Literature DB >> 22495751

CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.

Bo Qin1, Meng Zhou, Ying Ge, Len Taing, Tao Liu, Qian Wang, Su Wang, Junsheng Chen, Lingling Shen, Xikun Duan, Sheng'en Hu, Wei Li, Henry Long, Yong Zhang, X Shirley Liu.   

Abstract

SUMMARY: Transcription and chromatin regulators, and histone modifications play essential roles in gene expression regulation. We have created CistromeMap as a web server to provide a comprehensive knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human. We have also manually curated metadata to ensure annotation consistency, and developed a user-friendly display matrix for quick navigation and retrieval of data for specific factors, cells and papers. Finally, we provide users with summary statistics of ChIP-Seq and DNase-Seq studies.

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Mesh:

Year:  2012        PMID: 22495751      PMCID: PMC3348563          DOI: 10.1093/bioinformatics/bts157

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  8 in total

1.  A comprehensive view of nuclear receptor cancer cistromes.

Authors:  Qianzi Tang; Yiwen Chen; Clifford Meyer; Tim Geistlinger; Mathieu Lupien; Qian Wang; Tao Liu; Yong Zhang; Myles Brown; Xiaole Shirley Liu
Journal:  Cancer Res       Date:  2011-09-22       Impact factor: 12.701

Review 2.  Chromatin modifications and their function.

Authors:  Tony Kouzarides
Journal:  Cell       Date:  2007-02-23       Impact factor: 41.582

3.  hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.

Authors:  Li Chen; George Wu; Hongkai Ji
Journal:  Bioinformatics       Date:  2011-03-30       Impact factor: 6.937

4.  NCBI GEO: archive for high-throughput functional genomic data.

Authors:  Tanya Barrett; Dennis B Troup; Stephen E Wilhite; Pierre Ledoux; Dmitry Rudnev; Carlos Evangelista; Irene F Kim; Alexandra Soboleva; Maxim Tomashevsky; Kimberly A Marshall; Katherine H Phillippy; Patti M Sherman; Rolf N Muertter; Ron Edgar
Journal:  Nucleic Acids Res       Date:  2008-10-21       Impact factor: 16.971

Review 5.  Mechanisms of transcription factor selectivity.

Authors:  Yongping Pan; Chung-Jung Tsai; Buyong Ma; Ruth Nussinov
Journal:  Trends Genet       Date:  2010-01-13       Impact factor: 11.639

6.  NCBI GEO: archive for functional genomics data sets--10 years on.

Authors:  Tanya Barrett; Dennis B Troup; Stephen E Wilhite; Pierre Ledoux; Carlos Evangelista; Irene F Kim; Maxim Tomashevsky; Kimberly A Marshall; Katherine H Phillippy; Patti M Sherman; Rolf N Muertter; Michelle Holko; Oluwabukunmi Ayanbule; Andrey Yefanov; Alexandra Soboleva
Journal:  Nucleic Acids Res       Date:  2010-11-21       Impact factor: 16.971

7.  NCBI Epigenomics: a new public resource for exploring epigenomic data sets.

Authors:  Ian M Fingerman; Lee McDaniel; Xuan Zhang; Walter Ratzat; Tarek Hassan; Zhifang Jiang; Robert F Cohen; Gregory D Schuler
Journal:  Nucleic Acids Res       Date:  2010-11-12       Impact factor: 16.971

8.  Nuclear Receptor Signaling Atlas (www.nursa.org): hyperlinking the nuclear receptor signaling community.

Authors:  Rainer B Lanz; Zeljko Jericevic; William J Zuercher; Chris Watkins; David L Steffen; Ronald Margolis; Neil J McKenna
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

  8 in total
  24 in total

1.  RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets.

Authors:  Zhengyu Guo; Boriana Tzvetkova; Jennifer M Bassik; Tara Bodziak; Brianna M Wojnar; Wei Qiao; Md A Obaida; Sacha B Nelson; Bo Hua Hu; Peng Yu
Journal:  Bioinformatics       Date:  2015-08-30       Impact factor: 6.937

2.  Changes in Gene Expression and Estrogen Receptor Cistrome in Mouse Liver Upon Acute E2 Treatment.

Authors:  Gaëlle Palierne; Aurélie Fabre; Romain Solinhac; Christine Le Péron; Stéphane Avner; Françoise Lenfant; Coralie Fontaine; Gilles Salbert; Gilles Flouriot; Jean-François Arnal; Raphaël Métivier
Journal:  Mol Endocrinol       Date:  2016-05-10

3.  CistromeFinder for ChIP-seq and DNase-seq data reuse.

Authors:  Hanfei Sun; Bo Qin; Tao Liu; Qixuan Wang; Jing Liu; Juan Wang; Xueqiu Lin; Yulin Yang; Len Taing; Prakash K Rao; Myles Brown; Yong Zhang; Henry W Long; X Shirley Liu
Journal:  Bioinformatics       Date:  2013-03-18       Impact factor: 6.937

Review 4.  Nuclear receptors in cancer - uncovering new and evolving roles through genomic analysis.

Authors:  Vineet K Dhiman; Michael J Bolt; Kevin P White
Journal:  Nat Rev Genet       Date:  2017-12-27       Impact factor: 53.242

5.  EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types.

Authors:  Tianshun Gao; Bing He; Sheng Liu; Heng Zhu; Kai Tan; Jiang Qian
Journal:  Bioinformatics       Date:  2016-08-10       Impact factor: 6.937

Review 6.  Cistrome plasticity and mechanisms of cistrome reprogramming.

Authors:  Ivan Garcia-Bassets; Dong Wang
Journal:  Cell Cycle       Date:  2012-08-16       Impact factor: 4.534

Review 7.  Transcription factor-DNA binding: beyond binding site motifs.

Authors:  Sachi Inukai; Kian Hong Kock; Martha L Bulyk
Journal:  Curr Opin Genet Dev       Date:  2017-03-27       Impact factor: 5.578

8.  Integrative Analysis Reveals the Transcriptional Collaboration between EZH2 and E2F1 in the Regulation of Cancer-Related Gene Expression.

Authors:  Han Xu; Kexin Xu; Housheng H He; Chongzhi Zang; Chen-Hao Chen; Yiwen Chen; Qian Qin; Su Wang; Chenfei Wang; Shengen Hu; Fugen Li; Henry Long; Myles Brown; X Shirley Liu
Journal:  Mol Cancer Res       Date:  2015-12-09       Impact factor: 5.852

9.  Identifying gene regulatory network rewiring using latent differential graphical models.

Authors:  Dechao Tian; Quanquan Gu; Jian Ma
Journal:  Nucleic Acids Res       Date:  2016-07-04       Impact factor: 16.971

10.  Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data.

Authors:  Pedro Madrigal; Paweł Krajewski
Journal:  Front Genet       Date:  2012-10-31       Impact factor: 4.599

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