Difference between revisions of "Main Page"

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<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Data sources</div>
 
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Data sources</div>
<div style="padding:0.5em 0.5em;">LncRNAs in present database are collected from GENCODE V19, NONCODE V4, and LNCipedia V2.1.We used blastn to obtain the non-redundant lncRNAs in the three databases. When lncRNA transcripts show 100% sequence identity and are mapped to the same genomic location, they are considered to be the same transcript in different databases. We at last obtained 105,255 non-redundant lncRNA transcripts. To examine how many lncRNAs have been functionally studied, we blasted the 105,255 lncRNAs against lncRNA sequences in lncRNAdb (purple circle indicates lncRNAdb) (downloaded on 21 July, 2014; 223 lncRNAs in total).
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<div style="padding:0.5em 0.5em;">LncRNAs in present database are collected from GENCODE V19, NONCODE V4, and LNCipedia V2.1.We used blastn to obtain the non-redundant lncRNAs in the three databases. When lncRNA transcripts show 100% sequence identity and are mapped to the same genomic location, they are considered to be the same transcript in different databases. We at last obtained 105,255 non-redundant lncRNA transcripts. To examine how many lncRNAs have been functionally annotated, we blasted the 105,255 lncRNAs against lncRNA sequences in lncRNAdb (purple circle indicates lncRNAdb) (downloaded on 21 July, 2014; 223 lncRNAs in total) and found at most 103 lncRNAs have been functionally annotated to date, indicating a long-term process to fully annotate human lncRNAs.  
  
 
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Revision as of 16:09, 9 August 2014


Welcome to LncRNAWiki
105,256 human long non-coding RNAs inside
Introduction
LncRNAWiki is a wiki-based database for management of human lncRNAs, aiming to harness collective intelligence to collect, edit, and annotate information about human lncRNAs. This database is a publicly editable and open-content platform for community curation of human lncRNAs, bearing the potential to become a comprehensive and up-to-date knowledge base for human lncRNAs.

A featured lncRNA, ENST00000534336.1, that is overexpressed in many kinds of cancers and is closely associated with tumor growth and metastasis, is community-curated.


If a lncRNA is newly reported in a published paper or is annotated in a lncRNA database and this lncRNA is found not to be included by the present LncRNAWiki dataset after search, users can create a new page for this lncRNA. For example, LUNAR1, the recently discovered lncRNA, which is Notch-regulated and functions to enhance IGF1R (insulin-like growth factor receptor 1) mRNA expression to maintain human T cell acute lymphoblastic leukemia (T-ALL), has been added to LncRNAWiki.

Data sources
LncRNAs in present database are collected from GENCODE V19, NONCODE V4, and LNCipedia V2.1.We used blastn to obtain the non-redundant lncRNAs in the three databases. When lncRNA transcripts show 100% sequence identity and are mapped to the same genomic location, they are considered to be the same transcript in different databases. We at last obtained 105,255 non-redundant lncRNA transcripts. To examine how many lncRNAs have been functionally annotated, we blasted the 105,255 lncRNAs against lncRNA sequences in lncRNAdb (purple circle indicates lncRNAdb) (downloaded on 21 July, 2014; 223 lncRNAs in total) and found at most 103 lncRNAs have been functionally annotated to date, indicating a long-term process to fully annotate human lncRNAs.


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Classification

The classification of lncRNA based on genomic location is now the most feasible classification method and is suggested to be of great biological significance (Ma etal. 2013, RNA Biology).
We classified lncRNAs into seven groups (Intergenic, Intronic (S),Intronic (AS),Overlapping (S),Overlapping (AS), Sense and Antisense) based on their genomic location in respect to protein-coding genes. Help


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Publications
About Us
Our group works in the field of Computational Biology and Bioinformatics (CBB), currently with a particular focus on building biological knowledge wikis in aid of community curation of massive biological knowledge.
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