Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-seq data

PLoS Computational Biology

Volumn 7, Issue 7, 2011, Pages

  Chung, Dongjun ^a,b   Kuan, Pei Fen ^c   Li, Bo ^a   Sanalkumar, Rajendran ^d   Liang, Kun ^a,b   Bresnick, Emery H ^d   Dewey, Colin ^a,b   Keleş, Sündüz ^a,b  

^a University of Wisconsin Madison   (United States)

^b UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^c IL   (United States)

^d University of Wisconsin Health   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION; TRANSCRIPTION FACTORS;

ARRAY ANALYSIS; CHIP-CHIP; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN MODIFICATION; COMPUTATIONAL EXPERIMENT; HIGH-THROUGHPUT SEQUENCING; SEGMENTAL DUPLICATIONS; STATE OF THE ART; TILING ARRAY; TRANSCRIPTION FACTOR BINDING SITES;

BINDING SITES;

STAT1 PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GATA 1; GATA1 PROTEIN, MOUSE; STAT1 PROTEIN, HUMAN;

ARTICLE; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; GATA1 GENE; GENE; GENE IDENTIFICATION; GENE LOCUS; GENE TARGETING; GENETIC ASSOCIATION; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; MOLECULAR DYNAMICS; QUANTITATIVE ANALYSIS; SEGMENTAL DUPLICATION; SEQUENCE ANALYSIS; UPREGULATION; VALIDATION PROCESS; ANIMAL; CHROMOSOME MAP; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; GENOME; GENOMICS; HELA CELL; HIGH THROUGHPUT SCREENING; HUMAN; METABOLISM; METHODOLOGY; MOUSE; NUCLEOTIDE REPEAT; REPRODUCIBILITY;

ANIMALS; BASE COMPOSITION; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME MAPPING; GATA1 TRANSCRIPTION FACTOR; GENOME; GENOMICS; HELA CELLS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MICE; REPETITIVE SEQUENCES, NUCLEIC ACID; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; STAT1 TRANSCRIPTION FACTOR; TRANSCRIPTION FACTORS;

EID: 79960941563     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002111     Document Type: Article

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