-
2
-
-
0037819447
-
Transcription regulation and animal diversity
-
10.1038/nature01763, 12853946
-
Levine M, Tjian R. Transcription regulation and animal diversity. Nature 2003, 424:147-151. 10.1038/nature01763, 12853946.
-
(2003)
Nature
, vol.424
, pp. 147-151
-
-
Levine, M.1
Tjian, R.2
-
3
-
-
1842584947
-
Applied bioinformatics for the identification of regulatory elements
-
10.1038/nrg1315, 15131651
-
Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 2004, 5:276-287. 10.1038/nrg1315, 15131651.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 276-287
-
-
Wasserman, W.W.1
Sandelin, A.2
-
4
-
-
33846283385
-
The evolution of gene regulation by transcription factors and microRNAs
-
10.1038/nrg1990, 17230196
-
Chen K, Rajewsky N. The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet 2007, 8:93-103. 10.1038/nrg1990, 17230196.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 93-103
-
-
Chen, K.1
Rajewsky, N.2
-
5
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
10.1089/106652700750050961, 11108481
-
Friedman N, Linial M, Nachman I, Pe'er D. Using Bayesian networks to analyze expression data. J Comput Biol 2000, 7:601-620. 10.1089/106652700750050961, 11108481.
-
(2000)
J Comput Biol
, vol.7
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
Pe'er, D.4
-
6
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
10.1371/journal.pbio.0050008, 1764438, 17214507
-
Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 2007, 5:e8. 10.1371/journal.pbio.0050008, 1764438, 17214507.
-
(2007)
PLoS Biol
, vol.5
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
Mogno, I.4
Wierzbowski, J.5
Cottarel, G.6
Kasif, S.7
Collins, J.J.8
Gardner, T.S.9
-
7
-
-
33750353888
-
Reverse engineering cellular networks
-
Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A. Reverse engineering cellular networks. Nat Protocols 2006, 1:662-671.
-
(2006)
Nat Protocols
, vol.1
, pp. 662-671
-
-
Margolin, A.A.1
Wang, K.2
Lim, W.K.3
Kustagi, M.4
Nemenman, I.5
Califano, A.6
-
8
-
-
54949156075
-
Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks
-
10.1093/bioinformatics/btn482, 18784117
-
Reverter A, Chan EKF. Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks. Bioinformatics 2008, 24:2491-2497. 10.1093/bioinformatics/btn482, 18784117.
-
(2008)
Bioinformatics
, vol.24
, pp. 2491-2497
-
-
Reverter, A.1
Chan, E.K.F.2
-
9
-
-
77949500391
-
PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches
-
10.1093/bioinformatics/btp674, 20007253
-
Watson-Haigh NS, Kadarmideen HN, Reverter A. PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches. Bioinformatics 2010, 26:411-413. 10.1093/bioinformatics/btp674, 20007253.
-
(2010)
Bioinformatics
, vol.26
, pp. 411-413
-
-
Watson-Haigh, N.S.1
Kadarmideen, H.N.2
Reverter, A.3
-
10
-
-
33847008688
-
A network biology approach to prostate cancer
-
1828752, 17299418
-
Ergün A, Lawrence CA, Kohanski MA, Brennan TA, Collins JJ. A network biology approach to prostate cancer. Mol Syst Biol 2007, 3:82. 1828752, 17299418.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 82
-
-
Ergün, A.1
Lawrence, C.A.2
Kohanski, M.A.3
Brennan, T.A.4
Collins, J.J.5
-
11
-
-
21444452397
-
Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks
-
10.1038/nbt1075, 15765094
-
di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliott SJ, Schaus SE, Collins JJ. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol 2005, 23:377-383. 10.1038/nbt1075, 15765094.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 377-383
-
-
di Bernardo, D.1
Thompson, M.J.2
Gardner, T.S.3
Chobot, S.E.4
Eastwood, E.L.5
Wojtovich, A.P.6
Elliott, S.J.7
Schaus, S.E.8
Collins, J.J.9
-
12
-
-
34547886125
-
BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations
-
10.1093/bioinformatics/btm252, 17496321
-
Kerhornou A, Guigó R. BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations. Bioinformatics 2007, 23:1831-1833. 10.1093/bioinformatics/btm252, 17496321.
-
(2007)
Bioinformatics
, vol.23
, pp. 1831-1833
-
-
Kerhornou, A.1
Guigó, R.2
-
13
-
-
67349178206
-
Intra- and inter-individual genetic differences in gene expression
-
10.1007/s00335-009-9181-x, 2690833, 19424753
-
Cowley MJ, Cotsapas CJ, Williams RBH, Chan EKF, Pulvers JN, Liu MY, Luo OJ, Nott DJ, Little PFR. Intra- and inter-individual genetic differences in gene expression. Mamm Genome 2009, 20:281-295. 10.1007/s00335-009-9181-x, 2690833, 19424753.
