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LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.

Ma L, Li A, Zou D, Xu X, Xia L, Yu J, Bajic VB, Zhang Z - Nucleic Acids Res. (2014)

Bottom Line: Unlike existing databases, lncRNAWiki features comprehensive integration of information on human lncRNAs obtained from multiple different resources and allows not only existing lncRNAs to be edited, updated and curated by different users but also the addition of newly identified lncRNAs by any user.It harnesses community collective knowledge in collecting, editing and annotating human lncRNAs and rewards community-curated efforts by providing explicit authorship based on quantified contributions.LncRNAWiki relies on the underling knowledge of scientific community for collective and collaborative curation of human lncRNAs and thus has the potential to serve as an up-to-date and comprehensive knowledgebase for human lncRNAs.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

Show MeSH
Classification of lncRNAs based on their genomic location in respect of protein-coding genes. (A) lncRNA categories. Intergenic: lncRNAs are transcribed from intergenic regions; Intronic (S): lncRNAs are transcribed entirely from introns of protein-coding genes; Intronic (AS): lncRNAs are transcribed from antisense strand of protein-coding genes and the entire sequences are covered by introns of protein-coding genes; Overlapping (S): lncRNAs that contain coding genes within an intron on the sense strand; Overlapping (AS): lncRNAs that contain coding genes within an intron on the antisense strand; Sense: lncRNAs are transcribed from the sense strand of protein-coding genes and the entire sequence of lncRNAs are covered by protein-coding genes (Intronic lncRNAs are not included), or the entire sequence of protein-coding genes are covered by lncRNAs (Overlapping lncRNAs are not included), or both lncRNAs and protein-coding genes intersect each other partially; Antisense: lncRNAs are transcribed from the antisense strand of protein-coding genes and the entire sequence of lncRNAs are covered by protein-coding genes (Intronic lncRNAs are not included), or the entire sequence of protein-coding genes are covered by lncRNAs (Overlapping lncRNAs are not included), or both lncRNAs and protein-coding genes intersect each other partially. (B) Proportions of human lncRNAs in different categories.
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Figure 2: Classification of lncRNAs based on their genomic location in respect of protein-coding genes. (A) lncRNA categories. Intergenic: lncRNAs are transcribed from intergenic regions; Intronic (S): lncRNAs are transcribed entirely from introns of protein-coding genes; Intronic (AS): lncRNAs are transcribed from antisense strand of protein-coding genes and the entire sequences are covered by introns of protein-coding genes; Overlapping (S): lncRNAs that contain coding genes within an intron on the sense strand; Overlapping (AS): lncRNAs that contain coding genes within an intron on the antisense strand; Sense: lncRNAs are transcribed from the sense strand of protein-coding genes and the entire sequence of lncRNAs are covered by protein-coding genes (Intronic lncRNAs are not included), or the entire sequence of protein-coding genes are covered by lncRNAs (Overlapping lncRNAs are not included), or both lncRNAs and protein-coding genes intersect each other partially; Antisense: lncRNAs are transcribed from the antisense strand of protein-coding genes and the entire sequence of lncRNAs are covered by protein-coding genes (Intronic lncRNAs are not included), or the entire sequence of protein-coding genes are covered by lncRNAs (Overlapping lncRNAs are not included), or both lncRNAs and protein-coding genes intersect each other partially. (B) Proportions of human lncRNAs in different categories.

Mentions: Based on our previous study (7) and categories of Derrien et al. (35), we classified the 105 255 non-redundant lncRNA transcripts into seven groups according to their genomic location in respect to protein-coding genes, viz., Intergenic, Intronic (S), Intronic (AS), Overlapping (S), Overlapping (AS), Sense and Antisense (Figure 2). The difference between our classification and Derrien's (35) is that we classified lncRNAs that intersect protein-coding genes into Sense or Antisense by considering the whole transcript sequence instead of exonic region only.


LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.

