NONCODE v3.0: integrative annotation of long noncoding RNAs

Abstract

Facilitated by the rapid progress of high-throughput sequencing technology, a large number of long noncoding RNAs (lncRNAs) have been identified in mammalian transcriptomes over the past few years. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. Notably, a growing number of lncRNAs have been implicated in disease etiology. With the increasing number of published lncRNA studies, the experimental data on lncRNAs (e.g. expression profiles, molecular features and biological functions) have accumulated rapidly. In order to enable a systematic compilation and integration of this information, we have updated the NONCODE database (http://www.noncode.org) to version 3.0 to include the first integrated collection of expression and functional lncRNA data obtained from re-annotated microarray studies in a single database. NONCODE has a user-friendly interface with a variety of search or browse options, a local Genome Browser for visualization and a BLAST server for sequence-alignment search. In addition, NONCODE provides a platform for the ongoing collation of ncRNAs reported in the literature. All data in NONCODE are open to users, and can be downloaded through the website or obtained through the SOAP API and DAS services.

Long non-coding RNAs link extracellular matrix gene expression to ischemic cardiomyopathy

“…We used two lncRNA data sources for our analysis: the NONCODE 3.0 non-coding RNA database 21 and the Human Body Map lincRNAs Catalog. 22 Together, a collective lncRNA gene list containing over 30 000 annotated human lncRNA genes was used in this study.…”

“…22 Together, a collective lncRNA gene list containing over 30 000 annotated human lncRNA genes was used in this study. 21,22 All singleexon transcripts as well as any transcripts overlapping RefSeq genes and known protein-coding genes were removed to exclude potential protein-coding genes ( Figure 2A). To define a stringent set of candidate lncRNAs, transcripts were selected from the catalogue of expressed transcripts if they fulfilled both of the following criteria: (i) >200 bp long and (ii) expression of >0.5 RPKM in the sample (Methods; Figure 2A).…”

Genome-wide identification of cancer-related polyadenylated and non-polyadenylated RNAs in human breast and lung cell lines

“…Thus, the different forms of non-coding RNAs participate and influence tumorigenesis and tumor progression. Use of the coding-non-coding co-expression network to annotate the functions of the different forms of non-coding RNAs represents a novel tool for future research [41][42][43][44].…”

Tuning the engine

“…Users need to keep in mind that the data set size required for such an approach to produce meaningful results is quite high (in the order of tens, if not hundreds, of samples). NONCODE, 21 lncRNAdb 22 and NRED 23 are reference databases for ncRNAs and related expression information. Long-noncoding RNAs have been mostly regarded as chromatin-associated, and thus transcription-related, factors.…”

“…Available databases are focused mainly on UTRs annotation, 12,13 RBP-target interactions, 14,15 ncRNAs, [16][17][18][19][20][21][22][23][24] of which miRNAtarget interactions are the greater part, [16][17][18][19][20] with a limited number of resources focusing on lncRNAs, 22,23 and cis-elements. [25][26][27][28][29][30] Furthermore, a small number of resources integrating different data types is available.…”