-
(2009)
Mamm Genome
, vol.20
, pp. 281-295
-
-
Cowley, M.J.1
Cotsapas, C.J.2
Williams, R.B.H.3
Chan, E.K.F.4
Pulvers, J.N.5
Liu, M.Y.6
Luo, O.J.7
Nott, D.J.8
Little, P.F.R.9
-
14
-
-
77951151245
-
Functional annotation of novel lineage-specific genes using co-expression and promoter analysis
-
10.1186/1471-2164-11-161, 2848242, 20214810
-
Kumar CG, Everts RE, Loor JJ, Lewin HA. Functional annotation of novel lineage-specific genes using co-expression and promoter analysis. BMC Genomics 2010, 11:161. 10.1186/1471-2164-11-161, 2848242, 20214810.
-
(2010)
BMC Genomics
, vol.11
, pp. 161
-
-
Kumar, C.G.1
Everts, R.E.2
Loor, J.J.3
Lewin, H.A.4
-
15
-
-
60149084519
-
PASTAA: identifying transcription factors associated with sets of co-regulated genes
-
10.1093/bioinformatics/btn627, 2642637, 19073590
-
Roider HG, Manke T, O'Keeffe S, Vingron M, Haas SA. PASTAA: identifying transcription factors associated with sets of co-regulated genes. Bioinformatics 2009, 25:435-442. 10.1093/bioinformatics/btn627, 2642637, 19073590.
-
(2009)
Bioinformatics
, vol.25
, pp. 435-442
-
-
Roider, H.G.1
Manke, T.2
O'Keeffe, S.3
Vingron, M.4
Haas, S.A.5
-
16
-
-
60149110901
-
Module networks revisited: computational assessment and prioritization of model predictions
-
10.1093/bioinformatics/btn658, 19136553
-
Joshi A, De Smet R, Marchal K, Van de Peer Y, Michoel T. Module networks revisited: computational assessment and prioritization of model predictions. Bioinformatics 2009, 25:490-496. 10.1093/bioinformatics/btn658, 19136553.
-
(2009)
Bioinformatics
, vol.25
, pp. 490-496
-
-
Joshi, A.1
De Smet, R.2
Marchal, K.3
Van de Peer, Y.4
Michoel, T.5
-
17
-
-
33947382481
-
A gene coexpression network for bovine skeletal muscle inferred from microarray data
-
10.1152/physiolgenomics.00105.2006, 16985009
-
Reverter A, Hudson NJ, Wang Y, Tan S, Barris W, Byrne KA, McWilliam SM, Bottema CDK, Kister A, Greenwood PL, Harper GS, Lehnert SA, Dalrymple BP. A gene coexpression network for bovine skeletal muscle inferred from microarray data. Physiol Genomics 2006, 28:76-83. 10.1152/physiolgenomics.00105.2006, 16985009.
-
(2006)
Physiol Genomics
, vol.28
, pp. 76-83
-
-
Reverter, A.1
Hudson, N.J.2
Wang, Y.3
Tan, S.4
Barris, W.5
Byrne, K.A.6
McWilliam, S.M.7
Bottema, C.D.K.8
Kister, A.9
Greenwood, P.L.10
Harper, G.S.11
Lehnert, S.A.12
Dalrymple, B.P.13
-
18
-
-
70349668879
-
Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks
-
10.1371/journal.pone.0007249, 2749936, 19794913
-
Hudson NJ, Reverter A, Wang Y, Greenwood PL, Dalrymple BP. Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks. PLoS ONE 2009, 4:e7249. 10.1371/journal.pone.0007249, 2749936, 19794913.
-
(2009)
PLoS ONE
, vol.4
-
-
Hudson, N.J.1
Reverter, A.2
Wang, Y.3
Greenwood, P.L.4
Dalrymple, B.P.5
-
19
-
-
77951944593
-
Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data
-
10.1093/bioinformatics/btq051, 20144946
-
Reverter A, Hudson NJ, Nagaraj SH, Pérez-Enciso M, Dalrymple BP. Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data. Bioinformatics 2010, 26:896-904. 10.1093/bioinformatics/btq051, 20144946.
