-
1
-
-
0037453510
-
Assembly of cell regulatory systems through protein interaction domains
-
DOI 10.1126/science.1083653
-
Pawson, T. and Nash, P. (2003) Assembly of cell regulatory systems through protein interaction domains. Science, 300, 445-452 (Pubitemid 36444318)
-
(2003)
Science
, vol.300
, Issue.5618
, pp. 445-452
-
-
Pawson, T.1
Nash, P.2
-
2
-
-
0024396320
-
Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins
-
Mitchell, P.J. and Tjian, R. (1989) Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science, 245, 371-378 (Pubitemid 19203358)
-
(1989)
Science
, vol.245
, Issue.4916
, pp. 371-378
-
-
Mitchell, P.J.1
Tjian, R.2
-
3
-
-
17644391197
-
A rapid method for determining protein kinase phosphorylation specificity
-
Hutti, J.E., Jarrell, E.T., Chang, J.D., Abbott, D.W., Storz, P., Toker, A., Cantley, L.C. and Turk, B.E. (2004) A rapid method for determining protein kinase phosphorylation specificity. Nat. Methods, 1, 27-29
-
(2004)
Nat. Methods
, vol.1
, pp. 27-29
-
-
Hutti, J.E.1
Jarrell, E.T.2
Chang, J.D.3
Abbott, D.W.4
Storz, P.5
Toker, A.6
Cantley, L.C.7
Turk, B.E.8
-
4
-
-
77951969848
-
MOTIPS: Automated motif analysis for predicting targets of modular protein domains
-
Lam, H.Y.K., Kim, P.M., Mok, J., Tonikian, R., Sidhu, S.S., Turk, B.E., Snyder, M. and Gerstein, M.B. (2010) MOTIPS: automated motif analysis for predicting targets of modular protein domains. BMC Bioinformatics, 11, 243
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 243
-
-
Lam, H.Y.K.1
Kim, P.M.2
Mok, J.3
Tonikian, R.4
Sidhu, S.S.5
Turk, B.E.6
Snyder, M.7
Gerstein, M.B.8
-
5
-
-
55749111058
-
Linear motif atlas for phosphorylation-dependent signaling
-
Miller, M.L., Jensen, L.J., Diella, F., Jørgensen, C., Tinti, M., Li, L., Hsiung, M., Parker, S.A., Bordeaux, J., Sicheritz-Ponten, T. et al. (2008) Linear motif atlas for phosphorylation-dependent signaling. Sci. Signal., 1, ra2
-
(2008)
Sci. Signal.
, vol.1
-
-
Miller, M.L.1
Jensen, L.J.2
Diella, F.3
Jørgensen, C.4
Tinti, M.5
Li, L.6
Hsiung, M.7
Parker, S.A.8
Bordeaux, J.9
Sicheritz-Ponten, T.10
-
6
-
-
0035030510
-
SH3 domains: Complexity in moderation
-
Mayer, B.J. (2001) SH3 domains: complexity in moderation. J. Cell. Sci., 114, 1253-1263 (Pubitemid 32409462)
-
(2001)
Journal of Cell Science
, vol.114
, Issue.7
, pp. 1253-1263
-
-
Mayer, B.J.1
-
7
-
-
0030604722
-
Crystal structures of a complexed and peptide-free membrane protein- binding domain: Molecular basis of peptide recognition by PDZ
-
DOI 10.1016/S0092-8674(00)81307-0
-
Doyle, D.A., Lee, A., Lewis, J., Kim, E., Sheng, M. and MacKinnon, R. (1996) Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell, 85, 1067-1076 (Pubitemid 26231173)
-
(1996)
Cell
, vol.85
, Issue.7
, pp. 1067-1076
-
-
Doyle, D.A.1
Lee, A.2
Lewis, J.3
Kim, E.4
Sheng, M.5
MacKinnon, R.6
