-
1
-
-
33746826011
-
JAK/STAT signalling in Drosophila: insights into conserved regulatory and cellular functions
-
10.1242/dev.02411, 16794031
-
Arbouzova NI, Zeidler MP. JAK/STAT signalling in Drosophila: insights into conserved regulatory and cellular functions. Development 2006, 133:2605-2616. 10.1242/dev.02411, 16794031.
-
(2006)
Development
, vol.133
, pp. 2605-2616
-
-
Arbouzova, N.I.1
Zeidler, M.P.2
-
2
-
-
0036731485
-
Stats: transcriptional control and biological impact
-
Levy DE, Darnell JE. Stats: transcriptional control and biological impact. Nat Rev Mol Cell Biol 2002, 3:651-662.
-
(2002)
Nat Rev Mol Cell Biol
, vol.3
, pp. 651-662
-
-
Levy, D.E.1
Darnell, J.E.2
-
3
-
-
41149149301
-
Interpretation of cytokine signaling through the transcription factors STAT5A and STAT5B
-
10.1101/gad.1643908, 2394721,2394721, 18347089
-
Hennighausen L, Robinson GW. Interpretation of cytokine signaling through the transcription factors STAT5A and STAT5B. Genes Dev 2008, 22:711-721. 10.1101/gad.1643908, 2394721,2394721, 18347089.
-
(2008)
Genes Dev
, vol.22
, pp. 711-721
-
-
Hennighausen, L.1
Robinson, G.W.2
-
4
-
-
75649093758
-
Role of STAT5 in controlling cell survival and immunoglobulin gene recombination during pro-B cell development
-
2956121, 19946273
-
Malin S, McManus S, Cobaleda C, Novatchkova M, Delogu A, Bouillet P, Strasser A, Busslinger M. Role of STAT5 in controlling cell survival and immunoglobulin gene recombination during pro-B cell development. Nat Immunol 2010, 11:171-179. 2956121, 19946273.
-
(2010)
Nat Immunol
, vol.11
, pp. 171-179
-
-
Malin, S.1
McManus, S.2
Cobaleda, C.3
Novatchkova, M.4
Delogu, A.5
Bouillet, P.6
Strasser, A.7
Busslinger, M.8
-
5
-
-
79961002967
-
EsBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function
-
10.1038/ncb2285, 3155811, 21785422
-
Ho L, Miller EL, Ronan JL, Ho WQ, Jothi R, Crabtree GR. esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function. Nat Cell Biol 2011, 13:903-913. 10.1038/ncb2285, 3155811, 21785422.
-
(2011)
Nat Cell Biol
, vol.13
, pp. 903-913
-
-
Ho, L.1
Miller, E.L.2
Ronan, J.L.3
Ho, W.Q.4
Jothi, R.5
Crabtree, G.R.6
-
6
-
-
0029069145
-
Transcriptional responses to polypeptide ligands: the JAK-STAT pathway
-
10.1146/annurev.bi.64.070195.003201, 7574495
-
Schindler C, Darnell JE. Transcriptional responses to polypeptide ligands: the JAK-STAT pathway. Annu Rev Biochem 1995, 64:621-651. 10.1146/annurev.bi.64.070195.003201, 7574495.
-
(1995)
Annu Rev Biochem
, vol.64
, pp. 621-651
-
-
Schindler, C.1
Darnell, J.E.2
-
7
-
-
79953134246
-
Genomic views of STAT function in CD4+ T helper cell differentiation
-
10.1038/nri2958, 3070307, 21436836
-
O'Shea JJ, Lahesmaa R, Vahedi G, Laurence A, Kanno Y. Genomic views of STAT function in CD4+ T helper cell differentiation. Nat Rev Immunol 2011, 11:239-250. 10.1038/nri2958, 3070307, 21436836.
-
(2011)
Nat Rev Immunol
, vol.11
, pp. 239-250
-
-
O'Shea, J.J.1
Lahesmaa, R.2
Vahedi, G.3
Laurence, A.4
Kanno, Y.5
-
8
-
-
78651339534
-
NCBI GEO: archive for functional genomics data sets--10 years on
-
10.1093/nar/gkq1184, 3013736, 21097893
-
Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM. NCBI GEO: archive for functional genomics data sets--10 years on. Nucleic Acids Res 2011, 39:D1005-D1010. 10.1093/nar/gkq1184, 3013736, 21097893.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
Ledoux, P.4
Evangelista, C.5
Kim, I.F.6
Tomashevsky, M.7
Marshall, K.A.8
Phillippy, K.H.9
Sherman, P.M.10
-
9
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
10.1016/j.cell.2008.04.043, 18555785
-
Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133:1106-1117. 10.1016/j.cell.2008.04.043, 18555785.