-
(2010)
Bioinformatics
, vol.26
, pp. 896-904
-
-
Reverter, A.1
Hudson, N.J.2
Nagaraj, S.H.3
Pérez-Enciso, M.4
Dalrymple, B.P.5
-
20
-
-
2942572926
-
Quantifying the relationship between co-expression, co-regulation and gene function
-
10.1186/1471-2105-5-18, 375525, 15053845
-
Allocco DJ, Kohane IS, Butte AJ. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics 2004, 5:18. 10.1186/1471-2105-5-18, 375525, 15053845.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 18
-
-
Allocco, D.J.1
Kohane, I.S.2
Butte, A.J.3
-
21
-
-
0042706147
-
Genomic analysis of gene expression relationships in transcriptional regulatory networks
-
10.1016/S0168-9525(03)00175-6, 12902159
-
Yu H, Luscombe NM, Qian J, Gerstein M. Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet 2003, 19:422-427. 10.1016/S0168-9525(03)00175-6, 12902159.
-
(2003)
Trends Genet
, vol.19
, pp. 422-427
-
-
Yu, H.1
Luscombe, N.M.2
Qian, J.3
Gerstein, M.4
-
22
-
-
70349887776
-
Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster
-
10.1093/bioinformatics/btp462, 2752616, 19633094
-
Marco A, Konikoff C, Karr TL, Kumar S. Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. Bioinformatics 2009, 25:2473-2477. 10.1093/bioinformatics/btp462, 2752616, 19633094.
-
(2009)
Bioinformatics
, vol.25
, pp. 2473-2477
-
-
Marco, A.1
Konikoff, C.2
Karr, T.L.3
Kumar, S.4
-
23
-
-
33645018580
-
An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse
-
10.1186/1471-2105-7-44, 1403805, 16438730
-
Kim RS, Ji H, Wong WH. An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse. BMC Bioinformatics 2006, 7:44. 10.1186/1471-2105-7-44, 1403805, 16438730.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 44
-
-
Kim, R.S.1
Ji, H.2
Wong, W.H.3
-
24
-
-
77950381164
-
Conservation and divergence of known apicomplexan transcriptional regulons
-
10.1186/1471-2164-11-147, 2841118, 20199665
-
Essien K, Stoeckert CJ. Conservation and divergence of known apicomplexan transcriptional regulons. BMC Genomics 2010, 11:147. 10.1186/1471-2164-11-147, 2841118, 20199665.
-
(2010)
BMC Genomics
, vol.11
, pp. 147
-
-
Essien, K.1
Stoeckert, C.J.2
-
25
-
-
33749514099
-
Genomic analysis of the hierarchical structure of regulatory networks
-
10.1073/pnas.0508637103, 1595419, 17003135
-
Yu H, Gerstein M. Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci USA 2006, 103:14724-14731. 10.1073/pnas.0508637103, 1595419, 17003135.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 14724-14731
-
-
Yu, H.1
Gerstein, M.2
-
26
-
-
69249127529
-
Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture
-
10.1038/msb.2009.52, 2736650, 19690563
-
Jothi R, Balaji S, Wuster A, Grochow JA, Gsponer J, Przytycka TM, Aravind L, Babu MM. Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 2009, 5:294. 10.1038/msb.2009.52, 2736650, 19690563.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 294
-
-
Jothi, R.1
Balaji, S.2
Wuster, A.3
Grochow, J.A.4
Gsponer, J.5
Przytycka, T.M.6
Aravind, L.7
Babu, M.M.8
-
27
-
-
76949105103
-
Identification of interacting transcription factors regulating tissue gene expression in human
-
10.1186/1471-2164-11-49, 2822763, 20085649
-
Hu Z, Gallo SM. Identification of interacting transcription factors regulating tissue gene expression in human. BMC Genomics 2010, 11:49. 10.1186/1471-2164-11-49, 2822763, 20085649.
-
(2010)
BMC Genomics
, vol.11
, pp. 49
-
-
Hu, Z.1
Gallo, S.M.2
-
28
-
-
0025320694
-
The possible role of skeletal muscle in the adaptation to periods of energy deficiency
-
Henriksson J. The possible role of skeletal muscle in the adaptation to periods of energy deficiency. Eur J Clin Nutr 1990, 44(Suppl 1):55-64.
-
(1990)
Eur J Clin Nutr
, vol.44
, Issue.SUPPL 1
, pp. 55-64
-
-
Henriksson, J.1
-
29
-
-
3042514191
-
Coexpression analysis of human genes across many microarray data sets
-
10.1101/gr.1910904, 419787, 15173114
-
Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res 2004, 14:1085-1094. 10.1101/gr.1910904, 419787, 15173114.
