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CAGEd-oPOSSUM：基于CAGE衍生的转录起始位点的基序富集分析

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.

作者信息

Arenillas David J, Forrest Alistair R R, Kawaji Hideya, Lassmann Timo, Wasserman Wyeth W, Mathelier Anthony

机构信息

Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada.

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045 Japan.

出版信息

Bioinformatics. 2016 Sep 15;32(18):2858-60. doi: 10.1093/bioinformatics/btw337. Epub 2016 Jun 9.

DOI:10.1093/bioinformatics/btw337
PMID:27334471
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5018375/
Abstract

UNLABELLED

With the emergence of large-scale Cap Analysis of Gene Expression (CAGE) datasets from individual labs and the FANTOM consortium, one can now analyze the cis-regulatory regions associated with gene transcription at an unprecedented level of refinement. By coupling transcription factor binding site (TFBS) enrichment analysis with CAGE-derived genomic regions, CAGEd-oPOSSUM can identify TFs that act as key regulators of genes involved in specific mammalian cell and tissue types. The webtool allows for the analysis of CAGE-derived transcription start sites (TSSs) either provided by the user or selected from ∼1300 mammalian samples from the FANTOM5 project with pre-computed TFBS predicted with JASPAR TF binding profiles. The tool helps power insights into the regulation of genes through the study of the specific usage of TSSs within specific cell types and/or under specific conditions.

AVAILABILITY AND IMPLEMENTATION

The CAGEd-oPOSUM web tool is implemented in Perl, MySQL and Apache and is available at http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM CONTACTS: anthony.mathelier@ncmm.uio.no or wyeth@cmmt.ubc.ca

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

未标注

随着各个实验室和FANTOM联盟产生的大规模基因表达帽分析（CAGE）数据集的出现，现在人们能够以前所未有的精细程度分析与基因转录相关的顺式调控区域。通过将转录因子结合位点（TFBS）富集分析与CAGE衍生的基因组区域相结合，CAGEd - oPOSSUM可以识别在特定哺乳动物细胞和组织类型中作为基因关键调控因子的转录因子。该网络工具允许分析由用户提供的或从FANTOM5项目的约1300个哺乳动物样本中选择的CAGE衍生的转录起始位点（TSS），这些样本具有用JASPAR转录因子结合谱预先计算的TFBS。该工具通过研究特定细胞类型和/或特定条件下TSS的特定使用情况，有助于深入了解基因的调控。

可用性和实现方式

CAGEd - oPOSSUM网络工具用Perl、MySQL和Apache实现，可在http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM获取。

联系方式

anthony.mathelier@ncmm.uio.no或wyeth@cmmt.ubc.ca

补充信息

补充数据可在《生物信息学》在线获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/5018375/1c1154be85e8/btw337f1p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/5018375/1c1154be85e8/btw337f1p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/5018375/1c1154be85e8/btw337f1p.jpg

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