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<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to LncRNAWiki</div>
 
<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to LncRNAWiki</div>
<div style="padding:0em; font-size:100%">[[:Category:Transcripts|105,823]] human long non-coding RNAs inside</div>
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<div style="padding:0em; font-size:100%">[[:Category:Transcripts|105,824]] human long non-coding RNAs inside</div>
  
 
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*[[File:New5.png]][[LncRNAWiki:Featured|Featured LncRNAs]]
 
*[[File:New5.png]][[LncRNAWiki:Featured|Featured LncRNAs]]
*[[File:New5.png]][[LncRNAWiki:small peptides|Small Proteins]]
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*[[File:New5.png]][[LncRNAWiki:Small_proteins|Small Proteins]]
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*[[File:New5.png]][[LncRNAWiki:Disease|Disease]]
 
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*<span style="color: red;">Featured lncRNAs</span>: 633 lncRNAs with publications have been collected and curated in LncRNAWiki over the past two years, and there are 719 featured lncRNAs in total in the present version. Among the 719 lncRNAs, 289 are extensively studied and experimentally proved to be associated with cancer or other human diseases. Newly featured lncRNA:[[AATBC|''AATBC'']],[[ABALON|''ABALON'']], [[ENST00000444200.1|''APOA1-AS'']], [[NONHSAT121673|''APTR'']], [[Lnc-APBA1-3:1|''BANCR'']], [[ENST00000499008.3|''BDNF-AS'']], [[NONHSAT008995|''BLACAT1'']], [[ENST00000418282.1|''BPESC1'']], [[ENST00000604200.1|''CAHM'']], [[ENST00000502056.1|''CASC8'']], [[NONHSAT129017|''CCAT1'']], [[CCAT2|''CCAT2'']],[[NONHSAT028496|''CISTR'']], [[Lnc-IRX3-4:2|''CRNDE'']],  [[ENST00000357401.3|''CYYR1-AS1'']], [[DALIR|''DALIR'']], [[NONHSAT096369|''DANCR'']], [[NONHSAT099821|''DBET'']], [[NONHSAT035954|''DHRS4-AS1'']], [[NONHSAT033797|''DLEU1'']], [[NONHSAT033821|''DLEU2'']], [[Lnc-CHRAC1-2:1|''ERICD'']], [[ENST00000583516.1|''ESRG'']], [[Lnc-MTHFSD-2:1|''FENDRR'']], [[ENST00000427391.1|''FIRRE'']],[[Lnc-FOXC1-1:1|''FOXCUT'']], [[ENST00000602812.1|''FTX'']], [[GHET1|''GHET1'']], [[NONHSAT087920|''GHRLOS'']],  [[NONHSAT076558|''GPR1-AS'']], [[NONHSAT075638|''HAGLR'']], [[HEIH|''HEIH'']], [[JADDR|''JADRR'']], [[ENST00000604849.1|''KANTR'']], [[NONHSAT123382|''LINC-PINT'']], [[LINC00163|''LINC00163'']], [[NONHSAT087716|''LINC00312'']], [[LINC00850|''LINC00850'']], [[ENST00000412690.1|''LINC01191'']], [[LSINCT5|''LSINCT5'']], [[ENST00000511918.1|''LUCAT1'']], [[ENST00000574306.1|''MIR22HG'']], [[NONHSAT130385|''MIR31HG'']], [[ENST00000602580.1|''MIR99AHG'']], [[ENST00000531381.1|''MIR100HG'']], [[NONHSAT081499|''MIR155HG'']], [[ENST00000602507.1|''MIR222HG'']], [[ENST00000414769.1|''MIR503HG'']], [[ENST00000433810.1|''MYCNUT'']], [[ENST00000604258.1|''NAMA'']], [[ENST00000414795.1|''NRIR'']], [[ENST00000442621.1|''OVAAL'']], [[ENST00000608917.1|''PACERR'']], [[ENST00000506884.1|''PART-1'']], [[NONHSAT018635|''PAUPAR'']], [[ENST00000412654.1|''PCA3'']], [[ENST00000561978.1|''PCAT1'']], [[ENST00000504263.1|''PCAT4'']], [[ENST00000452148.2|''PCAT7'']], [[NONHSAT129019|''PRNCR1'']], [[ENST00000430058.1|''PTCSC2'']], [[ENST00000556013.2|''PTCSC3'']], [[ENST00000513868.2|''PVT1'']], [[NONHSAT040920|''PWRN1'']], [[NONHSAT040875|''PWRN2'']], [[RASSF1-AS1|''RASSF1-AS1'']], [[SCAANT1|''SCAANT1'']], [[NONHSAT075852|''SCHLAP1'']], [[ENST00000526269.2|''SENCR'']], [[ENST00000607033.1|''TARID'']], [[Lnc-HEATR6-1:4|''WFDC21P'']] ([[LncRNAWiki:Featured|see more]])
 
  
*<span style="color: red;">Small proteins</span>:Considering the potential functional significane of lncRNA-encoded small proteins(Anderson, D.M. et al.Cell,2015; Nelson, B.R. et al. Science, 2016), we developed computational approaches for automatic identification of small proteins in 105,823 human lncRNAs. As a result, we obtained '''9,390''' small proteins based on protein instability, secondary structure and transmembrane helix. Among the 9,390 small proteins, '''2,246''' transmembrane proteins are considered to be with high confidence. Accordingly, LncRNAWiki integrates all putative small proteins, their physical and chemical parameters, secondary structures, transmembrane helices and topology structures ([[LncRNAWiki:small peptides|lncRNAs and small proteins]], [[Help:Contents#Database content|help]]). We also provide download of all the information of predicted small proteins ([[LncRNAWiki:Download|see Downloads]]).
 
