Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data

BMC Bioinformatics

Volumn 16, Issue 1, 2015, Pages

  Dabrowski, Michal ^a   Dojer, Norbert ^b   Krystkowiak, Izabella ^a   Kaminska, Bozena ^a   Wilczynski, Bartek ^b  

^a NENCKI INSTITUTE OF EXPERIMENTAL BIOLOGY   (Poland)

^b UNIVERSITY OF WARSAW   (Poland)

Author keywords

Binding site; Motif database; Sequence motif; Transcription factor binding

Indexed keywords

DATABASE SYSTEMS; GENES; TRANSCRIPTION; TRANSCRIPTION FACTORS;

COMPREHENSIVE ANALYSIS; COMPREHENSIVE COMPARISONS; INFORMATION CONTENTS; POTENTIAL BINDING SITES; SCIENTIFIC COMMUNITY; SEQUENCE MOTIFS; TRANSCRIPTION FACTOR BINDING; TRANSCRIPTION FACTOR BINDING SITES;

BINDING SITES;

PROTEIN BINDING; TRANSCRIPTION FACTOR;

BINDING SITE; BIOLOGY; CHROMATIN IMMUNOPRECIPITATION; DNA SEQUENCE; FACTUAL DATABASE; GENETICS; HUMAN; HUMAN GENOME; METABOLISM; NUCLEOTIDE MOTIF; POSITION WEIGHT MATRIX; PROCEDURES;

BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; GENOME, HUMAN; HUMANS; NUCLEOTIDE MOTIFS; POSITION-SPECIFIC SCORING MATRICES; PROTEIN BINDING; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS;

EID: 84938956077     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0573-5     Document Type: Article

References (30)

1. Schneider TD, Stormo GD, Gold L, Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J Mol Biol. 1986; 188(3):415-31.
2. Xing EP, Jordan MI, Karp RM, Russell S. A hierarchical bayesian markovian model for motifs in biopolymer sequences In: Becker S, Thrun S, Obermayer K, editors. Advances in Neural Information Processing Systems 15. Vancouver Canada: MIT Press: 2003. p. 1513-20.
3. Zhao Y, Ruan S, Pandey M, Stormo GD. Improved models for transcription factor binding site identification using nonindependent interactions. Genetics. 2012; 191(3):781-90. Accessed 2015-03-10.
4. Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gordân R, et al. TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res. 2014; 42(Database issue):148-55. Accessed 2015-03-10.
5. Zhao Y, Stormo GD. Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat Biotech. 2011; 29(6):480-3.
6. Hertz GZ, Stormo GD. Identifying dna and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics. 1999; 15(7):563-77.
7. Rahmann S, Muller T, Vingron M. On the power of profiles for transcription factor binding site detection. Stat Appl Genet Mol Biol. 2003; 2(1):1032.
8. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, et al. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature. 2005; 434(7031):338-45.
9. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, et al.Transfac and its module transcompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 2006; 34(Database issue):108-10.
10. Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell. 2008; 133(7):1266-76.
11. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, et al.Diversity and complexity in DNA recognition by transcription factors. Science. 2009; 324(5935):1720-23.
12. Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, et al. Jaspar 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 2010; 38(Database issue):105-10.
13. Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, et al. Dna-binding specificities of human transcription factors. Cell. 2013; 152(1-2):327-39.
14. Kulakovskiy IV, Medvedeva YA, Schaefer U, Kasianov AS, Vorontsov IE, Bajic VB, et al. Hocomoco: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res. 2013; 41(Database issue):195-202.
15. Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E. Swissregulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Res. 2013; 41(Database issue):214-20.
16. Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014; 42(Database issue):142-7.
17. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012; 489(7414):57-74.
18. Kel AE, Gössling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E, MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 2003; 31(13):3576-579.
19. Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, et al.MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics. 2005; 21(13):2933-42.
20. Turatsinze JV, Thomas-Chollier M, Defrance M, van Helden J. Using rsat to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc. 2008; 3(10):1578-88.
21. Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, et al. Biopython: freely available python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009; 25(11):1422-3.
22. Wilczynski B, Dojer N, Patelak M, Tiuryn J. Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs. BMC Bioinformatics. 2009; 10:82.
23. Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, et al.Matinspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics. 2005; 21(13):2933-42.
24. Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from dna sequence and chromatin accessibility data. Genome Res. 2011; 21(3):447-55.
25. Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, et al. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early drosophila development. PLoS Genet. 2011; 7(2):1001290.
26. Mudunuri U, Che A, Yi M, Stephens RM. bioDBnet: the biological database network. Bioinformatics. 2009; 25(4):555-6.
27. Krystkowiak I, Lenart J, Debski K, Kuterba P, Petas M, Kaminska B, et al. Nencki genomics database-ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs. Database (Oxford). 2013; 2013:069.
28. Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, et al. Ensembl 2013. Nucleic Acids Res. 2013; 41(Database issue):48-55.
29. Worsley Hunt R, Mathelier A, del Peso L, Wasserman W. Improving analysis of transcription factor binding sites within chip-seq data based on topological motif enrichment. BMC Genomics. 2014; 15(1):472.
30. Quandt K, Frech K, Karas H, Wingender E, Werner T. MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res. 1995; 23(23):4878-884.