos, M.M.4
Nielsen, J.5
Kielland-Brandt, M.C.6
Regenberg, B.7
-
28
-
-
0038506725
-
Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8
-
10.1074/jbc.M301981200, 12676948
-
Young ET, Dombek KM, Tachibana C, Ideker T. Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8. J Biol Chem 2003, 278(28):26146-26158. 10.1074/jbc.M301981200, 12676948.
-
(2003)
J Biol Chem
, vol.278
, Issue.28
, pp. 26146-26158
-
-
Young, E.T.1
Dombek, K.M.2
Tachibana, C.3
Ideker, T.4
-
29
-
-
68249144372
-
A novel circuit overrides Adr1p control during expression of Saccharomyces cerevisiae 2-trans-enoyl-ACP reductase Etr1p of mitochondrial type 2 fatty acid synthase
-
10.1111/j.1574-6968.2009.01688.x, 2784040, 19583790
-
Gurvitz A. A novel circuit overrides Adr1p control during expression of Saccharomyces cerevisiae 2-trans-enoyl-ACP reductase Etr1p of mitochondrial type 2 fatty acid synthase. FEMS Microbiol Lett 2009, 297(2):255-260. 10.1111/j.1574-6968.2009.01688.x, 2784040, 19583790.
-
(2009)
FEMS Microbiol Lett
, vol.297
, Issue.2
, pp. 255-260
-
-
Gurvitz, A.1
-
30
-
-
78651333266
-
Reconstruction of gene regulatory networks by integrating ChIP-chip, knock out and expression data
-
Jiang LH, Li YX, Liu Q. Reconstruction of gene regulatory networks by integrating ChIP-chip, knock out and expression data. Progr Biochem Biophys 2010, 37(9):996-1005.
-
(2010)
Progr Biochem Biophys
, vol.37
, Issue.9
, pp. 996-1005
-
-
Jiang, L.H.1
Li, Y.X.2
Liu, Q.3
-
31
-
-
78651272522
-
YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface
-
3013800, 20972212
-
Abdulrehman D, Monteiro PT, Teixeira MC, Mira NP, Lourenço AB, Dos Santos SC, Cabrito TR, Francisco AP, Madeira SC, Aires RS, Oliveira AL, Sá-Correia I, Freitas AT. YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. Nucleic Acids Res 2011, 39(Database issue):D136-D140. 3013800, 20972212.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.DATABASE ISSUE
-
-
Abdulrehman, D.1
Monteiro, P.T.2
Teixeira, M.C.3
Mira, N.P.4
Lourenço, A.B.5
Dos Santos, S.C.6
Cabrito, T.R.7
Francisco, A.P.8
Madeira, S.C.9
Aires, R.S.10
Oliveira, A.L.11
Sá-Correia, I.12
Freitas, A.T.13
-
32
-
-
67650663220
-
Backup in gene regulatory networks explains differences between binding and knockout results
-
2710864, 19536199
-
Gitter A, Siegfried Z, Klutstein M, Fornes O, Oliva B, Simon I, Bar-Joseph Z. Backup in gene regulatory networks explains differences between binding and knockout results. Mol Syst Biol 2009, 5:276. 2710864, 19536199.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 276
-
-
Gitter, A.1
Siegfried, Z.2
Klutstein, M.3
Fornes, O.4
Oliva, B.5
Simon, I.6
Bar-Joseph, Z.7
-
34
-
-
34447279700
-
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
-
10.1186/1471-2105-8-188, 1906835, 17559637
-
Wu WS, Li WH, Chen BS. Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics 2007, 8:188. 10.1186/1471-2105-8-188, 1906835, 17559637.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 188
-
-
Wu, W.S.1
Li, W.H.2
Chen, B.S.3
-
35
-
-
78651307692
-
YPA: an integrated repository of promoter features in Saccharomyces cerevisiae
-
3013683, 21045055
-
Chang DTH, Huang CY, Wu CY, Wu WS. YPA: an integrated repository of promoter features in Saccharomyces cerevisiae. Nucleic Acids Res 2011, 39(1):D647-D652. 3013683, 21045055.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.1
-
-
Chang, D.T.H.1
Huang, C.Y.2
Wu, C.Y.3
Wu, W.S.4
|