 
*BLAST lncRNAs: If a lncRNA is newly reported in a published paper but is not found in LncRNAWiki after [[Special:BLAST|BLAST]], please consider to create a new page for this lncRNA to obtain its authorship in LncRNAWiki. See [[LncRNAWiki:FAQ#Curation|here]] for help.
 
 
*Community curation: Community-curated efforts are quantified and rewarded by giving explicit authorship. Please share your expertise and perform curations to have the authorship for lncRNAs of your interest.
 
 
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|-
 
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<!-----------Data sources------------>
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<!-----------Disease------------>
 
|valign="top" style="border:1px solid #66B3FF; background-color:transparent; "|
 
|valign="top" style="border:1px solid #66B3FF; background-color:transparent; "|
<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;">Disease</div>
<div style="padding:0.5em 0.5em;">[[File:web1a.png|left|350px|caption]] In version1, 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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<div style="padding:0.5em 0.5em;">[[File:Statistics5.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.  
  
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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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]]).  
  
<span style="color: red;">In the newly updated version, 633 lncRNAs with publications were added and curated. These lncRNAs are mainly obtained from HGNC.In total, there are 719 featured lncRNAs in present database.</span>
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Among these 719 lncRNAs, 304 have been experimentally proved to be associated with cancer and other diseases ([[LncRNAWiki:Disease|Disease]]).
 +
 
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''Top diseases and top cancers, and the lncRNA numbers are listed.''
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|}
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<!--------------main part two---------------->
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{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"
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|-
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<!-----------Data source------------>
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|valign="top" style="border:1px solid #66B3FF; background-color:transparent;width:35%;"|
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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|center|350px|caption]]
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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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<br /></div>
  
 
<!-----------------Classification---------------------->
 
<!-----------------Classification---------------------->
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|valign="top" style="border:1px solid #66B3FF; background-color:transparent;width:40%;"|
 
 
<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>
<div style="padding:0.5em 0.5em;">
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<div style="padding:0.5em 0.5em;">[[File:web2a.png|center|400px]]
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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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 (Ma etal. 2013, RNA Biology). [[Help:Contents#Database content|''Help'']]
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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<br /></div>
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<!-----------------Small protein---------------------->
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|valign="top" style="border:1px solid #66B3FF; background-color:transparent;30%;"|
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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-2.png|center|367px]]
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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]]).
 +
<br /></div>
  
<br />
 
[[File:web2a.png|center|400px]]
 
</div>
 
 
|}
 
|}
  
<!--------------main part two---------------->
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<!--------------main part three---------------->
 
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"
 
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"
 
<!------------- Participating---------------->
 
<!------------- Participating---------------->
 
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<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</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;">How to Cite</div>
 
<div style="padding:0.5em 1em;">
 
<div style="padding:0.5em 1em;">
* Lina Ma, Vladimir B. Bajic, Zhang Zhang. [https://www.landesbioscience.com/journals/rnabiology/article/24604/?nocache=227993923 On the classification of long non-coding RNAs.] (2013) ''RNA Biology'', 10(6),924-933.
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If you use any data or information in your work, please cite the following primary publication:
* Lina Ma#, Ang Li#, Dong Zou, Xingjian Xu, Lin Xia, Jun Yu, Vladimir B. Bajic and Zhang Zhang. [http://nar.oxfordjournals.org/content/early/2014/11/15/nar.gku1167.full LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.] (2015) ''Nucleic Acids Research'', 43:D187-92.
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* Lina Ma, Ang Li, Dong Zou, Xingjian Xu, Lin Xia, Jun Yu, Vladimir B. Bajic and Zhang Zhang. [http://nar.oxfordjournals.org/content/early/2014/11/15/nar.gku1167.full '''LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs'''.] (2015) ''Nucleic Acids Research'', 43:D187-92.
 +
 
 +
Related publication:
 +
* BIG Data Center Members: [http://nar.oxfordjournals.org/content/early/2016/11/28/nar.gkw1060.full '''The BIG Data Center: from deposition to integration to translation'''.] ''Nucleic Acids Research'' 2017, accepted and in press.
 +
* Lina Ma, Vladimir B. Bajic, Zhang Zhang. [https://www.landesbioscience.com/journals/rnabiology/article/24604/?nocache=227993923 '''On the classification of long non-coding RNAs'''.] (2013) ''RNA Biology'', 10(6),924-933.
 
</div>
 
</div>
  

Revision as of 08:13, 21 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
Statistics5.png

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).

Top diseases and top cancers, and the lncRNA numbers are listed.

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

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 (Ma etal. 2013, RNA Biology). Help


Small protein
SmallPRO-2.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.
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