TF2LncRNA : Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data
Joint Authors
Wu, Xiaoliang
Wang, Jixuan
Wang, Yadong
Jiang, Qinghua
Ma, Rui
Li, Yu
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-5, 5 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-03-04
Country of Publication
Egypt
No. of Pages
5
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Jiang, Qinghua& Wang, Jixuan& Wang, Yadong& Ma, Rui& Wu, Xiaoliang& Li, Yu. 2014. TF2LncRNA : Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data. BioMed Research International،Vol. 2014, no. 2014, pp.1-5.
https://search.emarefa.net/detail/BIM-463029
Modern Language Association (MLA)
Jiang, Qinghua…[et al.]. TF2LncRNA : Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data. BioMed Research International No. 2014 (2014), pp.1-5.
https://search.emarefa.net/detail/BIM-463029
American Medical Association (AMA)
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. BioMed Research International. 2014. Vol. 2014, no. 2014, pp.1-5.
https://search.emarefa.net/detail/BIM-463029
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-463029