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|style="width:50%; text-align:center; white-space:nowrap; color:#000"|
 
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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|106,063]] human long non-coding RNAs inside</div>
  
 
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*[[:Category:Transcripts|LncRNA Transcripts]]
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*[[:Category:Transcripts|Transcripts]]
 +
*[[:Category:Genes|Genes]]
 
*[[LncRNAWiki:Classification|Classification]]
 
*[[LncRNAWiki:Classification|Classification]]
 
|style="width:18%;|
 
|style="width:18%;|
*[[:Category:Genes|Genes]]
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*[[LncRNAWiki:Featured|Featured LncRNAs]]
*[[Special:BLAST|BLAST]]
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*[http://bigd.big.ac.cn/lncbook/disease Disease]
 +
*[http://bigd.big.ac.cn/lncbook/function Function]
 
|style="width:18%;|
 
|style="width:18%;|
*[[LncRNAWiki:Download|Downloads]]
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*[[LncRNAWiki:Small_proteins|Small Proteins]]
*[[LncRNAWiki:FAQ|FAQ]]
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*[http://bigd.big.ac.cn/lgc Prediction]
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*[http://bigd.big.ac.cn/lncbook/blast BLAST]
*[[File:New5.png]][[LncRNAWiki:Featured|Featured LncRNAs]]
 
*[[File:New5.png]][[LncRNAWiki:small peptides|Small Proteins]]
 
 
|}
 
|}
 
 
<!---------------welcome Box----------------->
 
<!---------------welcome Box----------------->
 
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{{LncRNAWiki:Summary}}
 
{{LncRNAWiki:Summary}}
<div style="padding:0.2em 0.5em;text-align:center;font-weight:bold;color:#2d2d2d;">''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''</div>
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<div style="padding:0.2em 0.5em;text-align:center;color:#2d2d2d;"> ''LncRNAWiki, an important component of '' [http://bigd.big.ac.cn/lncbook '''LncBook'''], ''provides community annotations of human lncRNAs''</div>
 
</div>
 
</div>
----
+
|}
*<span style="color: red;">Featured lncRNAs</span>: A total of 633 lncRNAs with publications have been collected and curated in LncRNAWiki over the last two years, and there are 719 such lncRNAs in total in the present version. Among all these lncRNAs, more than 200 of them have been extensively studied, and most of which are found to be associated with cancer and many 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]]).
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<!--------------main part one---------------->
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{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"
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|-
  
*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.
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<!-----------Featured lncRNAs------------>
 +
|valign="top" style="border:1px solid #66B3FF; background-color:transparent;width:50%;"|
 +
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">[http://lncrna.big.ac.cn/index.php/LncRNAWiki:Featured Featured lncRNAs]</div>
 +
<div style="padding:0.5em 0.5em;">[[File:Featured-2019-3.png|center|500px|link=LncRNAWiki:Featured]]</div>
  
*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.  
+
|style="padding:0px 4px;"|
 +
 
 +
<!-----------Top 10 lncRNA-associated diseases------------>
 +
|valign="top" style="border:1px solid #66B3FF; background-color:transparent;"|
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<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Top 10  [http://bigd.big.ac.cn/lncbook/disease lncRNA-associated diseases]</div>
 +
 
 +
<div style="padding:0.5em 0.5em;">
 +
''Diseases and their associated lncRNAs' counts are listed below.''
 +
 
 +
* [http://bigd.big.ac.cn/lncbook/disease?filter=diseasemesh&term=Neoplasms Neoplasms]: 1,077
 +
 
 +
* [http://bigd.big.ac.cn/lncbook/disease?filter=diseasemesh&term=Digestive%20System%20Diseases Digestive System Diseases]: 427
 +
 
 +
* [http://bigd.big.ac.cn/lncbook/disease?filter=diseasemesh&term=Male%20Urogenital%20Diseases Male Urogenital Diseases]: 117
 +
 
 +
* [http://bigd.big.ac.cn/lncbook/disease?filter=diseasemesh&term=Female%20Urogenital%20Diseases%20and%20Pregnancy%20Complications Female Urogenital Diseases and Pregnancy Complications]: 196
 +
 
 +
* [http://bigd.big.ac.cn/lncbook/disease?filter=diseasemesh&term=Respiratory%20Tract%20Diseases Respiratory Tract Diseases]: 224
 +
 
 +
* [http://bigd.big.ac.cn/lncbook/disease?filter=diseasemesh&term=Skin%20and%20Connective%20Tissue%20Diseases Skin and Connective Tissue Diseases]: 165
 +
 
 +
* [http://bigd.big.ac.cn/lncbook/disease?filter=diseasemesh&term=Endocrine%20System%20Diseases Endocrine System Diseases]: 129
 +
 
 +
* [http://bigd.big.ac.cn/lncbook/disease?filter=diseasemesh&term=Cardiovascular%20Diseases Cardiovascular Diseases]: 155
 +
 
 +
* [http://bigd.big.ac.cn/lncbook/disease?filter=diseasemesh&term=Congenital,%20Hereditary,%20and%20Neonatal%20Diseases%20and%20Abnormalities Congenital, Hereditary, and Neonatal Diseases and Abnormalities]: 150
 +
 
 +
* [http://bigd.big.ac.cn/lncbook/disease?filter=diseasemesh&term=Nervous%20System%20Diseases Nervous System Diseases]: 103
 +
 
 +
</div>
 
|}
 
|}
  
<!--------------main part one---------------->
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<!--------------main part two---------------->
 
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"
 
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|-
 
|-
<!-----------Data sources------------>
 
|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>
 
<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.
 
