Difference between revisions of "Main Page"

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{|style="width:100%; margin-top:10px; background-color:#f6f6f6; border:1px solid #d2d2d2; margin-bottom: 10px;"
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<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to LncRNAWiki</div>
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<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to LncRNAWiki 1.0</div>
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<div style="padding:0em; font-size:100%">[[:Category:Transcripts|105,257]] 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]]
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*[[:Category:Genes|Genes]]
 
*[[LncRNAWiki:Classification|Classification]]
 
*[[LncRNAWiki:Classification|Classification]]
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|style="width:15%;|
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*[[:Category:Genes|Genes]]
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*[[LncRNAWiki:Featured|Featured LncRNAs]]
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*[[Special:BLAST|BLAST]]
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*[https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&biological_context=Disease Disease]
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*[https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism= Function]
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*[[LncRNAWiki:Download|Downloads]]
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*[[LncRNAWiki:FAQ|FAQ]]
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*[[LncRNAWiki:Small_proteins|Small Proteins]]
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*[http://bigd.big.ac.cn/lgc Prediction]
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*[http://bigd.big.ac.cn/lncbook/blast BLAST]
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<div style="padding:0.5em 0.5em;">[[File:News2.png|center|150px|link=https://ngdc.cncb.ac.cn/lncrnawiki/]]</div>
 
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<!---------------welcome Box----------------->
 
<!---------------welcome Box----------------->
 
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{{LncRNAWiki:Summary}}
 
{{LncRNAWiki:Summary}}
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<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>
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----
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|}
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*Featured lncRNAs: [[ENST00000534336.1|''MALAT-1'']], [[LUNAR1|''LUNAR1'']], [[NONHSAT028508|''HOTAIR'']], [[NONHSAT137541|''Xist'']], [[ENST00000609176.1|''Air'']], [[ENST00000501122.2|''NEAT1'']], [[NONHSAT017524|''Kcnq1ot1'']], [[NONHSAT119717|''HOTTIP'']], [[Lnc-DLX5-3:1|''Evf2'']]  ([[LncRNAWiki:Featured|see more]])
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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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|-
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<!-----------Featured lncRNAs------------>
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|valign="top" style="border:1px solid #66B3FF; background-color:transparent;width:50%;"|
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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://lncrna.big.ac.cn/index.php/LncRNAWiki:Featured Featured lncRNAs]</div>
 +
<div style="padding:0.5em 0.5em;">[[File:Homepage-2020.png|center|500px|link=LncRNAWiki:Featured]]</div>
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|style="padding:0px 4px;"|
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<!-----------Top 10 lncRNA-associated diseases------------>
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|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  [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&biological_context=Disease lncRNA-associated diseases]</div>
 +
 
 +
<div style="padding:0.5em 0.5em;">
 +
''Diseases and their associated lncRNAs' counts are listed below.''
 +
* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&context_detail=hepatocellular%20cancer Hepatocellular cancer]: 361
 +
 
 +
* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&context_detail=colorectal%20cancer Colorectal cancer]: 305
 +
 
 +
* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&context_detail=lung%20cancer Lung cancer]: 296
 +
 
 +
* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&context_detail=breast%20cancer Breast cancer]: 282
  
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*Newly curated lncRNAs: [[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|''CCAT-1'']], [[CCAT2|''CCAT2'']],[[NONHSAT028496|''CISTR'']], [[Lnc-IRX3-4:2|''CRNDE'']],  [[ENST00000357401.3|''CYYR1-AS1'']], [[DALIR|''DALIR'']], [[NONHSAT096369|''DANCR'']], [[NONHSAT099821|''DBE-T'']], [[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|''JADDR'']], [[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|''MIG403HG'']], [[ENST00000433810.1|''MYCNUT'']], [[ENST00000604258.1|''NAMA'']], [[ENST00000414795.1|''NRIR'']], [[ENST00000442621.1|''OVAAL'']], [[ENST00000608917.1|''PACER'']], [[ENST00000506884.1|''PART-1'']], [[NONHSAT018635|''PAUPAR'']], [[ENST00000412654.1|''PCA3'']], [[ENST00000561978.1|''PCAT-1'']], [[ENST00000504263.1|''PCAT4'']], [[ENST00000452148.2|''PACT7'']], [[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'']]
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* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&context_detail=oral%20squamous%20cell%20cancer Oral squamous cell cancer]: 234
  