-
8
-
-
0034740693
-
Mechanisma and role of PDZ domains in signaling complex assembly
-
Harris, B.Z. and Lim, W.A. (2001) Mechanism and role of PDZ domains in signaling complex assembly. J. Cell. Sci., 114, 3219-3231 (Pubitemid 32998900)
-
(2001)
Journal of Cell Science
, vol.114
, Issue.18
, pp. 3219-3231
-
-
Harris, B.Z.1
Lim, W.A.2
-
9
-
-
0035930331
-
Recognition of specific DNA sequences
-
DOI 10.1016/S1097-2765(01)00392-6
-
Garvie, C.W. and Wolberger, C. (2001) Recognition of specific DNA sequences. Mol. Cell, 8, 937-946 (Pubitemid 34031797)
-
(2001)
Molecular Cell
, vol.8
, Issue.5
, pp. 937-946
-
-
Garvie, C.W.1
Wolberger, C.2
-
10
-
-
51349085386
-
Predicting PDZ domain-peptide interactions from primary sequences
-
Chen, J.R., Chang, B.H., Allen, J.E., Stiffler, M.A. and MacBeath, G. (2008) Predicting PDZ domain-peptide interactions from primary sequences. Nat. Biotechnol., 26, 1041-1045
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1041-1045
-
-
Chen, J.R.1
Chang, B.H.2
Allen, J.E.3
Stiffler, M.A.4
MacBeath, G.5
-
11
-
-
77949509793
-
Specificity landscapes of DNA binding molecules elucidate biological function
-
Carlson, C.D., Warren, C.L., Hauschild, K.E., Ozers, M.S., Qadir, N., Bhimsaria, D., Lee, Y., Cerrina, F. and Ansari, A.Z. (2010) Specificity landscapes of DNA binding molecules elucidate biological function. Proc. Natl Acad. Sci. USA, 107, 4544-4549
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 4544-4549
-
-
Carlson, C.D.1
Warren, C.L.2
Hauschild, K.E.3
Ozers, M.S.4
Qadir, N.5
Bhimsaria, D.6
Lee, Y.7
Cerrina, F.8
Ansari, A.Z.9
-
12
-
-
34547127612
-
PDZ domain binding selectivity is optimized across the mouse proteome
-
Stiffler, M.A., Chen, J.R., Grantcharova, V.P., Lei, Y., Fuchs, D., Allen, J.E., Zaslavskaia, L.A. and MacBeath, G. (2007) PDZ domain binding selectivity is optimized across the mouse proteome. Science, 317, 364-369
-
(2007)
Science
, vol.317
, pp. 364-369
-
-
Stiffler, M.A.1
Chen, J.R.2
Grantcharova, V.P.3
Lei, Y.4
Fuchs, D.5
Allen, J.E.6
Zaslavskaia, L.A.7
MacBeath, G.8
-
13
-
-
70350404403
-
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins
-
Tonikian, R., Xin, X., Toret, C.P., Gfeller, D., Landgraf, C., Panni, S., Paoluzi, S., Castagnoli, L., Currell, B., Seshagiri, S. et al. (2009) Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol., 7, e1000218
-
(2009)
PLoS Biol.
, vol.7
-
-
Tonikian, R.1
Xin, X.2
Toret, C.P.3
Gfeller, D.4
Landgraf, C.5
Panni, S.6
Paoluzi, S.7
Castagnoli, L.8
Currell, B.9
Seshagiri, S.10
-
14
-
-
62649175248
-
Inhibition of Wnt signaling by Dishevelled PDZ peptides
-
Zhang, Y., Appleton, B.A., Wiesmann, C., Lau, T., Costa, M., Hannoush, R.N. and Sidhu, S.S. (2009) Inhibition of Wnt signaling by Dishevelled PDZ peptides. Nat. Chem. Biol., 5, 217-219
-
(2009)
Nat. Chem. Biol.
