Figure 1.
Diagram of the genomic context of different lncRNA subtypes.
(a) CI: Completely Intronic lncRNA, IA: Intronic Antisense lncRNA and IO: Intron Overlapping lncRNA; (b) 3UO: 3/UTR Overlapping lncRNA, 5UO: 5/UTR Overlapping lncRNA, CD: CDS overlapping lncRNA and AN: Antisense lncRNA; (c) SO: Sense Overlapping lncRNA; (d) LI: Intergenic lncRNA;
Figure 2.
Distribution of non coding lncRNA subtypes.
Distribution of noncoding lncRNA subtypes in (a) human and (b) mouse. Abbreviations: (1) 3UO, 3/UTR overlapping lncRNAs (2) 5UO, 5/UTR overlapping lncRNAs (3) CDS, CDS overlapping lncRNAs (4) LI, Intergenic (linc) lncRNAs (5) AN, Antisense lncRNAs (6) CI, Completely Intronic (7) IA, Intronic Antisense lncRNAs (8) IO, Intron Overlapping lncRNA (9) PS, Pseudogene lncRNAs (10) SO, Sense Overlapping lncRNAs (11) AO, Ambiguous ORF transcripts (12) PT, Processed Transcripts (13) MI, miscRNAs (14) NC, Non coding transcripts.
Figure 3.
Distribution of putatively coding lncRNA subtypes.
Distribution of putatively coding lncRNA subtypes in (a) human and (b) mouse. Abbreviations: (1) 3UO, 3/UTR overlapping lncRNAs (2) 5UO, 5/UTR overlapping lncRNAs (3) CDS, CDS overlapping lncRNAs (4) LI, Intergenic (linc) lncRNAs (5) AN, Antisense lncRNAs (6) CI, Completely Intronic (7) IA, Intronic Antisense lncRNAs (8) IO, Intron Overlapping lncRNA (9) PS, Pseudogene lncRNAs (10) SO, Sense Overlapping lncRNAs (11) AO, Ambiguous ORF transcripts (12) PT, Processed Transcripts (13) MI, miscRNAs (14) NC, Non coding transcripts.
Figure 4.
Distribution of Repeat Elements across lncRNAs.
Distribution of different Repeat Families across lncRNAs in (a) human and (b) mouse compared to protein coding transcripts. (c) Repeat associated lncRNA subtypes in human and mouse. Abbreviations: (1) 3UO, 3/UTR overlapping lncRNAs (2) 5UO, 5/UTR overlapping lncRNAs (3) CDS, CDS overlapping lncRNAs (4) LI, Intergenic (linc) lncRNAs (5) AN, Antisense lncRNAs (6) CI, Completely Intronic (7) IA, Intronic Antisense lncRNAs (8) IO, Intron Overlapping lncRNA (9) PS, Pseudogene lncRNAs (10) SO, Sense Overlapping lncRNAs (11) AO, Ambiguous ORF transcripts (12) PT, Processed Transcripts (13) MI, miscRNAs (14) NC, Non coding transcripts.
Figure 5.
Distribution of CGI and non-CGI promoters among the various lncRNA subtypes.
CGI and non-CGI promoters of each subtype of lncRNA (a) in human (b) in mouse. Abbreviations: (1) 3UO, 3/UTR overlapping lncRNAs (2) 5UO, 5/UTR overlapping lncRNAs (3) CDS, CDS overlapping lncRNAs (4) LI, Intergenic (linc) lncRNAs (5) AN, Antisense lncRNAs (6) CI, Completely Intronic (7) IA, Intronic Antisense lncRNAs (8) IO, Intron Overlapping lncRNA (9) PS, Pseudogene lncRNAs (10) SO, Sense Overlapping lncRNAs (11) AO, Ambiguous ORF transcripts (12) PT, Processed Transcripts (13) MI, miscRNAs (14) NC, Non coding transcripts.
Figure 6.
Different web interfaces allow easy view of lncRNA information.
(a) Search page provides multiple options for searching lncRNA information. (b) General Output page displays basic information about an lncRNA transcript and provides multiple options for probing into further details. (c) Detailed Output page displays complete information about an lncRNA transcript. (d) LncRBrowse allows user to browse through different genomic annotation tracks.
Table 1.
Source of transcripts for LncRBase.
Figure 7.
Classification scheme for LncRBase transcripts.
The transcripts selected were either pre-annotated as lncRNAs or simply mentioned as non coding transcripts. In the former case, additional details were provided about the transcripts, while in the latter case, transcripts > = 200 nts were selected and characterized as lncRNAs.
Figure 8.
LncRBase is compiled by subsequent importing, naming, analysis and visualization of lncRNA transcripts. Every lncRNA transcript is subsequently characterised using multiple parameters, and the results are stored in the database. A web-interface built using Perl enables lncRNA visualization and database querying.