A short survey of computational analysis methods in analysing ChIP-seq data

Hyunmin Kim, Jihye Kim, Heather Selby, Dexiang Gao, Tiejun Tong, Tzu Lip Phang, Aik-Choon Tan

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Chromatin immunoprecipitation followed by massively parallel next-generation sequencing (ChIP-seq) is a valuable experimental strategy for assaying protein-DNA interaction over the whole genome. Many computational tools have been designed to find the peaks of the signals corresponding to protein binding sites. In this paper, three computational methods, ChIP-seq processing pipeline (spp), PeakSeq and CisGenome, used in ChIP-seq data analysis are reviewed. There is also a comparison of how they agree and disagree on finding peaks using the publically available Signal Transducers and Activators of Transcription protein 1 (STAT1) and RNA polymerase II (PolII) datasets with corresponding negative controls.

Original languageEnglish
Pages (from-to)117-123
Number of pages7
JournalHuman Genomics
Volume5
Issue number2
DOIs
Publication statusPublished - 2011 Jan 1
Externally publishedYes

Fingerprint

STAT Transcription Factors
STAT1 Transcription Factor
RNA Polymerase II
Chromatin Immunoprecipitation
Transcription Factor AP-1
Protein Binding
Binding Sites
Genome
DNA
Proteins
Datasets
Surveys and Questionnaires

Keywords

  • Bioinformatics
  • CHIP-Seq analysis
  • Comparative analysis
  • Next-generation sequencing

ASJC Scopus subject areas

  • Drug Discovery
  • Genetics
  • Molecular Biology
  • Molecular Medicine

Cite this

Kim, H., Kim, J., Selby, H., Gao, D., Tong, T., Phang, T. L., & Tan, A-C. (2011). A short survey of computational analysis methods in analysing ChIP-seq data. Human Genomics, 5(2), 117-123. https://doi.org/10.1186/1479-7364-5-2-117

A short survey of computational analysis methods in analysing ChIP-seq data. / Kim, Hyunmin; Kim, Jihye; Selby, Heather; Gao, Dexiang; Tong, Tiejun; Phang, Tzu Lip; Tan, Aik-Choon.

In: Human Genomics, Vol. 5, No. 2, 01.01.2011, p. 117-123.

Research output: Contribution to journalArticle

Kim, H, Kim, J, Selby, H, Gao, D, Tong, T, Phang, TL & Tan, A-C 2011, 'A short survey of computational analysis methods in analysing ChIP-seq data', Human Genomics, vol. 5, no. 2, pp. 117-123. https://doi.org/10.1186/1479-7364-5-2-117
Kim, Hyunmin ; Kim, Jihye ; Selby, Heather ; Gao, Dexiang ; Tong, Tiejun ; Phang, Tzu Lip ; Tan, Aik-Choon. / A short survey of computational analysis methods in analysing ChIP-seq data. In: Human Genomics. 2011 ; Vol. 5, No. 2. pp. 117-123.
@article{aa4e2dc415334ae482b2c8a36ddc6ca2,
title = "A short survey of computational analysis methods in analysing ChIP-seq data",
abstract = "Chromatin immunoprecipitation followed by massively parallel next-generation sequencing (ChIP-seq) is a valuable experimental strategy for assaying protein-DNA interaction over the whole genome. Many computational tools have been designed to find the peaks of the signals corresponding to protein binding sites. In this paper, three computational methods, ChIP-seq processing pipeline (spp), PeakSeq and CisGenome, used in ChIP-seq data analysis are reviewed. There is also a comparison of how they agree and disagree on finding peaks using the publically available Signal Transducers and Activators of Transcription protein 1 (STAT1) and RNA polymerase II (PolII) datasets with corresponding negative controls.",
keywords = "Bioinformatics, CHIP-Seq analysis, Comparative analysis, Next-generation sequencing",
author = "Hyunmin Kim and Jihye Kim and Heather Selby and Dexiang Gao and Tiejun Tong and Phang, {Tzu Lip} and Aik-Choon Tan",
year = "2011",
month = "1",
day = "1",
doi = "10.1186/1479-7364-5-2-117",
language = "English",
volume = "5",
pages = "117--123",
journal = "Human Genomics",
issn = "1473-9542",
publisher = "Henry Stewart Publications",
number = "2",

}

TY - JOUR

T1 - A short survey of computational analysis methods in analysing ChIP-seq data

AU - Kim, Hyunmin

AU - Kim, Jihye

AU - Selby, Heather

AU - Gao, Dexiang

AU - Tong, Tiejun

AU - Phang, Tzu Lip

AU - Tan, Aik-Choon

PY - 2011/1/1

Y1 - 2011/1/1

N2 - Chromatin immunoprecipitation followed by massively parallel next-generation sequencing (ChIP-seq) is a valuable experimental strategy for assaying protein-DNA interaction over the whole genome. Many computational tools have been designed to find the peaks of the signals corresponding to protein binding sites. In this paper, three computational methods, ChIP-seq processing pipeline (spp), PeakSeq and CisGenome, used in ChIP-seq data analysis are reviewed. There is also a comparison of how they agree and disagree on finding peaks using the publically available Signal Transducers and Activators of Transcription protein 1 (STAT1) and RNA polymerase II (PolII) datasets with corresponding negative controls.

AB - Chromatin immunoprecipitation followed by massively parallel next-generation sequencing (ChIP-seq) is a valuable experimental strategy for assaying protein-DNA interaction over the whole genome. Many computational tools have been designed to find the peaks of the signals corresponding to protein binding sites. In this paper, three computational methods, ChIP-seq processing pipeline (spp), PeakSeq and CisGenome, used in ChIP-seq data analysis are reviewed. There is also a comparison of how they agree and disagree on finding peaks using the publically available Signal Transducers and Activators of Transcription protein 1 (STAT1) and RNA polymerase II (PolII) datasets with corresponding negative controls.

KW - Bioinformatics

KW - CHIP-Seq analysis

KW - Comparative analysis

KW - Next-generation sequencing

UR - http://www.scopus.com/inward/record.url?scp=79955838994&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79955838994&partnerID=8YFLogxK

U2 - 10.1186/1479-7364-5-2-117

DO - 10.1186/1479-7364-5-2-117

M3 - Article

VL - 5

SP - 117

EP - 123

JO - Human Genomics

JF - Human Genomics

SN - 1473-9542

IS - 2

ER -