, vol.5
, pp. 217-219
-
-
Zhang, Y.1
Appleton, B.A.2
Wiesmann, C.3
Lau, T.4
Costa, M.5
Hannoush, R.N.6
Sidhu, S.S.7
-
15
-
-
9644268153
-
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
-
DOI 10.1038/ng1473
-
Mukherjee, S., Berger, M.F., Jona, G., Wang, X.S., Muzzey, D., Snyder, M., Young, R.A. and Bulyk, M.L. (2004) Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat. Genet., 36, 1331-1339 (Pubitemid 39577944)
-
(2004)
Nature Genetics
, vol.36
, Issue.12
, pp. 1331-1339
-
-
Mukherjee, S.1
Berger, M.F.2
Jona, G.3
Wang, X.S.4
Muzzey, D.5
Snyder, M.6
Young, R.A.7
Bulyk, M.L.8
-
16
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis, G., Berger, M.F., Philippakis, A.A., Talukder, S., Gehrke, A.R., Jaeger, S.A., Chan, E.T., Metzler, G., Vedenko, A., Chen, X. et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science, 324, 1720-1723
-
(2009)
Science
, vol.324
, pp. 1720-1723
-
-
Badis, G.1
Berger, M.F.2
Philippakis, A.A.3
Talukder, S.4
Gehrke, A.R.5
Jaeger, S.A.6
Chan, E.T.7
Metzler, G.8
Vedenko, A.9
Chen, X.10
-
17
-
-
4744353840
-
Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides
-
DOI 10.1016/j.jmb.2004.08.064, PII S0022283604010551
-
Wiedemann, U., Boisguerin, P., Leben, R., Leitner, D., Krause, G., Moelling, K., Volkmer-Engert, R. and Oschkinat, H. (2004) Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides. J. Mol. Biol., 343, 703-718 (Pubitemid 39311616)
-
(2004)
Journal of Molecular Biology
, vol.343
, Issue.3
, pp. 703-718
-
-
Wiedemann, U.1
Boisguerin, P.2
Leben, R.3
Leitner, D.4
Krause, G.5
Moelling, K.6
Volkmer-Engert, R.7
Oschkinat, H.8
-
18
-
-
77951644400
-
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
-
Olsen, J.V., Vermeulen, M., Santamaria, A., Kumar, C., Miller, M.L., Jensen, L.J., Gnad, F., Cox, J., Jensen, T.S., Nigg, E.A. et al. (2010) Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci. Signal., 3, ra3
-
(2010)
Sci. Signal.
, vol.3
-
-
Olsen, J.V.1
Vermeulen, M.2
Santamaria, A.3
Kumar, C.4
Miller, M.L.5
Jensen, L.J.6
Gnad, F.7
Cox, J.8
Jensen, T.S.9
Nigg, E.A.10
-
19
-
-
34250748507
-
Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries
-
DOI 10.1038/nprot.2007.151, PII NPROT.2007.151
-
Tonikian, R., Zhang, Y., Boone, C. and Sidhu, S.S. (2007) Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries. Nat. Protoc., 2, 1368-1386 (Pubitemid 46952319)
-
(2007)
Nature Protocols
, vol.2
, Issue.6
, pp. 1368-1386
-
-
Tonikian, R.1
Zhang, Y.2
Boone, C.3
Sidhu, S.S.4
-
20
-
-
20744440509
-
Identification of transcription factor binding sites with variable-order Bayesian networks
-
DOI 10.1093/bioinformatics/bti410
-
Ben-Gal, I., Shani, A., Gohr, A., Grau, J., Arviv, S., Shmilovici, A., Posch, S. and Grosse, I. (2005) Identification of transcription factor binding sites with variable-order Bayesian networks. Bioinformatics, 21, 2657-2666 (Pubitemid 40852312)
-
(2005)
Bioinformatics
, vol.21
, Issue.11
, pp. 2657-2666
-
-
Ben-Gal, I.1
Shani, A.2
Gohr, A.3
Grau, J.4
Arviv, S.5
Shmilovici, A.6
Posch, S.7
Grosse, I.8
-
21
-
-
0030869663
-
A method for identifying splice sites and translational start sites in eukaryotic mRNA
-
Salzberg, S.L. (1997) A method for identifying splice sites and translational start sites in eukaryotic mRNA. Comput. Appl. Biosci., 13, 365-376
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 365-376
-
-
Salzberg, S.L.1
-
22
-
-
75549083247
-
JASPAR 2010: The greatly expanded open-access database of transcription factor binding profiles
-
Portales-Casamar, E., Thongjuea, S., Kwon, A.T., Arenillas, D., Zhao, X., Valen, E., Yusuf, D., Lenhard, B., Wasserman, W.W. and Sandelin, A. (2010) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res., 38, D105-D110
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Portales-Casamar, E.1
Thongjuea, S.2
Kwon, A.T.3
Arenillas, D.4
Zhao, X.5
Valen, E.6
Yusuf, D.7
Lenhard, B.8
Wasserman, W.W.9
Sandelin, A.10
-
23
-
-
0042622251
-
Scansite 2.0: Proteome-wide prediction of cell signalling interactions using short sequence motifs
-
DOI 10.1093/nar/gkg584
