TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data
High-throughput genomic technologies like lncRNA microarray and RNA-Seq often generate a set of lncRNAs of interest, yet little is known about the transcriptional regulation of the set of lncRNA genes. Here, based on ChIP-Seq peak lists of transcription factors (TFs) from ENCODE and annotated human...
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Online Access: | http://dx.doi.org/10.1155/2014/317642 |
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doaj-b9789c5c2dd442e885b1432383a3e2582020-11-24T23:49:34ZengHindawi LimitedBioMed Research International2314-61332314-61412014-01-01201410.1155/2014/317642317642TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq DataQinghua Jiang0Jixuan Wang1Yadong Wang2Rui Ma3Xiaoliang Wu4Yu Li5School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, ChinaSchool of Software, Harbin Institute of Technology, Harbin, Heilongjiang 150001, ChinaSchool of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, ChinaSchool of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, ChinaSchool of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, ChinaSchool of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, ChinaHigh-throughput genomic technologies like lncRNA microarray and RNA-Seq often generate a set of lncRNAs of interest, yet little is known about the transcriptional regulation of the set of lncRNA genes. Here, based on ChIP-Seq peak lists of transcription factors (TFs) from ENCODE and annotated human lncRNAs from GENCODE, we developed a web-based interface titled “TF2lncRNA,” where TF peaks from each ChIP-Seq experiment are crossed with the genomic coordinates of a set of input lncRNAs, to identify which TFs present a statistically significant number of binding sites (peaks) within the regulatory region of the input lncRNA genes. The input can be a set of coexpressed lncRNA genes or any other cluster of lncRNA genes. Users can thus infer which TFs are likely to be common transcription regulators of the set of lncRNAs. In addition, users can retrieve all lncRNAs potentially regulated by a specific TF in a specific cell line of interest or retrieve all TFs that have one or more binding sites in the regulatory region of a given lncRNA in the specific cell line. TF2LncRNA is an efficient and easy-to-use web-based tool.http://dx.doi.org/10.1155/2014/317642 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Qinghua Jiang Jixuan Wang Yadong Wang Rui Ma Xiaoliang Wu Yu Li |
spellingShingle |
Qinghua Jiang Jixuan Wang Yadong Wang Rui Ma Xiaoliang Wu Yu Li TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data BioMed Research International |
author_facet |
Qinghua Jiang Jixuan Wang Yadong Wang Rui Ma Xiaoliang Wu Yu Li |
author_sort |
Qinghua Jiang |
title |
TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data |
title_short |
TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data |
title_full |
TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data |
title_fullStr |
TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data |
title_full_unstemmed |
TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data |
title_sort |
tf2lncrna: identifying common transcription factors for a list of lncrna genes from chip-seq data |
publisher |
Hindawi Limited |
series |
BioMed Research International |
issn |
2314-6133 2314-6141 |
publishDate |
2014-01-01 |
description |
High-throughput genomic technologies like lncRNA microarray and RNA-Seq often generate a set of lncRNAs of interest, yet little is known about the transcriptional regulation of the set of lncRNA genes. Here, based on ChIP-Seq peak lists of transcription factors (TFs) from ENCODE and annotated human lncRNAs from GENCODE, we developed a web-based interface titled “TF2lncRNA,” where TF peaks from each ChIP-Seq experiment are crossed with the genomic coordinates of a set of input lncRNAs, to identify which TFs present a statistically significant number of binding sites (peaks) within the regulatory region of the input lncRNA genes. The input can be a set of coexpressed lncRNA genes or any other cluster of lncRNA genes. Users can thus infer which TFs are likely to be common transcription regulators of the set of lncRNAs. In addition, users can retrieve all lncRNAs potentially regulated by a specific TF in a specific cell line of interest or retrieve all TFs that have one or more binding sites in the regulatory region of a given lncRNA in the specific cell line. TF2LncRNA is an efficient and easy-to-use web-based tool. |
url |
http://dx.doi.org/10.1155/2014/317642 |
work_keys_str_mv |
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