W-ChIPeaks: A comprehensive web application tool for processing ChIP-chip and ChIP-seq data

Bioinformatics

Volumn 27, Issue 3, 2011, Pages 428-430

  Lan, Xun ^a   Bonneville, Russell ^a   Apostolos, Jeff ^a   Wu, Wangcheng ^b   Jin, Victor X ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; DNA MICROARRAY; HIGH THROUGHPUT SEQUENCING; INTERNET; METHODOLOGY;

HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTERNET; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE;

EID: 79551590211     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq669     Document Type: Article

References (12)

1. Bapat,S.A. et al. (2010) Multivalent epigenetic marks confer microenvironment-responsive epigenetic plasticity to ovarian cancer cells. Epigenetics, 5, 716-729.
2. Cotterman,R. et al. (2008) N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor. Cancer Res., 68, 9654-9662.
3. Farnham,P.J. (2009) Insights from genomic profiling of transcription factors. Nature Rev. Genet., 10, 605-616.
4. Frietze,S. et al. (2010) Genomic targets of the KRAN and SCAN domain-containing zinc figer protein ZNF263. J. Biol. Chem., 285, 1393-1403.
5. Ji et al. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol., 26,1293-1300.
6. Jin,V.X. et al. (2006) A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data-a case study using E2F1. Genome Res., 16, 1585-1595.
7. Johnson,D.S. et al. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502.
8. Johnson,D.S. et al. (2008) Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res., 18, 393-403.
9. Kim,T.H. et al. (2005)Ahigh-resolution map of active promoters in the human genome. Nature, 436, 876-880.
10. Loh,Y.-H. et al. (2006) The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nature Genetics, 38, 431-440.
11. Park,P.J. (2009) ChIP-seq: advantages and challenges of a maturing technology. Nature Rev. Genet., 10, 669-680.
12. Zhang,Y. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biology, 9, R137.