-
(2008)
Cell
, vol.133
, pp. 1106-1117
-
-
Chen, X.1
Xu, H.2
Yuan, P.3
Fang, F.4
Huss, M.5
Vega, V.B.6
Wong, E.7
Orlov, Y.L.8
Zhang, W.9
Jiang, J.10
-
10
-
-
84855495283
-
IκB kinase epsilon (IKK(epsilon)) regulates the balance between type I and type II interferon responses
-
10.1073/pnas.1119137109, 3248534, 22171011
-
Ng SL, Friedman BA, Schmid S, Gertz J, Myers RM, Tenoever BR, Maniatis T. IκB kinase epsilon (IKK(epsilon)) regulates the balance between type I and type II interferon responses. Proc Natl Acad Sci USA 2011, 108:21170-21175. 10.1073/pnas.1119137109, 3248534, 22171011.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 21170-21175
-
-
Ng, S.L.1
Friedman, B.A.2
Schmid, S.3
Gertz, J.4
Myers, R.M.5
Tenoever, B.R.6
Maniatis, T.7
-
11
-
-
71749089605
-
Analysis of interleukin-21-induced Prdm1 gene regulation reveals functional cooperation of STAT3 and IRF4 transcription factors
-
10.1016/j.immuni.2009.10.008, 3272079, 20064451
-
Kwon H, Thierry-Mieg D, Thierry-Mieg J, Kim H-P, Oh J, Tunyaplin C, Carotta S, Donovan CE, Goldman ML, Tailor P, Ozato K, Levy DE, Nutt SL, Calame K, Leonard WJ. Analysis of interleukin-21-induced Prdm1 gene regulation reveals functional cooperation of STAT3 and IRF4 transcription factors. Immunity 2009, 31:941-952. 10.1016/j.immuni.2009.10.008, 3272079, 20064451.
-
(2009)
Immunity
, vol.31
, pp. 941-952
-
-
Kwon, H.1
Thierry-Mieg, D.2
Thierry-Mieg, J.3
Kim, H.-P.4
Oh, J.5
Tunyaplin, C.6
Carotta, S.7
Donovan, C.E.8
Goldman, M.L.9
Tailor, P.10
Ozato, K.11
Levy, D.E.12
Nutt, S.L.13
Calame, K.14
Leonard, W.J.15
-
12
-
-
77953917067
-
Discrete roles of STAT4 and STAT6 transcription factors in tuning epigenetic modifications and transcription during T helper cell differentiation
-
10.1016/j.immuni.2010.06.003, 2904651, 20620946
-
Wei L, Vahedi G, Sun HW, Watford WT, Takatori H, Ramos HL, Takahashi H, Liang J, Gutierrez-Cruz G, Zang C, Peng W, O'Shea JJ, Kanno Y. Discrete roles of STAT4 and STAT6 transcription factors in tuning epigenetic modifications and transcription during T helper cell differentiation. Immunity 2010, 32:840-851. 10.1016/j.immuni.2010.06.003, 2904651, 20620946.
-
(2010)
Immunity
, vol.32
, pp. 840-851
-
-
Wei, L.1
Vahedi, G.2
Sun, H.W.3
Watford, W.T.4
Takatori, H.5
Ramos, H.L.6
Takahashi, H.7
Liang, J.8
Gutierrez-Cruz, G.9
Zang, C.10
Peng, W.11
O'Shea, J.J.12
Kanno, Y.13
-
13
-
-
54549103162
-
Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression
-
10.1038/ni.1656, 2762127, 18820682
-
Liao W, Schones DE, Oh J, Cui Y, Cui K, Roh T-Y, Zhao K, Leonard WJ. Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression. Nat Immunol 2008, 9:1288-1296. 10.1038/ni.1656, 2762127, 18820682.
-
(2008)
Nat Immunol
, vol.9
, pp. 1288-1296
-
-
Liao, W.1
Schones, D.E.2
Oh, J.3
Cui, Y.4
Cui, K.5
Roh, T.-Y.6
Zhao, K.7
Leonard, W.J.8
-
14
-
-
79956085895
-
Modulation of cytokine receptors by IL-2 broadly regulates differentiation into helper T cell lineages
-
3304099, 21516110
-
Liao W, Lin J-X, Wang L, Li P, Leonard WJ. Modulation of cytokine receptors by IL-2 broadly regulates differentiation into helper T cell lineages. Nat Immunol 2011, 12:551-559. 3304099, 21516110.
