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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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Detalles Bibliográficos
Autores principales: Jiang, Qinghua, Wang, Jixuan, Wang, Yadong, Ma, Rui, Wu, Xiaoliang, Li, Yu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960524/
https://www.ncbi.nlm.nih.gov/pubmed/24729968
http://dx.doi.org/10.1155/2014/317642
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author Jiang, Qinghua
Wang, Jixuan
Wang, Yadong
Ma, Rui
Wu, Xiaoliang
Li, Yu
author_facet Jiang, Qinghua
Wang, Jixuan
Wang, Yadong
Ma, Rui
Wu, Xiaoliang
Li, Yu
author_sort Jiang, Qinghua
collection PubMed
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.
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spelling pubmed-39605242014-04-13 TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data Jiang, Qinghua Wang, Jixuan Wang, Yadong Ma, Rui Wu, Xiaoliang Li, Yu Biomed Res Int Research Article 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. Hindawi Publishing Corporation 2014 2014-03-04 /pmc/articles/PMC3960524/ /pubmed/24729968 http://dx.doi.org/10.1155/2014/317642 Text en Copyright © 2014 Qinghua Jiang et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Jiang, Qinghua
Wang, Jixuan
Wang, Yadong
Ma, Rui
Wu, Xiaoliang
Li, Yu
TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data
title 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_short 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
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960524/
https://www.ncbi.nlm.nih.gov/pubmed/24729968
http://dx.doi.org/10.1155/2014/317642
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