-
(2004)
Genome Res
, vol.14
, pp. 1085-1094
-
-
Lee, H.K.1
Hsu, A.K.2
Sajdak, J.3
Qin, J.4
Pavlidis, P.5
-
30
-
-
33746617003
-
Extracting Gene Networks for Low-Dose Radiation Using Graph Theoretical Algorithms
-
10.1371/journal.pcbi.0020089, 1513268, 16854212
-
Voy BH, Scharff JA, Perkins AD, Saxton AM, Borate B, Chesler EJ, Branstetter LK, Langston MA. Extracting Gene Networks for Low-Dose Radiation Using Graph Theoretical Algorithms. PLoS Comput Biol 2006, 2:e89. 10.1371/journal.pcbi.0020089, 1513268, 16854212.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Voy, B.H.1
Scharff, J.A.2
Perkins, A.D.3
Saxton, A.M.4
Borate, B.5
Chesler, E.J.6
Branstetter, L.K.7
Langston, M.A.8
-
31
-
-
70849119931
-
Transcriptome complexity in a genome-reduced bacterium
-
Güell M, van Noort V, Yus E, Chen W, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin A, Bork P, Serrano L. Transcriptome complexity in a genome-reduced bacterium. Science 2009, 326:1268-1271.
-
(2009)
Science
, vol.326
, pp. 1268-1271
-
-
Güell, M.1
van Noort, V.2
Yus, E.3
Chen, W.4
Leigh-Bell, J.5
Michalodimitrakis, K.6
Yamada, T.7
Arumugam, M.8
Doerks, T.9
Kühner, S.10
Rode, M.11
Suyama, M.12
Schmidt, S.13
Gavin, A.14
Bork, P.15
Serrano, L.16
-
32
-
-
33947219266
-
Large-scale mapping of human protein-protein interactions by mass spectrometry
-
10.1038/msb4100134, 1847948, 17353931
-
Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, O'Connor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert J, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams S, Moran MF, Morin GB, Topaloglou T, Figeys D. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol 2007, 3:89. 10.1038/msb4100134, 1847948, 17353931.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 89
-
-
Ewing, R.M.1
Chu, P.2
Elisma, F.3
Li, H.4
Taylor, P.5
Climie, S.6
McBroom-Cerajewski, L.7
Robinson, M.D.8
O'Connor, L.9
Li, M.10
Taylor, R.11
Dharsee, M.12
Ho, Y.13
Heilbut, A.14
Moore, L.15
Zhang, S.16
Ornatsky, O.17
Bukhman, Y.V.18
Ethier, M.19
Sheng, Y.20
Vasilescu, J.21
Abu-Farha, M.22
Lambert, J.23
Duewel, H.S.24
Stewart, I.I.25
Kuehl, B.26
Hogue, K.27
Colwill, K.28
Gladwish, K.29
Muskat, B.30
Kinach, R.31
Adams, S.32
Moran, M.F.33
Morin, G.B.34
Topaloglou, T.35
Figeys, D.36
more..
-
33
-
-
2442477788
-
Genomic analysis of essentiality within protein networks
-
10.1016/j.tig.2004.04.008, 15145574
-
Yu H, Greenbaum D, Xin Lu H, Zhu X, Gerstein M. Genomic analysis of essentiality within protein networks. Trends Genet 2004, 20:227-231. 10.1016/j.tig.2004.04.008, 15145574.
-
(2004)
Trends Genet
, vol.20
, pp. 227-231
-
-
Yu, H.1
Greenbaum, D.2
Xin Lu, H.3
Zhu, X.4
Gerstein, M.5
-
34
-
-
76049125511
-
ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells
-
10.1073/pnas.0904863106, 2789751, 19995984
-
Ouyang Z, Zhou Q, Wong WH. ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci USA 2009, 106:21521-21526. 10.1073/pnas.0904863106, 2789751, 19995984.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 21521-21526
-
-
Ouyang, Z.1
Zhou, Q.2
Wong, W.H.3
-
35
-
-
77955477557
-
Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets
-
10.1371/journal.pcbi.1000755, 2877725, 20523742
-
Bhardwaj N, Carson MB, Abyzov A, Yan K, Lu H, Gerstein MB. Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets. PLoS Comput Biol 2010, 6:e1000755. 10.1371/journal.pcbi.1000755, 2877725, 20523742.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Bhardwaj, N.1
Carson, M.B.2
Abyzov, A.3
Yan, K.4
Lu, H.5
Gerstein, M.B.6
-
36
-
-
2442526837
-
Just-in-time transcription program in metabolic pathways
-
10.1038/ng1348, 15107854
-
Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U. Just-in-time transcription program in metabolic pathways. Nat Genet 2004, 36:486-491. 10.1038/ng1348, 15107854.