-
Obenauer, J.C., Cantley, L.C. and Yaffe, M.B. (2003) Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res., 31, 3635-3641 (Pubitemid 37442212)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3635-3641
-
-
Obenauer, J.C.1
Cantley, L.C.2
Yaffe, M.B.3
-
24
-
-
79955569676
-
The multiple-specificity landscape of modular peptide recognition domains
-
Gfeller, D., Butty, F., Wierzbicka, M., Verschueren, E., Vanhee, P., Huang, H., Ernst, A., Dar, N., Stagljar, I., Serrano, L. et al. (2011) The multiple-specificity landscape of modular peptide recognition domains. Mol. Syst. Biol., 7, 1-12
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 1-12
-
-
Gfeller, D.1
Butty, F.2
Wierzbicka, M.3
Verschueren, E.4
Vanhee, P.5
Huang, H.6
Ernst, A.7
Dar, N.8
Stagljar, I.9
Serrano, L.10
-
25
-
-
0036399733
-
Hidden Markov model-based prediction of antigenic peptides that interact with MHC class II molecules
-
DOI 10.1016/S1389-1723(02)80160-8
-
Noguchi, H., Kato, R., Hanai, T., Matsubara, Y., Honda, H., Brusic, V. and Kobayashi, T. (2002) Hidden Markov model-based prediction of antigenic peptides that interact with MHC class II molecules. J. Biosci. Bioeng., 94, 264-270 (Pubitemid 35192075)
-
(2002)
Journal of Bioscience and Bioengineering
, vol.94
, Issue.3
, pp. 264-270
-
-
Noguchi, H.1
Kato, R.2
Hanai, T.3
Matsubara, Y.4
Honda, H.5
Brusic, V.6
Kobayashi, T.7
-
27
-
-
77956544553
-
Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing
-
Ernst, A., Gfeller, D., Kan, Z., Seshagiri, S., Kim, P.M., Bader, G.D. and Sidhu, S.S. (2010) Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing. Mol. Biosyst., 6, 1782-1790
-
(2010)
Mol. Biosyst.
, vol.6
, pp. 1782-1790
-
-
Ernst, A.1
Gfeller, D.2
Kan, Z.3
Seshagiri, S.4
Kim, P.M.5
Bader, G.D.6
Sidhu, S.S.7
-
28
-
-
77956338533
-
High-resolution mapping of protein sequence-function relationships
-
Fowler, D.M., Araya, C.L., Fleishman, S.J., Kellogg, E.H., Stephany, J.J., Baker, D. and Fields, S. (2010) High-resolution mapping of protein sequence-function relationships. Nat. Methods, 7, 741-746
-
(2010)
Nat. Methods
, vol.7
, pp. 741-746
-
-
Fowler, D.M.1
Araya, C.L.2
Fleishman, S.J.3
Kellogg, E.H.4
Stephany, J.J.5
Baker, D.6
Fields, S.7
-
29
-
-
77955019084
-
Parallelization of the MAFFT multiple sequence alignment program
-
Katoh, K. and Toh, H. (2010) Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics, 26, 1899-1900
-
(2010)
Bioinformatics
, vol.26
, pp. 1899-1900
-
-
Katoh, K.1
Toh, H.2
-
30
-
-
0000120766
-
Estimating the Dimension of a Model
-
Schwarz, G. (1978) Estimating the Dimension of a Model. Annals of Statistics, 6, 461-464
-
(1978)
Annals of Statistics
, vol.6
, pp. 461-464
-
-
Schwarz, G.1
-
31
-
-
51749088608
-
BioJava: An open-source framework for bioinformatics
-
Holland, R.C.G., Down, T.A., Pocock, M., Prlić, A., Huen, D., James, K., Foisy, S., Dräger, A., Yates, A., Heuer, M. et al. (2008) BioJava: an open-source framework for bioinformatics. Bioinformatics, 24, 2096-2097
-
(2008)
Bioinformatics
, vol.24
, pp. 2096-2097
-
-
Holland, R.C.G.1
Down, T.A.2
Pocock, M.3
Prlić, A.4
Huen, D.5
James, K.6
Foisy, S.7
Dräger, A.8
Yates, A.9
Heuer, M.10
-
32
-
-
0025008168
-
Sequence logos: A new way to display consensus sequences
-
Schneider, T.D. and Stephens, R.M. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 6097-6100
-
-
Schneider, T.D.1
Stephens, R.M.2
-
33
-
-
77951226627
-
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
-
Cock, P.J.A., Fields, C.J., Goto, N., Heuer, M.L. and Rice, P.M. (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res., 38, 1767-1771
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 1767-1771
-
-
Cock, P.J.A.1
Fields, C.J.2
Goto, N.3
Heuer, M.L.4
Rice, P.M.5
-
34
-
-
77954954652
-
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
-
Wei, G.-H., Badis, G., Berger, M.F., Kivioja, T., Palin, K., Enge, M., Bonke, M., Jolma, A., Varjosalo, M., Gehrke, A.R. et al. (2010) Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J., 29, 2147-2160
-
(2010)
EMBO J.
