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;">Disease</div>
 
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Disease</div>
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<div style="padding:0.5em 0.5em;">[[File:Statistics4.png|center|900px]]  
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<div style="padding:0.5em 0.5em;">[[File:Statistics4.png|left|900px]]  
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LncRNAWiki keeps frequent updates by community annotation of human lncRNAs and integration of newly identified lncRNAs with experimental evidence. In contrast to the previous version (released in 2014) that had 86 curated lncRNAs, the updated version has, a total of 719 lncRNAs that are community-curated (the detailed list is available at [[LncRNAWiki:Featured|Featured LncRNAs]]).  
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LncRNAWiki keeps frequent updates by community annotation of human lncRNAs and integration of newly identified lncRNAs with experimental evidence.  
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In contrast to the previous version (released in 2014) that had 86 curated lncRNAs, the updated version has, a total of 719 lncRNAs that are community-curated (the detailed list is available at [[LncRNAWiki:Featured|Featured LncRNAs]]).  
  
 
Among these 719 lncRNAs, 304 have been experimentally proved to be associated with cancer and other diseases ([[LncRNAWiki:Disease|Disease]])
 
Among these 719 lncRNAs, 304 have been experimentally proved to be associated with cancer and other diseases ([[LncRNAWiki:Disease|Disease]])
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<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Small Protein</div>
 
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We developed computational approaches for identification of small proteins in all the human lncRNAs in LncRNAWiki. As a result, we identified '''9,387''' lncRNAs potentially encoding small proteins and we further validated '''2,246''' such small proteins with high confidence by considering protein instability, secondary structure and transmembrane helix ([[LncRNAWiki:small proteins|lncRNAs and small proteins]], [[Help:Contents#Database content|help]]). 
 
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All putative small proteins as well as their relevant information on physical and chemical parameters, secondary structures, transmembrane helices and topology structures are integrated into LncRNAWiki (e.g., [[ENST00000608917.1|''ENST00000608917.1'']]) and also publicly available at [[LncRNAWiki:Download|Downloads]]. Expanding LncRNAWiki by this information provides a very new quality for lncRNA researchers.
 
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[[File:SmallPRO-1.png|center|400px]]
 
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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>
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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 source</div>
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<div style="padding:0.5em 0.5em;">[[File:web1a.png|left|350px|caption]]  
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<div style="padding:0.5em 0.5em;">[[File:web1a.png|center|350px|caption]]  
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In LncRNAWiki2014, we integrated lncRNA sequences and annotation information from three data sources: GENCODE (version 19; 23,898 human lncRNA transcripts), NONCODE (version 4.0; 95,135 human lncRNA transcripts), and LNCipedia (version 2.1; 32,181 human lncRNA transcripts). After the process of error and redundancy elimination, 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 that only about 100 human lncRNAs have been functionally annotated to date, indicating a long-term process of human lncRNA annotation.
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The majority of the lncRNA information was initially seeded with a subset of information from [http://www.gencodegenes.org/ GENCODE], [http://www.bioinfo.org/noncode/ NONCODE], [http://www.lncipedia.org/ LNCipedia], and [http://www.lncrnadb.org/ lncRNAdb](purple circle indicates lncRNAdb).
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The majority of the lncRNA information was initially seeded with a subset of information from [http://www.gencodegenes.org/ GENCODE], [http://www.bioinfo.org/noncode/ NONCODE], [http://www.lncipedia.org/ LNCipedia], and [http://www.lncrnadb.org/ lncRNAdb].
 
 
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<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Classification</div>
 
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Classification</div>
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<div style="padding:0.5em 0.5em;">[[File:web2a.png|center|400px]]
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Taking into account that the genomic context of lncRNAs may offer insights into their function, the classification of lncRNAs based on genomic location is of great biological significance in in-depth mining and analysis (Ma etal. 2013, RNA Biology). <br />
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Based on genomic location, we classified lncRNAs into seven groups (Ma etal. 2013, RNA Biology) ('''Intergenic''', '''Intronic (S)''','''Intronic (AS)''','''Overlapping (S)''','''Overlapping (AS)''', '''Sense''' and '''Antisense''') based on their genomic location in respect to protein-coding genes. [[Help:Contents#Database content|''Help'']]
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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:Contents#Database content|''Help'']]<br />
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<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Small Protein</div>
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<div style="padding:0.5em 0.5em;">[[File:SmallPRO-1.png|center|380px]]
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We developed computational approaches for identification of small proteins in all the human lncRNAs in LncRNAWiki. As a result, we identified '''9,387''' lncRNAs potentially encoding small proteins and we further validated '''2,246''' such small proteins with high confidence by considering protein instability, secondary structure and transmembrane helix ([[LncRNAWiki:small proteins|lncRNAs and small proteins]], [[Help:Contents#Database content|help]]).
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Revision as of 09:06, 20 June 2017


Welcome to LncRNAWiki
105,824 human long non-coding RNAs inside
Introduction

LncRNAWiki is a wiki-based, publicly editable and open-content platform for community curation of human long non-coding RNAs (lncRNAs), viz., a community-curated lncRNA knowledgebase. Unlike conventional biological databases based on expert curation, lncRNAWiki harnesses collective intelligence to collect, edit and annotate information about lncRNAs, quantifies users' contributions in each annotated lncRNA and provides explicit authorship to encourage more participation from the whole scientific community.

Imagine a world in which every single person on the planet has free access to the sum of all human knowledge. — Jimmy Wales, Founder of Wikipedia
Disease
900px

LncRNAWiki keeps frequent updates by community annotation of human lncRNAs and integration of newly identified lncRNAs with experimental evidence.

In contrast to the previous version (released in 2014) that had 86 curated lncRNAs, the updated version has, a total of 719 lncRNAs that are community-curated (the detailed list is available at Featured LncRNAs).

Among these 719 lncRNAs, 304 have been experimentally proved to be associated with cancer and other diseases (Disease)

Data source
caption

The majority of the lncRNA information was initially seeded with a subset of information from GENCODE, NONCODE, LNCipedia, and lncRNAdb(purple circle indicates lncRNAdb).


Classification
Web2a.png

Based on genomic location, we classified lncRNAs into seven groups (Ma etal. 2013, RNA Biology) (Intergenic, Intronic (S),Intronic (AS),Overlapping (S),Overlapping (AS), Sense and Antisense) based on their genomic location in respect to protein-coding genes. Help


Small Protein
SmallPRO-1.png

We developed computational approaches for identification of small proteins in all the human lncRNAs in LncRNAWiki. As a result, we identified 9,387 lncRNAs potentially encoding small proteins and we further validated 2,246 such small proteins with high confidence by considering protein instability, secondary structure and transmembrane helix (lncRNAs and small proteins, help).


How to Cite

If you use any data or information in your work, please cite the following primary publication:

Related publication:

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.
Visitor Statistics

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