-
(2004)
Nat Genet
, vol.36
, pp. 486-491
-
-
Zaslaver, A.1
Mayo, A.E.2
Rosenberg, R.3
Bashkin, P.4
Sberro, H.5
Tsalyuk, M.6
Surette, M.G.7
Alon, U.8
-
37
-
-
0036678794
-
Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics
-
10.1073/pnas.152046799, 124972, 12145321
-
Ronen M, Rosenberg R, Shraiman BI, Alon U. Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci USA 2002, 99:10555-10560. 10.1073/pnas.152046799, 124972, 12145321.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 10555-10560
-
-
Ronen, M.1
Rosenberg, R.2
Shraiman, B.I.3
Alon, U.4
-
38
-
-
14244266613
-
FHL3 negatively regulates human high-affinity IgE receptor beta-chain gene expression by acting as a transcriptional co-repressor of MZF-1
-
10.1042/BJ20040775, 1134781, 15453830
-
Takahashi K, Matsumoto C, Ra C. FHL3 negatively regulates human high-affinity IgE receptor beta-chain gene expression by acting as a transcriptional co-repressor of MZF-1. Biochem J 2005, 386:191-200. 10.1042/BJ20040775, 1134781, 15453830.
-
(2005)
Biochem J
, vol.386
, pp. 191-200
-
-
Takahashi, K.1
Matsumoto, C.2
Ra, C.3
-
39
-
-
61749091132
-
Human four-and-a-half LIM family members suppress tumor cell growth through a TGF-beta-like signaling pathway
-
2631293, 19139564
-
Ding L, Wang Z, Yan J, Yang X, Liu A, Qiu W, Zhu J, Han J, Zhang H, Lin J, Cheng L, Qin X, Niu C, Yuan B, Wang X, Zhu C, Zhou Y, Li J, Song H, Huang C, Ye Q. Human four-and-a-half LIM family members suppress tumor cell growth through a TGF-beta-like signaling pathway. J Clin Invest 2009, 119:349-361. 2631293, 19139564.
-
(2009)
J Clin Invest
, vol.119
, pp. 349-361
-
-
Ding, L.1
Wang, Z.2
Yan, J.3
Yang, X.4
Liu, A.5
Qiu, W.6
Zhu, J.7
Han, J.8
Zhang, H.9
Lin, J.10
Cheng, L.11
Qin, X.12
Niu, C.13
Yuan, B.14
Wang, X.15
Zhu, C.16
Zhou, Y.17
Li, J.18
Song, H.19
Huang, C.20
Ye, Q.21
more..
-
40
-
-
0033515620
-
A Smad transcriptional corepressor
-
10.1016/S0092-8674(00)80712-6, 10199400
-
Wotton D, Lo RS, Lee S, Massagué J. A Smad transcriptional corepressor. Cell 1999, 97:29-39. 10.1016/S0092-8674(00)80712-6, 10199400.
-
(1999)
Cell
, vol.97
, pp. 29-39
-
-
Wotton, D.1
Lo, R.S.2
Lee, S.3
Massagué, J.4
-
41
-
-
39149119250
-
Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes
-
10.1016/j.ygeno.2007.11.002, 18082363
-
Michalak P. Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 2008, 91:243-248. 10.1016/j.ygeno.2007.11.002, 18082363.
-
(2008)
Genomics
, vol.91
, pp. 243-248
-
-
Michalak, P.1
-
42
-
-
76249101086
-
Abundance of Ribosomal RNA Gene Copies Maintains Genome Integrity
-
10.1126/science.1179044, 20133573
-
Ide S, Miyazaki T, Maki H, Kobayashi T. Abundance of Ribosomal RNA Gene Copies Maintains Genome Integrity. Science 2010, 327:693-696. 10.1126/science.1179044, 20133573.
-
(2010)
Science
, vol.327
, pp. 693-696
-
-
Ide, S.1
Miyazaki, T.2
Maki, H.3
Kobayashi, T.4
-
43
-
-
58649119619
-
Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences
-
10.1186/gb-2008-9-12-r172, 2646276, 19087242
-
Ettwiller L, Budd A, Spitz F, Wittbrodt J. Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences. Genome Biol 2008, 9:R172. 10.1186/gb-2008-9-12-r172, 2646276, 19087242.
-
(2008)
Genome Biol
, vol.9
-
-
Ettwiller, L.1
Budd, A.2
Spitz, F.3
Wittbrodt, J.4
-
44
-
-
0031020729
-
Differential cell cycle effects induced by E2F1 mutants
-
10.1038/sj.onc.1200809, 9010232
-
Qin XQ, Barsoum J. Differential cell cycle effects induced by E2F1 mutants. Oncogene 1997, 14:53-62. 10.1038/sj.onc.1200809, 9010232.
