title: TF2LncRNA: identifying common transcription factors for a list of lncRNA genes from ChIP-Seq data.
abstract: 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.
authors.affiliation: School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Jiang
authors.affiliation: School of Software, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
authors.forename: Jixuan
authors.initials: J
authors.lastname: Wang
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
authors.forename: Yadong
authors.initials: Y
authors.lastname: Wang
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Ma
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
authors.forename: Xiaoliang
authors.initials: X
authors.lastname: Wu
authors.affiliation: School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Li
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020407:Internet; D008969:Molecular Sequence Data; D062085:RNA, Long Noncoding / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding; D014157:Transcription Factors
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