SIOMICS: A novel approach for systematic identification of motifs in ChIP-seq data

Nucleic Acids Research

Volumn 42, Issue 5, 2014, Pages

  Ding, Jun ^a   Hu, Haiyan ^a   Li, Xiaoman ^b  

^a UNIVERSITY OF CENTRAL FLORIDA   (United States)

^b UNIVERSITY OF CENTRAL FLORIDA COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

KRUPPEL LIKE FACTOR 4; MYC PROTEIN; OCTAMER TRANSCRIPTION FACTOR 4; PEPTIDES AND PROTEINS; PROTEIN ESRRB; PROTEIN TCFCP2L1; PROTEIN ZFX; SMAD1 PROTEIN; STAT3 PROTEIN; TRANSCRIPTION FACTOR CTCF; TRANSCRIPTION FACTOR E2F1; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; COMPARATIVE STUDY; COMPUTER PROGRAM; DNA BINDING MOTIF; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY;

BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; NUCLEOTIDE MOTIFS; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS;

EID: 84898988373     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1288     Document Type: Article

References (40)

1. Birney, E., Stamatoyannopoulos, J.A., Dutta, A., Guigo, R., Gingeras, T.R., Margulies, E.H., Weng, Z., Snyder, M., Dermitzakis, E.T., Thurman, R.E. et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799-816. (Pubitemid 46920138
2. Blanchette, M., Bataille, A.R., Chen, X., Poitras, C., Laganiere, J., Lefebvre, C., Deblois, G., Giguere, V., Ferretti, V., Bergeron, D. et al. (2006) Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res., 16, 656-668.
3. Cai, X., Hou, L., Su, N., Hu, H., Deng, M. and Li, X. (2010) Systematic identification of conserved motif modules in the human genome. BMC Genomics, 11, 567.
4. Wingender, E., Dietze, P., Karas, H. and Knuppel, R. (1996) TRANSFAC: A database on transcription factors and their DNA binding sites. Nucleic Acids Res., 24, 238-241. (Pubitemid 26085775
5. Stormo, G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23. (Pubitemid 30204197
6. Arnone, M.I. and Davidson, E.H. (1997) The hardwiring of development: Organization and function of genomic regulatory systems. Development, 124, 1851-1864. (Pubitemid 27270255
7. Ding, J., Hu, H. and Li, X. (2012) Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar. Plant Physiol., 158, 145-155.
8. Ding, J., Li, X. and Hu, H. (2012) Systematic prediction of cisregulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics. Plant Physiol., 160, 613-623.
9. Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A. et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods, 4, 651-657.
10. Ji, H., Jiang, H., Ma, W., Johnson, D.S., Myers, R.M. and Wong, W.H. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol., 26, 1293-1300.
11. Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W. et al. (2008) Model-based analysis of ChIP-Seq (MACS) Genome Boil., 9, R137.
12. Jothi, R., Cuddapah, S., Barski, A., Cui, K. and Zhao, K. (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res., 36, 5221-5231.
13. 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.
14. Bailey, T.L. (2011) DREME: Motif discovery in transcription factor ChIP-seq data. Bioinformatics, 27, 1653-1659.
15. Ding, J., Cai, X., Wang, Y., Hu, H. and Li, X. (2013) Chipmodule: Systematic discovery of transcription factors and their cofactors from chip-seq data. Pac. Symp. Biocomput., 18, 320-331.
16. Sun, H., Guns, T., Fierro, A.C., Thorrez, L., Nijssen, S. and Marchal, K. (2012) Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection. Nucleic Acids Res., 40, e90.
17. Hu, M., Yu, J., Taylor, J.M., Chinnaiyan, A.M. and Qin, Z.S. (2010) On the detection and refinement of transcription factor binding sites using ChIP-Seq data. Nucleic Acids Res., 38, 2154-2167.
18. Thomas-Chollier, M., Herrmann, C., Defrance, M., Sand, O., Thieffry, D. and van Helden, J. (2012) RSAT peak-motifs: Motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res., 40, e31.