  
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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<!-----------------Extensively curated---------------------->
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|valign="top" style="border:1px solid #66B3FF; background-color:transparent;width:50%;"|
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{|style="width:100%;"
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<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Extensively curated</div>
 +
 
 +
|style="width:33%;|
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* [[NONHSAT028508|''HOTAIR'']]
 +
 
 +
* [[ENST00000534336.1|''MALAT-1'']]
 +
 
 +
* [[NONHSAT017465|''H19'']]
 +
 
 +
* [[NONHSAT039745|''MEG3'']]
 +
 
 +
* [[ENST00000501122.2|''NEAT1'']]
  
<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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* [[ENST00000513868.2|''PVT1'']]
<br /></div>
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 +
* [[NONHSAT007663|''GAS5'']]
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 +
* [[Lnc-C9orf53-2:1|''CDKN2B-AS1'']]
 +
 
 +
* [[NONHSAT119717|''HOTTIP'']]
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 +
* [[NONHSAT113149|''7SK'']]
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 +
|style="width:33%;|
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* [[BANCR|''BANCR'']]
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 +
* [[BTG3-AS1|''BTG3-AS1'']]
 +
 
 +
* [[CERNA2|''CERNA2'']]
 +
 
 +
* [[FLICR|''FLICR'']]
 +
 
 +
* [[GUARDIN|''GUARDIN'']]
 +
 
 +
* [[LINC-ROR|''LINC-ROR'']]
 +
 
 +
* [[PINCR|''PINCR'']]
 +
 
 +
* [[PLUT|''PLUT'']]
 +
 
 +
* [[LUNAR1|''LUNAR1'']]
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 +
* [[Lnc-SRA1-1:1|''SRA'']]
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 +
|style="width:34%;|
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* [[NONHSAT017524|''KCNQ1OT1'']]
 +
 
 +
* [[NONHSAT076153|''PCGEM1'']]
 +
 
 +
* [[NONHSAT137541|''XIST'']]
 +
 
 +
* [[Lnc-EPCAM-1:2|''BCYRN1'']]
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 +
* [[NONHSAT084827|''TUG1'']]
 +
 
 +
* [[Lnc-OR10H5-1:1|''UCA1'']]
 +
 
 +
* [[NONHSAT107640|''HULC'']]
 +
 
 +
* [[NONHSAT129019|''PRNCR1'']]
 +
 
 +
* [[TP53COR1|''TP53COR1'']]
 +
 
 +
* [[Lnc-CDKN1A-1:1|''PANDAR'']]
 +
|}
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<!-----------------Function---------------------->
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<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">[http://bigd.big.ac.cn/lncbook/function Function]</div>
  
<!-----------------Classification---------------------->
 
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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="padding:0.5em 0.5em;">
 
<div style="padding:0.5em 0.5em;">
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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''Functional mechanisms and their associated lncRNAs' counts are listed below.''
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 />
+
 
 +
* [http://bigd.big.ac.cn/lncbook/function?filter=functionmec&term=transcriptional%20regulation Transcriptional regulation]: 282
 +
* [http://bigd.big.ac.cn/lncbook/function?filter=functionmec&term=ceRNA ceRNA]: 73
 +
* [http://bigd.big.ac.cn/lncbook/function?filter=functionmec&term=translational%20control Translational control]: 13
 +
* [http://bigd.big.ac.cn/lncbook/function?filter=functionmec&term=protein%20localization Protein localization]: 6
 +
* [http://bigd.big.ac.cn/lncbook/function?filter=functionmec&term=splicing%20regulation Splicing regulation]: 4
  
<br />
 
[[File:web2a.png|center|400px]]
 
 
</div>
 
</div>
 
|}
 
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<!------------- 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.
+
If you use any data or information in your work, please cite the following publications.
* 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.
+
 
</div>
+
Primary publication:
 +
* [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.
  
<!-------------Lab Information-------------->
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Related publication:
|style="padding:0px 4px;"|
+
* [https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.82 '''Community Curation and Expert Curation of Human Long Noncoding RNAs with LncRNAWiki and LncBook'''.] '' Curr Protoc Bioinformatics 2019''.
|valign="top" style="border:1px solid #66B3FF; background-color:transparent; width:33%"|
 
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">About Us</div>
 
<div style="padding:0.5em 1em;">Our group works in the field of [http://cbb.big.ac.cn Computational Biology and Bioinformatics] (CBB), currently with a particular focus on building biological knowledge wikis in aid of community curation of massive biological knowledge.
 
 
</div>
 
</div>
  

Latest revision as of 08:01, 16 September 2019



Welcome to LncRNAWiki
106,063 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.

LncRNAWiki, an important component of LncBook, provides community annotations of human lncRNAs
Featured-2019-3.png
Extensively curated

Functional mechanisms and their associated lncRNAs' counts are listed below.

How to Cite

If you use any data or information in your work, please cite the following publications.

Primary publication:

Related publication:

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