Issue 2, 2015

A global view of network of lncRNAs and their binding proteins

Abstract

Recently, the long non-coding RNAs (lncRNAs) have obtained wide attention because they have broad and crucial functions in regulating complex biological processes. Many lncRNAs functioned by interfacing with corresponding RNA binding proteins and the complexity of lncRNAs' function was attributed to multiple lncRNA–protein interactions. To gain insights into the global relationship between lncRNAs and their binding proteins, here we constructed a lncRNA–protein network (LPN) based on experimentally determined functional interactions between them. This network included 177 lncRNAs, 92 proteins and 683 relationships between them. Cluster analysis of LPN revealed that some proteins (such as AGO and IGFBP families) and lncRNA (such as XIST and MALAT1) were densely connected, suggesting the potential co-regulated mechanism and functional cross-talk of different lncRNAs. We then characterized the lncRNA functions and found that lncRNA binding proteins (LBPs) enriched in many cancer or cancer-related pathways. Finally, we investigated the different topological properties of LBPs in PPIs network. Compared with disease proteins and average ones, LBPs tend to have significantly higher degree, betweenness, and closeness but a relatively lower clustering coefficient, indicating their centrality and essentiality in the context of a biological network.

Graphical abstract: A global view of network of lncRNAs and their binding proteins

Supplementary files

Article information

Article type
Paper
Submitted
11 Jul 2014
Accepted
20 Nov 2014
First published
21 Nov 2014

Mol. BioSyst., 2015,11, 656-663

A global view of network of lncRNAs and their binding proteins

D. Shang, H. Yang, Y. Xu, Q. Yao, W. Zhou, X. Shi, J. Han, F. Su, B. Su, C. Zhang, C. Li and X. Li, Mol. BioSyst., 2015, 11, 656 DOI: 10.1039/C4MB00409D

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Spotlight

Advertisements