LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns.
Accumulating evidences suggest that long non-coding RNAs (lncRNAs) perform important functions. Genome-wide chromatin-states area rich source of information about cellular state, yielding insights beyond what is typically obtained by transcriptome profiling. We propose an integrative method for genome-wide functional predictions of lncRNAs by combining chromatin states data with gene expression patterns. We first validated the method using protein-coding genes with known function annotations. Our validation results indicated that our integrative method performs better than co-expression analysis, and is accurate across different conditions. Next, by applying the integrative model genome-wide, we predicted the probable functions for more than 97% of human lncRNAs. The putative functions inferred by our method match with previously annotated by the targets of lncRNAs. Moreover, the linkage from the cellular processes influenced by cancer-associated lncRNAs to the cancer hallmarks provided a "lncRNA point-of-view" on tumor biology. Our approach provides a functional annotation of the lncRNAs, which we developed into a web-based application, LncRNA Ontology, to provide visualization, analysis, and downloading of lncRNA putative functions.
College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Nangang, Harbin, Heilongjiang, China.
Yongsheng
Y
Li
College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Nangang, Harbin, Heilongjiang, China.
Hong
H
Chen
College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Nangang, Harbin, Heilongjiang, China.
Tao
T
Pan
College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Nangang, Harbin, Heilongjiang, China.
Chunjie
C
Jiang
College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Nangang, Harbin, Heilongjiang, China.
Zheng
Z
Zhao
College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Nangang, Harbin, Heilongjiang, China.
Zishan
Z
Wang
College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Nangang, Harbin, Heilongjiang, China.
Jinwen
J
Zhang
College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Nangang, Harbin, Heilongjiang, China.
Juan
J
Xu
College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Nangang, Harbin, Heilongjiang, China.
Xia
X
Li
D000465:Algorithms; D002460:Cell Line; D045744:Cell Line, Tumor; D002478:Cells, Cultured; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D006367:HeLa Cells; D056945:Hep G2 Cells; D006657:Histones / Q000378:metabolism; D006801:Humans; D020014:K562 Cells; D008239:Lysine / Q000378:metabolism; D008745:Methylation; D008957:Models, Genetic; D009369:Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D011401:Promoter Regions, Genetic / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D024363:Transcription Initiation Site
D002843:Chromatin; D006657:Histones; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D008239:Lysine
chromatin pattern; integrated model; lncRNA functions; lncRNA ontology; long non-coding RNA