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PMID: 24263090 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Target analysis by integration of transcriptome and ChIP-seq data with BETA.

Nature protocols ·Vol. 8 ·No. 12 ·2013-12-00 ·Pages 2502-15

Wang S, Sun H, Ma J, Zang C, Wang C, Wang J, Tang Q, Meyer CA, Zhang Y, Liu XS

Abstract

The combination of ChIP-seq and transcriptome analysis is a compelling approach to unravel the regulation of gene expression. Several recently published methods combine transcription factor (TF) binding and gene expression for target prediction, but few of them provide an efficient software package for the community. Binding and expression target analysis (BETA) is a software package that integrates ChIP-seq of TFs or chromatin regulators with differential gene expression data to infer direct target genes. BETA has three functions: (i) to predict whether the factor has activating or repressive function; (ii) to infer the factor's target genes; and (iii) to identify the motif of the factor and its collaborators, which might modulate the factor's activating or repressive function. Here we describe the implementation and features of BETA to demonstrate its application to several data sets. BETA requires ~1 GB of RAM, and the procedure takes 20 min to complete. BETA is available open source at http://cistrome.org/BETA/.

MeSH Terms
Chromatin Immunoprecipitation/methods Gene Expression Profiling/methods Software Transcriptome
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Wang Su
Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China.
Sun Hanfei
Ma Jian
Zang Chongzhi
Wang Chenfei
Wang Juan
Tang Qianzi
Meyer Clifford A
Zhang Yong
Liu X Shirley
References (40)
40 references, click to expand
  1. Computational analysis of protein-DNA interactions from ChIP-seq data.
    Methods Mol Biol. 2012;786:263-73 PMID: 21938632
  2. ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor.
    Nucleic Acids Res. 2011 Jul;39(Web Server issue):W430-6 PMID: 21586587
  3. Genome-wide analysis of estrogen receptor binding sites.
    Nat Genet. 2006 Nov;38(11):1289-97 PMID: 17013392
  4. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.
    Nucleic Acids Res. 2007 Jul;35(Web Server issue):W169-75 PMID: 17576678
  5. A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth.
    Mol Cell. 2007 Aug 3;27(3):380-92 PMID: 17679089
  6. The human genome browser at UCSC.
    Genome Res. 2002 Jun;12(6):996-1006 PMID: 12045153
  7. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.
    Bioinformatics. 2009 Aug 1;25(15):1952-8 PMID: 19505939
  8. A chromatin-mediated mechanism for specification of conditional transcription factor targets.
    Nat Genet. 2006 Dec;38(12):1446-51 PMID: 17099712
  9. Androgen receptor-associated protein complex binds upstream of the androgen-responsive elements in the promoters of human prostate-specific antigen and kallikrein 2 genes.
    Nucleic Acids Res. 1997 Aug 15;25(16):3318-25 PMID: 9241247
  10. Model-based analysis of tiling-arrays for ChIP-chip.
    Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12457-62 PMID: 16895995
  11. A comprehensive view of nuclear receptor cancer cistromes.
    Cancer Res. 2011 Nov 15;71(22):6940-7 PMID: 21940749
  12. TFCat: the curated catalog of mouse and human transcription factors.
    Genome Biol. 2009;10(3):R29 PMID: 19284633
  13. TRED: a transcriptional regulatory element database, new entries and other development.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D137-40 PMID: 17202159
  14. Cistrome: an integrative platform for transcriptional regulation studies.
    Genome Biol. 2011 Aug 22;12(8):R83 PMID: 21859476
  15. CCCTC-binding factor confines the distal action of estrogen receptor.
    Cancer Res. 2008 Nov 1;68(21):9041-9 PMID: 18974150
  16. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
    Genome Biol. 2009;10(3):R25 PMID: 19261174
  17. Discovering transcription factor regulatory targets using gene expression and binding data.
    Bioinformatics. 2012 Jan 15;28(2):206-13 PMID: 22084256
  18. Reactivation of androgen receptor-regulated TMPRSS2:ERG gene expression in castration-resistant prostate cancer.
    Cancer Res. 2009 Aug 1;69(15):6027-32 PMID: 19584279
  19. Model-based method for transcription factor target identification with limited data.
    Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7793-8 PMID: 20385836
  20. The UCSC Genome Browser database: update 2011.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82 PMID: 20959295
  21. Identifying ChIP-seq enrichment using MACS.
    Nat Protoc. 2012 Sep;7(9):1728-40 PMID: 22936215
  22. Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.
    Bioinformatics. 2003 Oct 12;19(15):1917-26 PMID: 14555624
  23. The analysis of ChIP-Seq data.
    Methods Enzymol. 2011;497:51-73 PMID: 21601082
  24. Core transcriptional regulatory circuitry in human embryonic stem cells.
    Cell. 2005 Sep 23;122(6):947-56 PMID: 16153702
  25. MOODS: fast search for position weight matrix matches in DNA sequences.
    Bioinformatics. 2009 Dec 1;25(23):3181-2 PMID: 19773334
  26. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data.
    Nucleic Acids Res. 2005 Nov 10;33(20):e175 PMID: 16284200
  27. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
    Nat Protoc. 2012 Mar 01;7(3):562-78 PMID: 22383036
  28. A bioinformatics-based functional analysis shows that the specifically androgen-regulated gene SARG contains an active direct repeat androgen response element in the first intron.
    J Mol Endocrinol. 2004 Oct;33(2):477-91 PMID: 15525603
  29. Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana.
    BMC Bioinformatics. 2007 Nov 18;8:454 PMID: 18021423
  30. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
    Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50 PMID: 16199517
  31. DAVID gene ID conversion tool.
    Bioinformation. 2008 Jul 30;2(10):428-30 PMID: 18841237
  32. Model-based analysis of ChIP-Seq (MACS).
    Genome Biol. 2008;9(9):R137 PMID: 18798982
  33. A novel Bayesian DNA motif comparison method for clustering and retrieval.
    PLoS Comput Biol. 2008 Feb 29;4(2):e1000010 PMID: 18463706
  34. GREAT improves functional interpretation of cis-regulatory regions.
    Nat Biotechnol. 2010 May;28(5):495-501 PMID: 20436461
  35. TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles.
    Bioinformatics. 2011 Dec 1;27(23):3221-7 PMID: 22039215
  36. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity.
    Nature. 2011 May 19;473(7347):343-8 PMID: 21490601
  37. On the detection and refinement of transcription factor binding sites using ChIP-Seq data.
    Nucleic Acids Res. 2010 Apr;38(7):2154-67 PMID: 20056654
  38. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
    Brief Bioinform. 2013 Mar;14(2):178-92 PMID: 22517427
  39. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments.
    FEBS Lett. 2004 Aug 27;573(1-3):83-92 PMID: 15327980
  40. Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages.
    EMBO J. 2011 Feb 2;30(3):494-509 PMID: 21179004
Article Info
Journal
Nature protocols
Abbr.
Nat Protoc
ISSN
1750-2799
DOI
10.1038/nprot.2013.150
Published
2013-12-00
Epub
2013-00-21
Pages
2502-15
Language
English
Region
England
NLM ID
101284307
PMCID
PMC4135175
Subset
IM
Grants
NHGRI NIH HHS · R01 HG004069 · United States
NHGRI NIH HHS · U41 HG007000 · United States
NHGRI NIH HHS · HG4069 · United States
External Links
PubMed source DOI: 10.1038/nprot.2013.150 PMC Full Text View journal details
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