-
(2011)
Nat Immunol
, vol.12
, pp. 551-559
-
-
Liao, W.1
Lin, J.-X.2
Wang, L.3
Li, P.4
Leonard, W.J.5
-
15
-
-
79954992662
-
Extensive chromatin remodelling and establishment of transcription factor " hotspots" during early adipogenesis
-
10.1038/emboj.2011.65, 3102274, 21427703
-
Siersbæk R, Nielsen R, John S, Sung M-H, Baek S, Loft A, Hager GL, Mandrup S. Extensive chromatin remodelling and establishment of transcription factor " hotspots" during early adipogenesis. EMBO J 2011, 30:1459-1472. 10.1038/emboj.2011.65, 3102274, 21427703.
-
(2011)
EMBO J
, vol.30
, pp. 1459-1472
-
-
Siersbæk, R.1
Nielsen, R.2
John, S.3
Sung, M.-H.4
Baek, S.5
Loft, A.6
Hager, G.L.7
Mandrup, S.8
-
16
-
-
84863011066
-
Dynamic, sex-differential STAT5 and BCL6 binding to sex-biased, growth hormone-regulated genes in adult mouse liver
-
10.1128/MCB.06312-11, 3272977, 22158971
-
Zhang Y, Laz EV, Waxman DJ. Dynamic, sex-differential STAT5 and BCL6 binding to sex-biased, growth hormone-regulated genes in adult mouse liver. Mol Cell Biol 2012, 32:880-896. 10.1128/MCB.06312-11, 3272977, 22158971.
-
(2012)
Mol Cell Biol
, vol.32
, pp. 880-896
-
-
Zhang, Y.1
Laz, E.V.2
Waxman, D.J.3
-
17
-
-
84861563048
-
Genome-wide analyses reveal the extent of opportunistic STAT5 binding that does not yield transcriptional activation of neighboring genes
-
10.1093/nar/gks056, 3378893, 22319210
-
Zhu BM, Kang K, Yu JH, Chen W, Smith HE, Lee D, Sun HW, Wei L, Hennighausen L. Genome-wide analyses reveal the extent of opportunistic STAT5 binding that does not yield transcriptional activation of neighboring genes. Nucleic Acids Res 2012, 40:4461-4472. 10.1093/nar/gks056, 3378893, 22319210.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 4461-4472
-
-
Zhu, B.M.1
Kang, K.2
Yu, J.H.3
Chen, W.4
Smith, H.E.5
Lee, D.6
Sun, H.W.7
Wei, L.8
Hennighausen, L.9
-
18
-
-
81255154496
-
Epigenetic repression of the Igk locus by STAT5-mediated recruitment of the histone methyltransferase Ezh2
-
10.1038/ni.2136, 3233979, 22037603
-
Mandal M, Powers SE, Maienschein-Cline M, Bartom ET, Hamel KM, Kee BL, Dinner AR, Clark MR. Epigenetic repression of the Igk locus by STAT5-mediated recruitment of the histone methyltransferase Ezh2. Nat Immunol 2011, 12:1212-1220. 10.1038/ni.2136, 3233979, 22037603.
-
(2011)
Nat Immunol
, vol.12
, pp. 1212-1220
-
-
Mandal, M.1
Powers, S.E.2
Maienschein-Cline, M.3
Bartom, E.T.4
Hamel, K.M.5
Kee, B.L.6
Dinner, A.R.7
Clark, M.R.8
-
19
-
-
84859968982
-
Critical Role of STAT5 Transcription Factor Tetramerization for Cytokine Responses and Normal Immune Function
-
10.1016/j.immuni.2012.02.017, 22520852
-
Lin JX, Li P, Liu D, Jin HT, He J, Rasheed MAU, Rochman Y, Wang L, Cui K, Liu C, Kelsall BL, Ahmed R, Leonard WJ. Critical Role of STAT5 Transcription Factor Tetramerization for Cytokine Responses and Normal Immune Function. Immunity 2012, 36:586-599. 10.1016/j.immuni.2012.02.017, 22520852.
-
(2012)
Immunity
, vol.36
, pp. 586-599
-
-
Lin, J.X.1
Li, P.2
Liu, D.3
Jin, H.T.4
He, J.5
Rasheed, M.A.U.6
Rochman, Y.7
Wang, L.8
Cui, K.9
Liu, C.10
Kelsall, B.L.11
Ahmed, R.12
Leonard, W.J.13
-
20
-
-
84861964081
-
Systematic evaluation of factors influencing ChIP-seq fidelity
-
10.1038/nmeth.1985, 3477507, 22522655
-
Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim T, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS. Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods 2012, 9:609-614. 10.1038/nmeth.1985, 3477507, 22522655.
