Data analysed by TRAWLER

MAMMAL DATA

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. . . . . . . . . . . .
Transcription factors Dataset used Motif from literature Motif from Trawler
Sox2 From Boyer et al. [1] C[AT]TTGTT [2]
Oct4 From Boyer et al. [1] ATTTGCAT [2]
Creb From Zhang et al. [3] [4]
E2f From Ren et al. [5] [4]
Myod From Cao et al. [6] [4]
Nfkb From Schreiber et al. [7] [4]
Hnf4 From Odom et al. [8] [4]
Hnf6 From Odom et al. [8] ATCGAT [2]
Notch (CSL) From Palomero et al. [9] TGGGAA [9]
ERa to fill. [9] to fill [9]
ETS1 to fill. [9] [jaspar]
Nrf1 to fill. [9] To fill [9]
SRF to fill. [9] [jaspar]
To fill to fill. [9] [jaspar]

Additional datasets analysed by Trawler can be found here

Sequences used (in fasta format) can be uploaded from here

YEAST DATA

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for detailed analysis
(*) The reverse complement motif has been found by Trawler.

Transcription factor Motif from reference [10] Motif from Trawler
Abf1 (*)
Ace2 not found
Aft2 (*)
Azf1 not found
Bas1 (*)
Cad1
Cbf1
Cin5
Dal82 (*)
Dig1
Fhl1
Fkh1
Fkh2
Gal4 not found
Gat1
Gcn4
Gln3 (*)
Hap1
Hap4
Hsf1
Ime1 not found
Ino2
Ino4
Leu3
Mbp1
Mcm1
Met4 (*)
Msn2
Ndd1 not found
Nrg1
Pdr1 (*)
Phd1
Pho2
Pho4
Rap1
Rcs1
Rds1
Reb1 (*)
Rfx1
Rlr1 not found
Rpn4 (*)
Sfp1 (*)
Sig1 not found
Sip4
Skn7
Snt2
Sok2
Spt2 not found
Spt23
Stb1
Stb4
Stb5 (*)
Ste12
Sum1
Sut1
Swi4
SWI6
TEC1
Thi2 not found
Tye7
Ume6
Yap1
Yap7
Ydr026c
Zap1 not found


REFERENCE


[1] Core transcriptional regulatory circuitry in human embryonic stem cells. Laurie A Boyer, Tong Ihn Lee, Megan F Cole, Sarah E Johnstone, Stuart S Levine, Jacob P Zucker, Matthew G Guenther, Roshan M Kumar, Heather L Murray, Richard G Jenner, David K Gifford, Douglas A Melton, Rudolf Jaenisch, Richard A Young. Cell. 2005 vol. 122 pp. 947-56.

[2] A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Macisaac KD, Gordon DB, Nekludova L, Odom DT, Schreiber J,Gifford DK, Young RA, Fraenkel E. Bioinformatics. 2006 Feb 15;22(4):423-9.

[3]Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Xinmin Zhang, Duncan T Odom, Seung-Hoi Koo, Michael D Conkright, Gianluca Canettieri, Jennifer Best, Huaming Chen, Richard Jenner, Elizabeth Herbolsheimer, Elizabeth Jacobsen, Shilpa Kadam, Joseph R Ecker, Beverly Emerson, John B Hogenesch, Terry Unterman, Richard A Young, Marc Montminy. Proc. Natl. Acad. Sci. U.S.A. 2005 vol. 102 pp. 4459-64

[4] TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M,Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E. Nucleic Acids Res. 2006 Jan 1;34(Database issue)

[5]E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Bing Ren, Hieu Cam, Yasuhiko Takahashi, Thomas Volkert, Jolyon Terragni, Richard A Young, Brian David Dynlacht. Genes Dev. 2002 vol. 16 pp. 245-56

[6] Global and gene-specific analyses show distinct roles for Myod and Myog at a common set of promoters. Yi Cao, Roshan M Kumar, Bennett H Penn, Charlotte A Berkes, Charles Kooperberg, Laurie A Boyer, Richard A Young, Stephen J Tapscott. EMBO J. 2006 vol. 25 pp. 502-11.

[7] Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide. Proc. Natl. Acad. Sci. U.S.A.2006 vol. 103 pp. 5899-904.

[8] Control of pancreas and liver gene expression by HNF transcription factors. Duncan T Odom, Nora Zizlsperger, D Benjamin Gordon, George W Bell, Nicola J Rinaldi, Heather L Murray, Tom L Volkert, Jšrg Schreiber, P Alexander Rolfe, David K Gifford, Ernest Fraenkel, Graeme I Bell, Richard A Young. Science. 2004 vol. 303 pp. 1378-81.

[9] NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth.Palomero T, Lim WK, Odom DT, Sulis ML, Real PJ, Margolin A, Barnes KC, O'Neil J, Neuberg D, Weng AP,Aster JC, Sigaux F, Soulier J, Look AT, Young RA, Califano A, Ferrando AA.

[10] Transcriptional regulatory code of a eukaryotic genome. 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. Nature. 2004 Sep 2;431(7004):99-104.