Ma L, Li A, Zou D, Xu X, Xia L, Yu J, Bajic VB, Zhang Z - Nucleic Acids Res. (2014)

Classification of lncRNAs based on their genomic location in respect of protein-coding genes. (A) lncRNA categories. Intergenic: lncRNAs are transcribed from intergenic regions; Intronic (S): lncRNAs are transcribed entirely from introns of protein-coding genes; Intronic (AS): lncRNAs are transcribed from antisense strand of protein-coding genes and the entire sequences are covered by introns of protein-coding genes; Overlapping (S): lncRNAs that contain coding genes within an intron on the sense strand; Overlapping (AS): lncRNAs that contain coding genes within an intron on the antisense strand; Sense: lncRNAs are transcribed from the sense strand of protein-coding genes and the entire sequence of lncRNAs are covered by protein-coding genes (Intronic lncRNAs are not included), or the entire sequence of protein-coding genes are covered by lncRNAs (Overlapping lncRNAs are not included), or both lncRNAs and protein-coding genes intersect each other partially; Antisense: lncRNAs are transcribed from the antisense strand of protein-coding genes and the entire sequence of lncRNAs are covered by protein-coding genes (Intronic lncRNAs are not included), or the entire sequence of protein-coding genes are covered by lncRNAs (Overlapping lncRNAs are not included), or both lncRNAs and protein-coding genes intersect each other partially. (B) Proportions of human lncRNAs in different categories.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4383965&req=5

Figure 2: Classification of lncRNAs based on their genomic location in respect of protein-coding genes. (A) lncRNA categories. Intergenic: lncRNAs are transcribed from intergenic regions; Intronic (S): lncRNAs are transcribed entirely from introns of protein-coding genes; Intronic (AS): lncRNAs are transcribed from antisense strand of protein-coding genes and the entire sequences are covered by introns of protein-coding genes; Overlapping (S): lncRNAs that contain coding genes within an intron on the sense strand; Overlapping (AS): lncRNAs that contain coding genes within an intron on the antisense strand; Sense: lncRNAs are transcribed from the sense strand of protein-coding genes and the entire sequence of lncRNAs are covered by protein-coding genes (Intronic lncRNAs are not included), or the entire sequence of protein-coding genes are covered by lncRNAs (Overlapping lncRNAs are not included), or both lncRNAs and protein-coding genes intersect each other partially; Antisense: lncRNAs are transcribed from the antisense strand of protein-coding genes and the entire sequence of lncRNAs are covered by protein-coding genes (Intronic lncRNAs are not included), or the entire sequence of protein-coding genes are covered by lncRNAs (Overlapping lncRNAs are not included), or both lncRNAs and protein-coding genes intersect each other partially. (B) Proportions of human lncRNAs in different categories.
Mentions: Based on our previous study (7) and categories of Derrien et al. (35), we classified the 105 255 non-redundant lncRNA transcripts into seven groups according to their genomic location in respect to protein-coding genes, viz., Intergenic, Intronic (S), Intronic (AS), Overlapping (S), Overlapping (AS), Sense and Antisense (Figure 2). The difference between our classification and Derrien's (35) is that we classified lncRNAs that intersect protein-coding genes into Sense or Antisense by considering the whole transcript sequence instead of exonic region only.

Bottom Line: Unlike existing databases, lncRNAWiki features comprehensive integration of information on human lncRNAs obtained from multiple different resources and allows not only existing lncRNAs to be edited, updated and curated by different users but also the addition of newly identified lncRNAs by any user.It harnesses community collective knowledge in collecting, editing and annotating human lncRNAs and rewards community-curated efforts by providing explicit authorship based on quantified contributions.LncRNAWiki relies on the underling knowledge of scientific community for collective and collaborative curation of human lncRNAs and thus has the potential to serve as an up-to-date and comprehensive knowledgebase for human lncRNAs.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

Show MeSH