-
(2012)
Nat Methods
, vol.9
, pp. 609-614
-
-
Chen, Y.1
Negre, N.2
Li, Q.3
Mieczkowska, J.O.4
Slattery, M.5
Liu, T.6
Zhang, Y.7
Kim, T.8
He, H.H.9
Zieba, J.10
Ruan, Y.11
Bickel, P.J.12
Myers, R.M.13
Wold, B.J.14
White, K.P.15
Lieb, J.D.16
Liu, X.S.17
-
21
-
-
84861397707
-
Picking ChIP-seq peak detectors for analyzing chromatin modification experiments
-
10.1093/nar/gks048, 3351193, 22307239
-
Micsinai M, Parisi F, Strino F, Asp P, Dynlacht BD, Kluger Y. Picking ChIP-seq peak detectors for analyzing chromatin modification experiments. Nucleic Acids Res 2012, 40:e70. 10.1093/nar/gks048, 3351193, 22307239.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Micsinai, M.1
Parisi, F.2
Strino, F.3
Asp, P.4
Dynlacht, B.D.5
Kluger, Y.6
-
22
-
-
74549114755
-
A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
-
10.1186/1471-2164-10-618, 2804666, 20017957
-
Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo LL. A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics 2009, 10:618. 10.1186/1471-2164-10-618, 2804666, 20017957.
-
(2009)
BMC Genomics
, vol.10
, pp. 618
-
-
Laajala, T.D.1
Raghav, S.2
Tuomela, S.3
Lahesmaa, R.4
Aittokallio, T.5
Elo, L.L.6
-
23
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
10.1016/j.molcel.2010.05.004, 2898526, 20513432
-
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 2010, 38:576-589. 10.1016/j.molcel.2010.05.004, 2898526, 20513432.
-
(2010)
Mol Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
Benner, C.2
Spann, N.3
Bertolino, E.4
Lin, Y.C.5
Laslo, P.6
Cheng, J.X.7
Murre, C.8
Singh, H.9
Glass, C.K.10
-
24
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
10.1186/gb-2008-9-9-r137, 2592715, 18798982
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9:R137. 10.1186/gb-2008-9-9-r137, 2592715, 18798982.
-
(2008)
Genome Biol
, vol.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nussbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
Liu, X.S.11
-
25
-
-
84864041695
-
Genome-wide location analysis reveals distinct transcriptional circuitry by paralogous regulators Foxa1 and Foxa2
-
Bochkis IM, Schug J, Ye DZ, Kurinna S, Stratton SA, Barton MC, Kaestner KH. Genome-wide location analysis reveals distinct transcriptional circuitry by paralogous regulators Foxa1 and Foxa2. PLoS gen 2012, 8:e1002770.
-
(2012)
PLoS gen
, vol.8
-
-
Bochkis, I.M.1
Schug, J.2
Ye, D.Z.3
Kurinna, S.4
Stratton, S.A.5
Barton, M.C.6
Kaestner, K.H.7
-
26
-
-
75949117507
-
MOODS: fast search for position weight matrix matches in DNA sequences
-
10.1093/bioinformatics/btp554, 2778336, 19773334
-
Korhonen J, Martinmäki P, Pizzi C, Rastas P, Ukkonen E. MOODS: fast search for position weight matrix matches in DNA sequences. Bioinformatics 2009, 25:3181-3182. 10.1093/bioinformatics/btp554, 2778336, 19773334.
-
(2009)
Bioinformatics
, vol.25
, pp. 3181-3182
-
-
Korhonen, J.1
Martinmäki, P.2
Pizzi, C.3
Rastas, P.4
Ukkonen, E.5
-
27
-
-
38549096565
-
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
-
10.1093/nar/gkn449, 2238834, 18006571
-
Bryne JC, Valen E, Tang M-HE, Marstrand T, Winther O, Da Piedade I, Krogh A, Lenhard B, Sandelin A. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 2008, 36:D102-D106. 10.1093/nar/gkn449, 2238834, 18006571.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Bryne, J.C.1
Valen, E.2
Tang, M.-H.E.3
Marstrand, T.4
Winther, O.5
Da Piedade, I.6
Krogh, A.7
Lenhard, B.8
Sandelin, A.9
-
28
-
-
77952214662
-
GREAT improves functional interpretation of cis-regulatory regions
-
McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. GREAT improves functional interpretation of cis-regulatory regions. Nature biotechnol 2010, 28:495-501.