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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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* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&context_detail=Gastric%20cancer Gastric cancer]: 233
  
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*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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* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&context_detail=prostate%20cancer Prostate cancer]: 213
 +
 
 +
* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&context_detail=b%20acute%20lymphoblastic%20leukemia%20with%20t B acute lymphoblastic leukemia with t(1;19)(q23;p13.3)]: 173
 +
 
 +
* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&context_detail=papillary%20thyroid%20cancer Papillary thyroid cancer]: 157
 +
 
 +
* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&context_detail=obesity Obesity]: 151
 +
 
 +
 
 +
</div>
 
|}
 
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<!--------------main part one---------------->
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<!-----------Data sources------------>
 
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|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;">Data sources</div>
 
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<div style="padding:0.5em 0.5em;">[[File:web1a.png|left|350px|caption]] 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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<br /></div>
 
  
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<!-----------------Classification---------------------->
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<!-----------------Extensively curated---------------------->
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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;">Classification</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;">Extensively curated</div>
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|style="width:33%;|
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* [[NONHSAT028508|''HOTAIR'']]
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* [[ENST00000534336.1|''MALAT-1'']]
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* [[NONHSAT017465|''H19'']]
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* [[NONHSAT039745|''MEG3'']]
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 +
* [[ENST00000501122.2|''NEAT1'']]
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* [[ENST00000513868.2|''PVT1'']]
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* [[NONHSAT007663|''GAS5'']]
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* [[Lnc-C9orf53-2:1|''CDKN2B-AS1'']]
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* [[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'']]
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* [[CERNA2|''CERNA2'']]
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* [[FLICR|''FLICR'']]
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* [[GUARDIN|''GUARDIN'']]
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* [[LINC-ROR|''LINC-ROR'']]
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* [[PINCR|''PINCR'']]
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* [[PLUT|''PLUT'']]
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* [[LUNAR1|''LUNAR1'']]
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* [[Lnc-SRA1-1:1|''SRA'']]
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|style="width:34%;|
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* [[NONHSAT017524|''KCNQ1OT1'']]
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* [[NONHSAT076153|''PCGEM1'']]
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* [[NONHSAT137541|''XIST'']]
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* [[Lnc-EPCAM-1:2|''BCYRN1'']]
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* [[NONHSAT084827|''TUG1'']]
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* [[Lnc-OR10H5-1:1|''UCA1'']]
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* [[NONHSAT107640|''HULC'']]
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* [[NONHSAT129019|''PRNCR1'']]
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* [[TP53COR1|''TP53COR1'']]
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* [[Lnc-CDKN1A-1:1|''PANDAR'']]
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|}
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<!-----------------Function---------------------->
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|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;">[https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism= Functional mechanism]</div>
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<div style="padding:0.5em 0.5em;">
 
<div style="padding:0.5em 0.5em;">
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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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''Functional mechanisms and their associated lncRNAs' counts are listed below.''
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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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* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism=ceRNA ceRNA]: 194
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* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism=Transcriptional%20regulation Transcriptional regulation]: 85
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* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism=Epigenetic%20regulation Epigenetic regulation]: 84
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* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism=Post-transcriptional%20regulation Post-transcriptional regulation]: 12
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* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism=Translational%20regulation Translational regulation]: 2
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<br />
 
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[[File:web2a.png|center|400px]]
 
 
</div>
 
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<!--------------main part three---------------->
 
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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;">
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* 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 publications.
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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.] (2014) ''Nucleic Acids Research''. doi:10.1093/nar/gku1167.
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</div>
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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.
  
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<!-------------Lab Information-------------->
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Related publication:
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* [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''.
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<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">About Us</div>
 
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<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 10:38, 18 September 2021



Welcome to LncRNAWiki 1.0
106,063 human long non-coding RNAs inside
News2.png
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
Homepage-2020.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:

Visitor Statistics

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