, vol.29
, pp. 2147-2160
-
-
Wei, G.-H.1
Badis, G.2
Berger, M.F.3
Kivioja, T.4
Palin, K.5
Enge, M.6
Bonke, M.7
Jolma, A.8
Varjosalo, M.9
Gehrke, A.R.10
-
35
-
-
45449115390
-
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
-
DOI 10.1016/j.cell.2008.05.024, PII S0092867408006831
-
Berger, M.F., Badis, G., Gehrke, A.R., Talukder, S., Philippakis, A.A., Pena-Castillo, L., Alleyne, T.M., Mnaimneh, S., Botvinnik, O.B., Chan, E.T. et al. (2008) Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell, 133, 1266-1276 (Pubitemid 351852913)
-
(2008)
Cell
, vol.133
, Issue.7
, pp. 1266-1276
-
-
Berger, M.F.1
Badis, G.2
Gehrke, A.R.3
Talukder, S.4
Philippakis, A.A.5
Pena-Castillo, L.6
Alleyne, T.M.7
Mnaimneh, S.8
Botvinnik, O.B.9
Chan, E.T.10
Khalid, F.11
Zhang, W.12
Newburger, D.13
Jaeger, S.A.14
Morris, Q.D.15
Bulyk, M.L.16
Hughes, T.R.17
-
36
-
-
58149200952
-
UniPROBE: An online database of protein binding microarray data on protein-DNA interactions
-
Newburger, D.E. and Bulyk, M.L. (2009) UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res., 37, D77-D82
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Newburger, D.E.1
Bulyk, M.L.2
-
37
-
-
74549209548
-
Inferring binding energies from selected binding sites
-
Zhao, Y., Granas, D. and Stormo, G.D. (2009) Inferring binding energies from selected binding sites. PLoS Comput. Biol., 5, e1000590
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Zhao, Y.1
Granas, D.2
Stormo, G.D.3
-
39
-
-
0031784899
-
ASAP1, a phospholipid-dependent Arf GTPase-activating protein that associates with and is phosphorylated by Src
-
Brown, M.T., Andrade, J., Radhakrishna, H., Donaldson, J.G., Cooper, J.A. and Randazzo, P.A. (1998) ASAP1, a phospholipid-dependent arf GTPase-activating protein that associates with and is phosphorylated by Src. Mol. Cell. Biol., 18, 7038-7051 (Pubitemid 28533024)
-
(1998)
Molecular and Cellular Biology
, vol.18
, Issue.12
, pp. 7038-7051
-
-
Brown, M.T.1
Andrade, J.2
Radhakrishna, H.3
Donaldson, J.G.4
Cooper, J.A.5
Randazzo, P.A.6
-
40
-
-
0033539612
-
Specificity in transforming growth factor beta-induced transcription of the plasminogen activator inhibitor-1 gene: Interactions of promoter DNA transcription factor muE3, and Smad proteins
-
Hua, X., Miller, Z.A., Wu, G., Shi, Y. and Lodish, H.F. (1999) Specificity in transforming growth factor beta-induced transcription of the plasminogen activator inhibitor-1 gene: interactions of promoter DNA, transcription factor muE3, and Smad proteins. Proc. Natl Acad. Sci. USA, 96, 13130-13135
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 13130-13135
-
-
Hua, X.1
Miller, Z.A.2
Wu, G.3
Shi, Y.4
Lodish, H.F.5
-
41
-
-
0032101178
-
Direct binding of Smad3 and Smad4 to critical TGFβ-inducible elements in the promoter of human plasminogen activator inhibitor-type 1 gene
-
DOI 10.1093/emboj/17.11.3091
-
Dennler, S., Itoh, S., Vivien, D., ten Dijke, P., Huet, S. and Gauthier, J.M. (1998) Direct binding of Smad3 and Smad4 to critical TGF beta-inducible elements in the promoter of human plasminogen activator inhibitor-type 1 gene. EMBO J., 17, 3091-3100 (Pubitemid 28254381)
-
(1998)