-
(2010)
Nature biotechnol
, vol.28
, pp. 495-501
-
-
McLean, C.Y.1
Bristor, D.2
Hiller, M.3
Clarke, S.L.4
Schaar, B.T.5
Lowe, C.B.6
Wenger, A.M.7
Bejerano, G.8
-
29
-
-
17044368752
-
Gene regulatory networks for development
-
10.1073/pnas.0408031102, 555974, 15788537
-
Levine M, Davidson EH. Gene regulatory networks for development. Proc Natl Acad Sci USA 2005, 102:4936-4942. 10.1073/pnas.0408031102, 555974, 15788537.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 4936-4942
-
-
Levine, M.1
Davidson, E.H.2
-
30
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
10.1101/gr.3715005, 1182216, 16024819
-
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005, 15:1034-1050. 10.1101/gr.3715005, 1182216, 16024819.
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
Rosenbloom, K.6
Clawson, H.7
Spieth, J.8
Hillier, L.W.9
Richards, S.10
Weinstock, G.M.11
Wilson, R.K.12
Gibbs, R.A.13
Kent, W.J.14
Miller, W.15
Haussler, D.16
-
31
-
-
84859992161
-
The JAK-STAT Pathway at Twenty
-
10.1016/j.immuni.2012.03.013, 22520844
-
Stark GR, Darnell JE. The JAK-STAT Pathway at Twenty. Immunity 2012, 36:503-514. 10.1016/j.immuni.2012.03.013, 22520844.
-
(2012)
Immunity
, vol.36
, pp. 503-514
-
-
Stark, G.R.1
Darnell, J.E.2
-
32
-
-
80053179656
-
Decoding the genome with an integrative analysis tool: Combinatorial CRM Decoder
-
10.1093/nar/gkr516, 3177223, 21724599
-
Kang K, Kim J, Chung JH, Lee D. Decoding the genome with an integrative analysis tool: Combinatorial CRM Decoder. Nucleic Acids Res 2011, 39:e116. 10.1093/nar/gkr516, 3177223, 21724599.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Kang, K.1
Kim, J.2
Chung, J.H.3
Lee, D.4
-
33
-
-
38749127589
-
Predicting expression patterns from regulatory sequence in Drosophila segmentation
-
10.1038/nature06496, 18172436
-
Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U. Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 2008, 451:535-540. 10.1038/nature06496, 18172436.
-
(2008)
Nature
, vol.451
, pp. 535-540
-
-
Segal, E.1
Raveh-Sadka, T.2
Schroeder, M.3
Unnerstall, U.4
Gaul, U.5
-
34
-
-
0028937707
-
Spacing of palindromic half sites as a determinant of selective STAT (signal transducers and activators of transcription) DNA binding and transcriptional activity
-
10.1073/pnas.92.7.3041, 42355, 7708771
-
Seidel HM, Milocco LH, Lamb P, Darnell JE, Stein RB, Rosen J. Spacing of palindromic half sites as a determinant of selective STAT (signal transducers and activators of transcription) DNA binding and transcriptional activity. Proc Natl Acad Sci USA 1995, 92:3041-3045. 10.1073/pnas.92.7.3041, 42355, 7708771.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 3041-3045
-
-
Seidel, H.M.1
Milocco, L.H.2
Lamb, P.3
Darnell, J.E.4
Stein, R.B.5
Rosen, J.6
-
35
-
-
79958117256
-
MEME-ChIP: motif analysis of large DNA datasets
-
10.1093/bioinformatics/btr189, 3106185, 21486936
-
Machanick P, Bailey TL. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 2011, 27:1696-1697. 10.1093/bioinformatics/btr189, 3106185, 21486936.
-
(2011)
Bioinformatics
, vol.27
, pp. 1696-1697
-
-
Machanick, P.1
Bailey, T.L.2
-
36
-
-
34447506667
-
Quantifying similarity between motifs
-
10.1186/gb-2007-8-2-r24, 1852410, 17324271
-
Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS. Quantifying similarity between motifs. Genome Biol 2007, 8:R24. 10.1186/gb-2007-8-2-r24, 1852410, 17324271.
-
(2007)
Genome Biol
, vol.8
-
-
Gupta, S.1
Stamatoyannopoulos, J.A.2
Bailey, T.L.3
Noble, W.S.4
-
37
-
-
34547744867
-
The role of the runx transcription factors in thymocyte differentiation and in homeostasis of naive T cells
-
10.1084/jem.20070133, 2118679, 17646406
-
Egawa T, Tillman RE, Naoe Y, Taniuchi I, Littman DR. The role of the runx transcription factors in thymocyte differentiation and in homeostasis of naive T cells. J Exp Med 2007, 204:1945-1957. 10.1084/jem.20070133, 2118679, 17646406.