-
(1997)
Oncogene
, vol.14
, pp. 53-62
-
-
Qin, X.Q.1
Barsoum, J.2
-
45
-
-
0037031982
-
Regulation of smooth muscle cell differentiation by AT-rich interaction domain transcription factors Mrf2alpha and Mrf2beta
-
10.1161/01.RES.0000033593.05545.7B, 12215486
-
Watanabe M, Layne MD, Hsieh C, Maemura K, Gray S, Lee M, Jain MK. Regulation of smooth muscle cell differentiation by AT-rich interaction domain transcription factors Mrf2alpha and Mrf2beta. Circ Res 2002, 91:382-389. 10.1161/01.RES.0000033593.05545.7B, 12215486.
-
(2002)
Circ Res
, vol.91
, pp. 382-389
-
-
Watanabe, M.1
Layne, M.D.2
Hsieh, C.3
Maemura, K.4
Gray, S.5
Lee, M.6
Jain, M.K.7
-
46
-
-
58149171655
-
Sustained NF-kappaB activation produces a short-term cell proliferation block in conjunction with repressing effectors of cell cycle progression controlled by E2F or FoxM1
-
10.1002/jcp.21596, 2581928, 18803232
-
Penzo M, Massa PE, Olivotto E, Bianchi F, Borzi RM, Hanidu A, Li X, Li J, Marcu KB. Sustained NF-kappaB activation produces a short-term cell proliferation block in conjunction with repressing effectors of cell cycle progression controlled by E2F or FoxM1. J Cell Physiol 2009, 218:215-227. 10.1002/jcp.21596, 2581928, 18803232.
-
(2009)
J Cell Physiol
, vol.218
, pp. 215-227
-
-
Penzo, M.1
Massa, P.E.2
Olivotto, E.3
Bianchi, F.4
Borzi, R.M.5
Hanidu, A.6
Li, X.7
Li, J.8
Marcu, K.B.9
-
47
-
-
77951089274
-
NF-kappaB signaling: a tale of two pathways in skeletal myogenesis
-
10.1152/physrev.00040.2009, 20393192
-
Bakkar N, Guttridge DC. NF-kappaB signaling: a tale of two pathways in skeletal myogenesis. Physiol Rev 2010, 90:495-511. 10.1152/physrev.00040.2009, 20393192.
-
(2010)
Physiol Rev
, vol.90
, pp. 495-511
-
-
Bakkar, N.1
Guttridge, D.C.2
-
48
-
-
10944232632
-
Profiling molecular targets of TGF-beta1 in prostate fibroblast-to-myofibroblast transdifferentiation
-
10.1016/j.mad.2004.09.023, 15610763
-
Untergasser G, Gander R, Lilg C, Lepperdinger G, Plas E, Berger P. Profiling molecular targets of TGF-beta1 in prostate fibroblast-to-myofibroblast transdifferentiation. Mech Ageing Dev 2005, 126:59-69. 10.1016/j.mad.2004.09.023, 15610763.
-
(2005)
Mech Ageing Dev
, vol.126
, pp. 59-69
-
-
Untergasser, G.1
Gander, R.2
Lilg, C.3
Lepperdinger, G.4
Plas, E.5
Berger, P.6
-
49
-
-
33748035384
-
MEF2 activates a genetic program promoting chamber dilation and contractile dysfunction in calcineurin-induced heart failure
-
10.1161/CIRCULATIONAHA.105.608968, 16847152
-
van Oort RJ, van Rooij E, Bourajjaj M, Schimmel J, Jansen MA, van der Nagel R, Doevendans PA, Schneider MD, van Echteld CJA, De Windt LJ. MEF2 activates a genetic program promoting chamber dilation and contractile dysfunction in calcineurin-induced heart failure. Circulation 2006, 114:298-308. 10.1161/CIRCULATIONAHA.105.608968, 16847152.
-
(2006)
Circulation
, vol.114
, pp. 298-308
-
-
van Oort, R.J.1
van Rooij, E.2
Bourajjaj, M.3
Schimmel, J.4
Jansen, M.A.5
van der Nagel, R.6
Doevendans, P.A.7
Schneider, M.D.8
van Echteld, C.J.A.9
De Windt, L.J.10
-
50
-
-
77954050386
-
MEF2C silencing attenuates load-induced left ventricular hypertrophy by modulating mTOR/S6K pathway in mice
-
10.1371/journal.pone.0008472, 2794538, 20041152
-
Pereira AHM, Clemente CFMZ, Cardoso AC, Theizen TH, Rocco SA, Judice CC, Guido MC, Pascoal VDB, Lopes-Cendes I, Souza JRM, Franchini KG. MEF2C silencing attenuates load-induced left ventricular hypertrophy by modulating mTOR/S6K pathway in mice. PLoS ONE 2009, 4:e8472. 10.1371/journal.pone.0008472, 2794538, 20041152.
