Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

被引:0
|
作者
Victor G Levitsky
Ivan V Kulakovskiy
Nikita I Ershov
Dmitry Yu Oshchepkov
Vsevolod J Makeev
T C Hodgman
Tatyana I Merkulova
机构
[1] Institute of Cytology and Genetics of the Siberian Division of Russian Academy of Sciences,Engelhardt Institute of Molecular Biology
[2] Novosibirsk State University,Department of Computational Systems Biology, Vavilov Institute of General Genetics
[3] Russian Academy of Sciences,Multidisciplinary Centre for Integrative Biology, School of Biosciences
[4] Russian Academy of Sciences,undefined
[5] University of Nottingham,undefined
来源
BMC Genomics | / 15卷
关键词
ChIP-Seq; EMSA; Transcription factor binding sites; FoxA; SiteGA; PWM; Transcription factor binding model; Dinucleotide frequencies;
D O I
暂无
中图分类号
学科分类号
摘要
引用
收藏
相关论文
共 50 条
  • [41] NUCLEOSOME DISTRIBUTION AROUND TRANSCRIPTION FACTOR BINDING SITES ENRICHED FROM GENOME-WIDE CHIP-SEQ
    Wang Wei
    Lu Zuhong
    IFPT'6: PROGRESS ON POST-GENOME TECHNOLOGIES, PROCEEDINGS, 2009, : 392 - 395
  • [42] A ChIP-Seq Benchmark Shows That Sequence Conservation Mainly Improves Detection of Strong Transcription Factor Binding Sites
    Handstad, Tony
    Rye, Morten Beck
    Drablos, Finn
    Saetrom, Pal
    PLOS ONE, 2011, 6 (04):
  • [43] Detecting differential binding of transcription factors with ChIP-seq
    Liang, Kun
    Keles, Sunduz
    BIOINFORMATICS, 2012, 28 (01) : 121 - 122
  • [44] MotifGenie: a Python']Python application for searching transcription factor binding sequences using ChIP-Seq datasets
    Oguztuzun, Cerag
    Yasar, Pelin
    Yavuz, Kerim
    Muyan, Mesut
    Can, Tolga
    BIOINFORMATICS, 2021, 37 (22) : 4238 - 4239
  • [45] Studying the evolution of transcription factor binding events using multi-species ChIP-Seq data
    Zheng, Wei
    Zhao, Hongyu
    STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY, 2013, 12 (01) : 1 - 15
  • [46] CISMAPPER: predicting regulatory interactions from transcription factor ChIP-seq data
    O'Connor, Timothy
    Boden, Mikael
    Bailey, Timothy L.
    NUCLEIC ACIDS RESEARCH, 2017, 45 (04) : e19
  • [47] A short survey of computational analysis methods in analysing ChIP-seq data
    Kim H.
    Kim J.
    Selby H.
    Gao D.
    Tong T.
    Phang T.L.
    Tan A.C.
    Human Genomics, 5 (2) : 117 - 123
  • [48] Genome-Wide Analysis of MAMSTR Transcription Factor-Binding Sites via ChIP-Seq in Porcine Skeletal Muscle Fibroblasts
    Li, Chenlei
    Zhang, Zhe
    Wei, Yilin
    Qi, Kunlong
    Dou, Yaqing
    Song, Chenglei
    Liu, Yingke
    Li, Xinjian
    Li, Xiuling
    Wang, Kejun
    Qiao, Ruimin
    Yang, Feng
    Han, Xuelei
    ANIMALS, 2023, 13 (11):
  • [49] Python in ChIP-Seq data analysis
    Zhang, Li
    Hu, Yuansen
    Wang, Jinshui
    Zhang, Guangle
    Journal of Chemical and Pharmaceutical Research, 2014, 6 (03) : 1002 - 1007
  • [50] TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets
    Puente-Santamaria, Laura
    Wasserman, Wyeth W.
    del Peso, Luis
    BIOINFORMATICS, 2019, 35 (24) : 5339 - 5340