-
(2007)
J Exp Med
, vol.204
, pp. 1945-1957
-
-
Egawa, T.1
Tillman, R.E.2
Naoe, Y.3
Taniuchi, I.4
Littman, D.R.5
-
38
-
-
33344457703
-
Codependence of growth hormone-responsive, sexually dimorphic hepatic gene expression on signal transducer and activator of transcription 5b and hepatic nuclear factor 4alpha
-
Holloway MG, Laz EV, Waxman DJ. Codependence of growth hormone-responsive, sexually dimorphic hepatic gene expression on signal transducer and activator of transcription 5b and hepatic nuclear factor 4alpha. Mol Endo 2006, 20:647-660.
-
(2006)
Mol Endo
, vol.20
, pp. 647-660
-
-
Holloway, M.G.1
Laz, E.V.2
Waxman, D.J.3
-
39
-
-
43449139993
-
Physical and functional interactions between STAT5 and Runx transcription factors
-
Ogawa S, Satake M, Ikuta K. Physical and functional interactions between STAT5 and Runx transcription factors. J Biol Chem 2008, 143:695-709.
-
(2008)
J Biol Chem
, vol.143
, pp. 695-709
-
-
Ogawa, S.1
Satake, M.2
Ikuta, K.3
-
40
-
-
77955149398
-
In islets and liver Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver
-
10.1101/gr.104356.109, 2909568, 20551221
-
Hoffman BG, Robertson G, Zavaglia B, Hoffman BG, Robertson G, Zavaglia B, Beach M, Cullum R, Lee S, Soukhatcheva G, Li L, Wederell ED, Thiessen N, Bilenky M, Cezard T, Tam A, Kamoh B, Birol I, Dai D, Zhao Y, Hirst M, Verchere CB, Helgason CD, Marra MA, Jones SJM, Hoodless PA. In islets and liver Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. Genome Res 2010, 20:1037-1051. 10.1101/gr.104356.109, 2909568, 20551221.
-
(2010)
Genome Res
, vol.20
, pp. 1037-1051
-
-
Hoffman, B.G.1
Robertson, G.2
Zavaglia, B.3
Hoffman, B.G.4
Robertson, G.5
Zavaglia, B.6
Beach, M.7
Cullum, R.8
Lee, S.9
Soukhatcheva, G.10
Li, L.11
Wederell, E.D.12
Thiessen, N.13
Bilenky, M.14
Cezard, T.15
Tam, A.16
Kamoh, B.17
Birol, I.18
Dai, D.19
Zhao, Y.20
Hirst, M.21
Verchere, C.B.22
Helgason, C.D.23
Marra, M.A.24
Jones, S.J.M.25
Hoodless, P.A.26
more..
-
41
-
-
77954586080
-
A quantitative model of transcriptional regulation reveals the influence of binding location on expression
-
10.1371/journal.pcbi.1000773, 2861697, 20442865
-
Macisaac KD, Lo KA, Gordon W, Motola S, Mazor T, Fraenkel E. A quantitative model of transcriptional regulation reveals the influence of binding location on expression. PLoS Comput Biol 2010, 6:e1000773. 10.1371/journal.pcbi.1000773, 2861697, 20442865.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Macisaac, K.D.1
Lo, K.A.2
Gordon, W.3
Motola, S.4
Mazor, T.5
Fraenkel, E.6
-
42
-
-
77953062527
-
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
-
10.1126/science.1186176, 3008766, 20378774
-
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 2010, 328:1036-1040. 10.1126/science.1186176, 3008766, 20378774.
-
(2010)
Science
, vol.328
, pp. 1036-1040
-
-
Schmidt, D.1
Wilson, M.D.2
Ballester, B.3
Schwalie, P.C.4
Brown, G.D.5
Marshall, A.6
Kutter, C.7
Watt, S.8
Martinez-Jimenez, C.P.9
Mackay, S.10
Talianidis, I.11
Flicek, P.12
Odom, D.T.13
-
43
-
-
49149090637
-
Hepatocyte-specific ablation of Foxa2 alters bile acid homeostasis and results in endoplasmic reticulum stress
-
Bochkis IM, Rubins NE, White P, Furth EE, Friedman JR, Kaestner KH. Hepatocyte-specific ablation of Foxa2 alters bile acid homeostasis and results in endoplasmic reticulum stress. Nat Medicine 2008, 14:828-836.
