Oncotarget

Research Papers:

LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns

Yongsheng Li, Hong Chen, Tao Pan, Chunjie Jiang, Zheng Zhao, Zishan Wang, Jinwen Zhang, Juan Xu, Xia Li _

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Oncotarget. 2015; 6:39793-39805. https://doi.org/10.18632/oncotarget.5794

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Abstract

Yongsheng Li1,*, Hong Chen1,*, Tao Pan1,*, Chunjie Jiang1, Zheng Zhao1, Zishan Wang1, Jinwen Zhang1, Juan Xu1 and Xia Li1

1 College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Nangang, Harbin, Heilongjiang, China

* These authors should be regarded as joint First Authors

Correspondence to:

Xia Li, email:

Juan Xu, email:

Keywords: long non-coding RNA, chromatin pattern, lncRNA ontology, lncRNA functions, integrated model

Received: July 06, 2015 Accepted: September 05, 2015 Published: September 22, 2015

Abstract

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.

Author Information

Yongsheng Li

Hong Chen

Tao Pan

Chunjie Jiang

Zheng Zhao

Zishan Wang

Jinwen Zhang

Juan Xu

Xia Li
Primary Contact  _


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