19. Kulakovskiy, I.V., Boeva, V.A., Favorov, A.V. and Makeev, V.J. (2010) Deep and wide digging for binding motifs in ChIP-Seq data. Bioinformatics, 26, 2622-2623.
20. Stamatoyannopoulos, J.A. (2012) What does our genome encode? Genome Res., 22, 1602-1611.
21. Chen, X., Xu, H., Yuan, P., Fang, F., Huss, M., Vega, V.B., Wong, E., Orlov, Y.L., Zhang, W., Jiang, J. et al. (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell, 133, 1106-1117. (Pubitemid 351787745
22. Edgar, R., Domrachev, M. and Lash, A.E. (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210. (Pubitemid 34679544
23. Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M. and Haussler, D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006. (Pubitemid 34662293
24. Liu, X.S., Brutlag, D.L. and Liu, J.S. (2002) An algorithm for finding protein-DNA binding sites with applications to chromatinimmunoprecipitation microarray experiments. Nat. Biotechnol., 20, 835-839.
25. Li, X. and Wong, W.H. (2005) Sampling motifs on phylogenetic trees. Proc. Natl Acad. Sci. USA, 102, 9481-9486.
26. Li, X., Zhong, S. and Wong, W.H. (2005) Reliable prediction of transcription factor binding sites by phylogenetic verification. Proc. Natl Acad. Sci. USA, 102, 16945-16950.
27. Aldous, D. (1989) Probability Approximations via the Poisson Clumping Heuristic. Springer-Verlag, New York.
28. Hu, J., Hu, H. and Li, X. (2008) MOPAT: A graph-based method to predict recurrent cis-regulatory modules from known motifs. Nucleic Acids Res., 36, 4488-4497.
29. Chatr-Aryamontri, A., Breitkreutz, B.J., Heinicke, S., Boucher, L., Winter, A., Stark, C., Nixon, J., Ramage, L., Kolas, N., O'Donnell, L. et al. (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res., 41, D816-D823.
30. Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W.W. and Lenhard, B. (2004) JASPAR: An open-Access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res., 32, D91-D94. (Pubitemid 38081611
31. Mahony, S. and Benos, P.V. (2007) STAMP: A web tool for exploring DNA-binding motif similarities. Nucleic Acids Res., 35, W253-W258.
32. Amr, A.G., Mohamed, A.M., Mohamed, S.F., Abdel-Hafez, N.A. and Hammam Ael, F. (2006) Anticancer activities of some newly synthesized pyridine, pyrane, and pyrimidine derivatives. Bioorg. Med. Chem., 14, 5481-5488.
33. Fogel, B.L., Wexler, E., Wahnich, A., Friedrich, T., Vijayendran, C., Gao, F., Parikshak, N., Konopka, G. and Geschwind, D.H. (2012) RBFOX1 regulates both splicing and transcriptional networks in human neuronal development. Hum. Mol. Genet., 21, 4171-4186.
34. Pardo, M., Lang, B., Yu, L., Prosser, H., Bradley, A., Babu, M.M. and Choudhary, J. (2010) An expanded Oct4 interaction network: Implications for stem cell biology, development, and disease. Cell Stem Cell, 6, 382-395.
35. Foshay, K.M. and Gallicano, G.I. (2008) Regulation of Sox2 by STAT3 initiates commitment to the neural precursor cell fate. StemCells Dev., 17, 269-278. (Pubitemid 351630169
36. Donohoe, M.E., Silva, S.S., Pinter, S.F., Xu, N. and Lee, J.T. (2009) The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting. Nature, 460, 128-132.
37. Nakashima, K. (1999) Synergistic Signaling in Fetal Brain by STAT3-Smad1 Complex Bridged by p300. Science, 284, 479-482. (Pubitemid 29289619
38. Que, J., Okubo, T., Goldenring, J.R., Nam, K.T., Kurotani, R., Morrisey, E.E., Taranova, O., Pevny, L.H. and Hogan, B.L. (2007) Multiple dose-dependent roles for Sox2 in the patterning and differentiation of anterior foregut endoderm. Development, 134, 2521-2531. (Pubitemid 47074146
39. Zhou, Q. and Wong, W.H. (2004) CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proc. Natl Acad.Sci. USA, 101, 12114-12119.
40. Zhang, W., Geiman, D.E., Shields, J.M., Dang, D.T., Mahatan, C.S., Kaestner, K.H., Biggs, J.R., Kraft, A.S. and Yang, V.W. (2000) The gut-enriched Kruppel-like factor (Kruppel-like factor 4) mediates the transactivating effect of p53 on the p21WAF1/Cip1 promoter. J. Biol. Chem., 275, 18391-18398.