-
(2008)
Nat Medicine
, vol.14
, pp. 828-836
-
-
Bochkis, I.M.1
Rubins, N.E.2
White, P.3
Furth, E.E.4
Friedman, J.R.5
Kaestner, K.H.6
-
44
-
-
67651002855
-
Foxa1 and Foxa2 regulate bile duct development in mice
-
10.1172/JCI38201, 2689124, 19436110
-
Li Z, White P, Tuteja G, Rubins N, Sackett S, Kaestner KH. Foxa1 and Foxa2 regulate bile duct development in mice. J Clin Invest 2009, 119:1537-1545. 10.1172/JCI38201, 2689124, 19436110.
-
(2009)
J Clin Invest
, vol.119
, pp. 1537-1545
-
-
Li, Z.1
White, P.2
Tuteja, G.3
Rubins, N.4
Sackett, S.5
Kaestner, K.H.6
-
45
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat protocols 2012, 7:562-578.
-
(2012)
Nat protocols
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
Pertea, G.4
Kim, D.5
Kelley, D.R.6
Pimentel, H.7
Salzberg, S.L.8
Rinn, J.L.9
Pachter, L.10
-
46
-
-
84864462544
-
A map of the cis-regulatory sequences in the mouse genome
-
10.1038/nature11243, 22763441
-
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. A map of the cis-regulatory sequences in the mouse genome. Nature 2012, 488:116-120. 10.1038/nature11243, 22763441.
-
(2012)
Nature
, vol.488
, pp. 116-120
-
-
Shen, Y.1
Yue, F.2
McCleary, D.F.3
Ye, Z.4
Edsall, L.5
Kuan, S.6
Wagner, U.7
Dixon, J.8
Lee, L.9
Lobanenkov, V.V.10
Ren, B.11
-
47
-
-
0036071235
-
A note on the calculation of empirical P values from Monte Carlo procedures
-
10.1086/341527, 379178, 12111669
-
North BV, Curtis D, Sham PC. A note on the calculation of empirical P values from Monte Carlo procedures. Am J Hum Genet 2002, 71:439-441. 10.1086/341527, 379178, 12111669.
-
(2002)
Am J Hum Genet
, vol.71
, pp. 439-441
-
-
North, B.V.1
Curtis, D.2
Sham, P.C.3
-
48
-
-
79952184341
-
Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
-
10.1038/ng.759, 21258342
-
John S, Sabo PJ, Thurman RE, Sung M-H, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet 2011, 43:264-268. 10.1038/ng.759, 21258342.
-
(2011)
Nat Genet
, vol.43
, pp. 264-268
-
-
John, S.1
Sabo, P.J.2
Thurman, R.E.3
Sung, M.-H.4
Biddie, S.C.5
Johnson, T.A.6
Hager, G.L.7
Stamatoyannopoulos, J.A.8
-
49
-
-
78649723495
-
Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression
-
10.1128/MCB.00601-10, 2976433, 20876297
-
Ling G, Sugathan A, Mazor T, Fraenkel E, Waxman DJ. Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression. Mol Cell Biol 2010, 30:5531-5544. 10.1128/MCB.00601-10, 2976433, 20876297.
-
(2010)
Mol Cell Biol
, vol.30
, pp. 5531-5544
-
-
Ling, G.1
Sugathan, A.2
Mazor, T.3
Fraenkel, E.4
Waxman, D.J.5
-
50
-
-
54249099196
-
Species-specific transcription in mice carrying human chromosome 21
-
10.1126/science.1160930, 18787134
-
Cellino A, Paolicchi P, Binzel RP, Grundy WM, Chiang EI, Margot JL, Kern SD, Barucci A, Boehnhardt H, Cruikshank D, Morbidelli A, Brown ME, Trujillo CA, Sari R, Stansberry JA, Gladman G, Holman M, Marsden BG, Van Laerhoven C. Species-specific transcription in mice carrying human chromosome 21. Science 2008, 322:434-438. 10.1126/science.1160930, 18787134.