-
(2009)
PLoS ONE
, vol.4
-
-
Pereira, A.H.M.1
Clemente, C.F.M.Z.2
Cardoso, A.C.3
Theizen, T.H.4
Rocco, S.A.5
Judice, C.C.6
Guido, M.C.7
Pascoal, V.D.B.8
Lopes-Cendes, I.9
Souza, J.R.M.10
Franchini, K.G.11
-
51
-
-
77049114286
-
Nfix regulates fetal-specific transcription in developing skeletal muscle
-
10.1016/j.cell.2010.01.027, 20178747
-
Messina G, Biressi S, Monteverde S, Magli A, Cassano M, Perani L, Roncaglia E, Tagliafico E, Starnes L, Campbell CE, Grossi M, Goldhamer DJ, Gronostajski RM, Cossu G. Nfix regulates fetal-specific transcription in developing skeletal muscle. Cell 2010, 140:554-566. 10.1016/j.cell.2010.01.027, 20178747.
-
(2010)
Cell
, vol.140
, pp. 554-566
-
-
Messina, G.1
Biressi, S.2
Monteverde, S.3
Magli, A.4
Cassano, M.5
Perani, L.6
Roncaglia, E.7
Tagliafico, E.8
Starnes, L.9
Campbell, C.E.10
Grossi, M.11
Goldhamer, D.J.12
Gronostajski, R.M.13
Cossu, G.14
-
52
-
-
1842509855
-
ATF6 modulates SREBP2-mediated lipogenesis
-
10.1038/sj.emboj.7600106, 381012, 14765107
-
Zeng L, Lu M, Mori K, Luo S, Lee AS, Zhu Y, Shyy JY. ATF6 modulates SREBP2-mediated lipogenesis. EMBO J 2004, 23:950-958. 10.1038/sj.emboj.7600106, 381012, 14765107.
-
(2004)
EMBO J
, vol.23
, pp. 950-958
-
-
Zeng, L.1
Lu, M.2
Mori, K.3
Luo, S.4
Lee, A.S.5
Zhu, Y.6
Shyy, J.Y.7
-
53
-
-
67349266612
-
Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger
-
10.1038/nature08036, 2697266, 19430464
-
Wang GG, Song J, Wang Z, Dormann HL, Casadio F, Li H, Luo J, Patel DJ, Allis CD. Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger. Nature 2009, 459:847-851. 10.1038/nature08036, 2697266, 19430464.
-
(2009)
Nature
, vol.459
, pp. 847-851
-
-
Wang, G.G.1
Song, J.2
Wang, Z.3
Dormann, H.L.4
Casadio, F.5
Li, H.6
Luo, J.7
Patel, D.J.8
Allis, C.D.9
-
54
-
-
77950930524
-
Gene expression changes in mononuclear cells in patients with metabolic syndrome after acute intake of phenol-rich virgin olive oil
-
10.1186/1471-2164-11-253, 2874810, 20406432
-
Camargo A, Ruano J, Fernandez JM, Parnell LD, Jimenez A, Santos-Gonzalez M, Marin C, Perez-Martinez P, Uceda M, Lopez-Miranda J, Perez-Jimenez F. Gene expression changes in mononuclear cells in patients with metabolic syndrome after acute intake of phenol-rich virgin olive oil. BMC Genomics 2010, 11:253. 10.1186/1471-2164-11-253, 2874810, 20406432.
-
(2010)
BMC Genomics
, vol.11
, pp. 253
-
-
Camargo, A.1
Ruano, J.2
Fernandez, J.M.3
Parnell, L.D.4
Jimenez, A.5
Santos-Gonzalez, M.6
Marin, C.7
Perez-Martinez, P.8
Uceda, M.9
Lopez-Miranda, J.10
Perez-Jimenez, F.11
-
55
-
-
77951742701
-
Meis1 maintains stemness signature in MLL-AF9 leukemia
-
10.1182/blood-2010-01-264564, 20430967
-
Kumar AR, Sarver AL, Wu B, Kersey JH. Meis1 maintains stemness signature in MLL-AF9 leukemia. Blood 2010, 115:3642-3643. 10.1182/blood-2010-01-264564, 20430967.
-
(2010)
Blood
, vol.115
, pp. 3642-3643
-
-
Kumar, A.R.1
Sarver, A.L.2
Wu, B.3
Kersey, J.H.4
-
56
-
-
76449086120
-
An evolutionarily conserved Myostatin proximal promoter/enhancer confers basal levels of transcription and spatial specificity in vivo
-
10.1007/s00427-009-0312-x, 20052486
-
Grade CVC, Salerno MS, Schubert FR, Dietrich S, Alvares LE. An evolutionarily conserved Myostatin proximal promoter/enhancer confers basal levels of transcription and spatial specificity in vivo. Dev Genes Evol 2009, 219:497-508. 10.1007/s00427-009-0312-x, 20052486.
