LncRNA Ontology v2.0

The advent of large-scale sequencing has resulted in identifying thousands of long non-coding RNAs (lncRNAs) that potentially play critical roles of diverse cellular processes. Determining the biologic function of individual lncRNAs has been poorly understood. Although a considerable portion of genomes is transcribed as lncRNAs, the vast majority are functionally uncharacterized. Genetic loss-of-function strategies can be used to study the function of lncRNAs in vivo, however, it is time-consuming and expensive. Alternatively, the rule of 'association of guilty' is widely used to identify the protein-coding genes that are associated with lncRNAs, and these genes are further used to predict lncRNA functions. We describe the LncRNA Ontology database version 2.0 (LO v.2.0), an updated database that specifically stored and annotated the functional ontology of human long non-coding RNAs (lncRNAs), and their associated genes. This database integrated genome, transcriptome, epigenome (including DNA methylation and nine kinds of histone modifications), and regulatome at both transcription and post-transcription level. The majority of lncRNAs were annotated with one or more GO nodes in each of the tree GO categories. LO v2.0 documents totally 22,803,010 associations among 87,614 lncRNAs and 14848 GO annotations in human. LO v2.0 will be of help in uncovering the lncRNA biological roles in human.

we developed three flexible online querying modules:

'Lnc-Ann' module provided the comprehensive annotation of lncRNAs, including chromosomal localization, exon, intron, transcript information and so on, which are also displayed graphically.

'Lnc-genes' module provided a convenient querying for retrieving the genes that are associated with interesting lncRNAs, either based on individual omics data or the integrated results.

'Lnc-Ontology' module provides the predicted functions of lncRNAs based on their associated genes identified at each omics level or the integration.

Users can query, browse and manipulate these lncRNA functional annotations. Annotations from LO v2.0 are freely available and are accessible through most of the regular web browser.

    LO v2.0 is tested to work with the following web browsers with 1024*768: 1.Google Chrome (version 17 and later) 2.Mozilla Firefox (version 10 and later) 3.Apple Safari (version 5 and later).

• 1. The number of lncRNAs were greatly increased (including 87,614) and
  the annotation information of lncRNAs were further layout in the form of text and graphical display.
• 2. The function information were also expanded, including 9,942 biological processes, 3,644 molecular functions,
  and 1,262 cellular components. Moreover, the predicted lncRNA-function pairs increase 5.5 times compared with the first version.
• 3. Besides the predicted functions of lncRNAs, we also provided the protein coding genes that are associated with each lncRNA.
  The users can query and download the associated genes identified based individual omics data and the integrated gene lists identified
  from integration of multiple omics datasets.
• 4. Three additional types of omics data were integrated in the updated version, including the genome-wide lncRNA-gene interaction pairs
  identified based on genome, regulatome at the transcription and post-transcription levels. There are additional 2,175,095 lncRNA-gene
  interactions identified by integration of transcriptional regulation from ~10,200 curated ChIP-seq datasets and miRNA regulation from
  117 CLIP-seq datasets. This increased the types of omics data from two to five.
• 5. We updated the transcriptome data from ENCODE to the Genotype-Tissue Expression (GTEx) project, increased the number of samples
  to 8,555 across 30 tissues.

• lncRNA-gene pairs:
• Co-expression: 825,034
• Co-epigentics: 15,888,032
• Co-TF: 13,782,314
• Co-miRNA: 2,211,818
• Sequence similarity: 2,175,095
• Integration: 778,859
• lncRNA-function pairs:
• Co-expression: 493,974
• Co-epigentics: 14,255,487
• Co-TF: 5,622,804
• Co-miRNA: 2,176,206
• Sequence similarity: 1,629,486
• Integration: 801,258

• LncRNA Ontology
  (Yongsheng Li et al., Oncotarget, 2015)