-
(2008)
Science
, vol.322
, pp. 434-438
-
-
Cellino, A.1
Paolicchi, P.2
Binzel, R.P.3
Grundy, W.M.4
Chiang, E.I.5
Margot, J.L.6
Kern, S.D.7
Barucci, A.8
Boehnhardt, H.9
Cruikshank, D.10
Morbidelli, A.11
Brown, M.E.12
Trujillo, C.A.13
Sari, R.14
Stansberry, J.A.15
Gladman, G.16
Holman, M.17
Marsden, B.G.18
Van Laerhoven, C.19
-
51
-
-
57149119464
-
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
-
10.1371/journal.pcbi.1000216, 2570626, 18989395
-
Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 2008, 4:e1000216. 10.1371/journal.pcbi.1000216, 2570626, 18989395.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Field, Y.1
Kaplan, N.2
Fondufe-Mittendorf, Y.3
Moore, I.K.4
Sharon, E.5
Lubling, Y.6
Widom, J.7
Segal, E.8
-
52
-
-
33747500567
-
A genomic code for nucleosome positioning
-
10.1038/nature04979, 2623244, 16862119
-
Segal E, Fondufe-Mittendorf Y, Chen L, Thåström A, Field Y, Moore IK, Wang J-PZ, Widom J. A genomic code for nucleosome positioning. Nature 2006, 442:772-778. 10.1038/nature04979, 2623244, 16862119.
-
(2006)
Nature
, vol.442
, pp. 772-778
-
-
Segal, E.1
Fondufe-Mittendorf, Y.2
Chen, L.3
Thåström, A.4
Field, Y.5
Moore, I.K.6
Wang, J.-P.Z.7
Widom, J.8
-
53
-
-
75149177340
-
Hepatocyte nuclear factor 4alpha coordinates a transcription factor network regulating hepatic fatty acid metabolism
-
10.1128/MCB.00927-09, 2812226, 19933841
-
Martinez-Jimenez CP, Kyrmizi I, Cardot P, Gonzalez FJ, Talianidis I. Hepatocyte nuclear factor 4alpha coordinates a transcription factor network regulating hepatic fatty acid metabolism. Mol Cell Biol 2010, 30:565-577. 10.1128/MCB.00927-09, 2812226, 19933841.
-
(2010)
Mol Cell Biol
, vol.30
, pp. 565-577
-
-
Martinez-Jimenez, C.P.1
Kyrmizi, I.2
Cardot, P.3
Gonzalez, F.J.4
Talianidis, I.5
-
54
-
-
0028564903
-
CCAAT/enhancer binding protein
-
10.1073/pnas.91.19.8757, 44685, 8090719
-
Lin F, Lane MD. CCAAT/enhancer binding protein. Proc Natl Acad Sci USA 1994, 91:8757-8761. 10.1073/pnas.91.19.8757, 44685, 8090719.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 8757-8761
-
-
Lin, F.1
Lane, M.D.2
-
55
-
-
80155137594
-
Master transcription factors determine cell-type-specific responses to TGF-β signaling
-
10.1016/j.cell.2011.08.050, 3212730, 22036565
-
Mullen AC, Orlando DA, Newman JJ, Lovén J, Kumar RM, Bilodeau S, Reddy J, Guenther MG, De Koter RP, Young RA. Master transcription factors determine cell-type-specific responses to TGF-β signaling. Cell 2011, 147:565-576. 10.1016/j.cell.2011.08.050, 3212730, 22036565.
-
(2011)
Cell
, vol.147
, pp. 565-576
-
-
Mullen, A.C.1
Orlando, D.A.2
Newman, J.J.3
Lovén, J.4
Kumar, R.M.5
Bilodeau, S.6
Reddy, J.7
Guenther, M.G.8
De Koter, R.P.9
Young, R.A.10
-
56
-
-
84861133568
-
A computational pipeline for comparative ChIP-seq analyses
-
Bardet AF, He Q, Zeitlinger J, Stark A. A computational pipeline for comparative ChIP-seq analyses. Nat Protoc 2012, 7:45-61.
-
(2012)
Nat Protoc
, vol.7
, pp. 45-61
-
-
Bardet, A.F.1
He, Q.2
Zeitlinger, J.3
Stark, A.4
-
57
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
10.1186/gb-2009-10-3-r25, 2690996, 19261174
-
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
58
-
-
3142756502
-
Open source clustering software
-
10.1093/bioinformatics/bth078, 14871861
-
De Hoon MJL, Imoto S, Nolan J, Miyano S. Open source clustering software. Bioinformatics 2004, 20:1453-1454. 10.1093/bioinformatics/bth078, 14871861.
-
(2004)
Bioinformatics
, vol.20
, pp. 1453-1454
-
-
De Hoon, M.J.L.1
Imoto, S.2
Nolan, J.3
Miyano, S.4
-
59
-
-
77955183656
-
PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci.
-
Dvinge H, Tammoja K, Bertone P. PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci. BMC Bioinforma 2010, 11:415.
-
(2010)
BMC Bioinforma
, vol.11
, pp. 415
-
-
Dvinge, H.1
Tammoja, K.2
Bertone, P.3
|