NONCODEv4: exploring the world of long non-coding RNA genes

Abstract

NONCODE (http://www.bioinfo.org/noncode/) is an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs). Non-coding RNAs (ncRNAs) have been implied in diseases and identified to play important roles in various biological processes. Since NONCODE version 3.0 was released 2 years ago, discovery of novel ncRNAs has been promoted by high-throughput RNA sequencing (RNA-Seq). In this update of NONCODE, we expand the ncRNA data set by collection of newly identified ncRNAs from literature published in the last 2 years and integration of the latest version of RefSeq and Ensembl. Particularly, the number of long non-coding RNA (lncRNA) has increased sharply from 73 327 to 210 831. Owing to similar alternative splicing pattern to mRNAs, the concept of lncRNA genes was put forward to help systematic understanding of lncRNAs. The 56 018 and 46 475 lncRNA genes were generated from 95 135 and 67 628 lncRNAs for human and mouse, respectively. Additionally, we present expression profile of lncRNA genes by graphs based on public RNA-seq data for human and mouse, as well as predict functions of these lncRNA genes. The improvements brought to the database also include an incorporation of an ID conversion tool from RefSeq or Ensembl ID to NONCODE ID and a service of lncRNA identification. NONCODE is also accessible through http://www.noncode.org/.

Figure 1.

Overview of updates in NONCODE version 4.0. Through processes of data collection, redundancy elimination and filtration, the number of ncRNA entries in NONCODE version 4.0 has increased to 595 854. For lncRNAs from human and mouse, different transcripts that intersect any exon of other other and reside on the same DNA strand are considered to belong to the same gene and clustered into a single gene record. This step results in 56 018 genes from 95 135 transcripts in human and 46 475 genes from 67 628 transcripts in mouse. Using public RNA-seq data of human and mouse, presentation of expression and assignment of function is annotated for each lncRNA gene. All tools and services in NONCODE have been updated. In addition, ID conversion tool and iLncRNA is new in this version. The two fields marked with asterisk (*) are specifically for lncRNAs.

Figure 2.

Details of lncRNA transcripts and genes. (A) Exon number distribution of human and mouse lncRNA transcripts. (B) Length distribution of human and mouse lncRNA transcripts. (C) Number of transcripts per gene for human and mouse. (D). Distribution of human and mouse lncRNA genes according to categorization.

Figure 3.

Pipeline for identification of lncRNAs for users. Refer to main text for details.