-
(2009)
Dev Genes Evol
, vol.219
, pp. 497-508
-
-
Grade, C.V.C.1
Salerno, M.S.2
Schubert, F.R.3
Dietrich, S.4
Alvares, L.E.5
-
57
-
-
0347088945
-
GATA transcription factors and fat cell formation
-
10.1358/dnp.2003.16.9.829340, 14702139
-
Tong Q, Tsai J, Hotamisligil GS. GATA transcription factors and fat cell formation. Drug News Perspect 2003, 16:585-588. 10.1358/dnp.2003.16.9.829340, 14702139.
-
(2003)
Drug News Perspect
, vol.16
, pp. 585-588
-
-
Tong, Q.1
Tsai, J.2
Hotamisligil, G.S.3
-
58
-
-
13944284208
-
Gli2 and Gli3 have redundant and context-dependent function in skeletal muscle formation
-
10.1242/dev.01537, 15604102
-
McDermott A, Gustafsson M, Elsam T, Hui C, Emerson CP, Borycki A. Gli2 and Gli3 have redundant and context-dependent function in skeletal muscle formation. Development 2005, 132:345-357. 10.1242/dev.01537, 15604102.
-
(2005)
Development
, vol.132
, pp. 345-357
-
-
McDermott, A.1
Gustafsson, M.2
Elsam, T.3
Hui, C.4
Emerson, C.P.5
Borycki, A.6
-
59
-
-
65349085291
-
Global networks of functional coupling in eukaryotes from comprehensive data integration
-
10.1101/gr.087528.108, 2694487, 19246318
-
Alexeyenko A, Sonnhammer ELL. Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res 2009, 19:1107-1116. 10.1101/gr.087528.108, 2694487, 19246318.
-
(2009)
Genome Res
, vol.19
, pp. 1107-1116
-
-
Alexeyenko, A.1
Sonnhammer, E.L.L.2
-
60
-
-
16344362648
-
Validation of alternative methods of data normalization in gene co-expression studies
-
10.1093/bioinformatics/bti124, 15564293
-
Reverter A, Barris W, McWilliam S, Byrne KA, Wang YH, Tan SH, Hudson N, Dalrymple BP. Validation of alternative methods of data normalization in gene co-expression studies. Bioinformatics 2005, 21:1112-1120. 10.1093/bioinformatics/bti124, 15564293.
-
(2005)
Bioinformatics
, vol.21
, pp. 1112-1120
-
-
Reverter, A.1
Barris, W.2
McWilliam, S.3
Byrne, K.A.4
Wang, Y.H.5
Tan, S.H.6
Hudson, N.7
Dalrymple, B.P.8
-
61
-
-
77951956867
-
Assigning roles to DNA regulatory motifs using comparative genomics
-
10.1093/bioinformatics/btq049, 2844991, 20147307
-
Buske FA, Bodén M, Bauer DC, Bailey TL. Assigning roles to DNA regulatory motifs using comparative genomics. Bioinformatics 2010, 26:860-866. 10.1093/bioinformatics/btq049, 2844991, 20147307.
-
(2010)
Bioinformatics
, vol.26
, pp. 860-866
-
-
Buske, F.A.1
Bodén, M.2
Bauer, D.C.3
Bailey, T.L.4
-
62
-
-
21444443478
-
MatInspector and beyond: promoter analysis based on transcription factor binding sites
-
10.1093/bioinformatics/bti473, 15860560
-
Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, Frisch M, Bayerlein M, Werner T. MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 2005, 21:2933-2942. 10.1093/bioinformatics/bti473, 15860560.
-
(2005)
Bioinformatics
, vol.21
, pp. 2933-2942
-
-
Cartharius, K.1
Frech, K.2
Grote, K.3
Klocke, B.4
Haltmeier, M.5
Klingenhoff, A.6
Frisch, M.7
Bayerlein, M.8
Werner, T.9
-
63
-
-
16344389891
-
PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order
-
10.1093/bioinformatics/bti141, 15546938
-
Caraux G, Pinloche S. PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order. Bioinformatics 2005, 21:1280-1281. 10.1093/bioinformatics/bti141, 15546938.
-
(2005)
Bioinformatics
, vol.21
, pp. 1280-1281
-
-
Caraux, G.1
Pinloche, S.2
-
64
-
-
67749140118
-
Scale-free networks: a decade and beyond
-
Barabási A. Scale-free networks: a decade and beyond. Science 2009, 325:412-413.
-
(2009)
Science
, vol.325
, pp. 412-413
-
-
Barabási, A.1
-
65
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
Barabási A, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabási, A.1
Oltvai, Z.N.2
|