EMBO Journal
, vol.17
, Issue.11
, pp. 3091-3100
-
-
Dennler, S.1
Itoh, S.2
Vivien, D.3
Dijke, P.T.4
Huet, S.5
Gauthier, J.-M.6
-
42
-
-
1542314236
-
Transforming Growth Factor β-Mediated Transcriptional Repression of c-myc Is Dependent on Direct Binding of Smad3 to a Novel Repressive Smad Binding Element
-
DOI 10.1128/MCB.24.6.2546-2559.2004
-
Frederick, J.P., Liberati, N.T., Waddell, D.S., Shi, Y. and Wang, X.-F. (2004) Transforming growth factor beta-mediated transcriptional repression of c-myc is dependent on direct binding of Smad3 to a novel repressive Smad binding element. Mol. Cell. Biol., 24, 2546-2559 (Pubitemid 38326008)
-
(2004)
Molecular and Cellular Biology
, vol.24
, Issue.6
, pp. 2546-2559
-
-
Frederick, J.P.1
Liberati, N.T.2
Waddell, D.S.3
Shi, Y.4
Wang, X.-F.5
-
43
-
-
23044466047
-
Specificity and versatility in TGF-β signaling through smads
-
DOI 10.1146/annurev.cellbio.21.022404.142018
-
Feng, X.-H. and Derynck, R. (2005) Specificity and versatility in tgf-beta signaling through Smads. Annu. Rev. Cell Dev. Biol., 21, 659-693 (Pubitemid 41740650)
-
(2005)
Annual Review of Cell and Developmental Biology
, vol.21
, pp. 659-693
-
-
Feng, X.-H.1
Derynck, R.2
-
44
-
-
0042905768
-
YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation
-
DOI 10.1093/nar/gkg618
-
Sinha, S. and Tompa, M. (2003) YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res., 31, 3586-3588 (Pubitemid 37442203)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3586-3588
-
-
Sinha, S.1
Tompa, M.2
-
45
-
-
3242884167
-
Weeder web: Discovery of transcription factor binding sites in a set of sequences from co-regulated genes
-
DOI 10.1093/nar/gkh465
-
Pavesi, G., Mereghetti, P., Mauri, G. and Pesole, G. (2004) Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res., 32, W199-W203 (Pubitemid 38997329)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.WEB SERVER ISS.
-
-
Pavesi, G.1
Mereghetti, P.2
Mauri, G.3
Pesole, G.4
-
46
-
-
0036108622
-
A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes
-
DOI 10.1089/10665270252935566
-
Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouzé, P. and Moreau, Y. (2002) A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J. Comput. Biol., 9, 447-464 (Pubitemid 34548275)
-
(2002)
Journal of Computational Biology
, vol.9
, Issue.2
, pp. 447-464
-
-
Thijs, G.1
Marchal, K.2
Lescot, M.3
Rombauts, S.4
De Moor, B.5
Rouze, P.6
Moreau, Y.7
-
47
-
-
68949213578
-
Insights from genomic profiling of transcription factors
-
Farnham, P.J. (2009) Insights from genomic profiling of transcription factors. Nat. Rev. Genet., 10, 605-616
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 605-616
-
-
Farnham, P.J.1
-
48
-
-
50849090969
-
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
-
Valouev, A., Johnson, D.S., Sundquist, A., Medina, C., Anton, E., Batzoglou, S., Myers, R.M. and Sidow, A. (2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods, 5, 829-834.
-
(2008)
Nat. Methods
, vol.5
, pp. 829-834
-
-
Valouev, A.1
Johnson, D.S.2
Sundquist, A.3
Medina, C.4
Anton, E.5
Batzoglou, S.6
Myers, R.M.7
Sidow, A.8
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