Difference between revisions of "Main Page"

Latest revision as of 10:38, 18 September 2021

Welcome to LncRNAWiki 1.0

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 lncRNAs

Top 10 lncRNA-associated diseases

Diseases and their associated lncRNAs' counts are listed below.

Hepatocellular cancer: 361

Colorectal cancer: 305

Lung cancer: 296

Breast cancer: 282

Oral squamous cell cancer: 234

Gastric cancer: 233

Prostate cancer: 213

B acute lymphoblastic leukemia with t(1;19)(q23;p13.3): 173

Papillary thyroid cancer: 157

Obesity: 151

Extensively curated

HOTAIR

MALAT-1

H19

MEG3

NEAT1

PVT1

GAS5

CDKN2B-AS1

HOTTIP

7SK

BANCR

BTG3-AS1

CERNA2

FLICR

GUARDIN

LINC-ROR

PINCR

PLUT

LUNAR1

SRA

KCNQ1OT1

PCGEM1

XIST

BCYRN1

TUG1

UCA1

HULC

PRNCR1

TP53COR1

PANDAR

Functional mechanism

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:

LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. (2015) Nucleic Acids Research, 43:D187-92.

Related publication:

Community Curation and Expert Curation of Human Long Noncoding RNAs with LncRNAWiki and LncBook. Curr Protoc Bioinformatics 2019.

Visitor Statistics

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 __NOTOC__
 __NOEDITSECTION__
 <!-----------------title--------------------->
 {|style="width:100%; margin-top:10px; background-color:#f6f6f6; border:1px solid #d2d2d2; margin-bottom: 10px;"
-|style="width:50%; text-align:center; white-space:nowrap; color:#000"|
+|style="width:40%; text-align:center; white-space:nowrap; color:#000"|
-<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 1.0</div>
-<div style="padding:0em; font-size:100%">[[:Category:Transcripts|105,824]] human long non-coding RNAs inside</div>
+<div style="padding:0em; font-size:100%">[[:Category:Transcripts|106,063]] human long non-coding RNAs inside</div>
-|style="width:18%;|
+|style="width:15%;|
-*[[:Category:Transcripts|LncRNA Transcripts]]
+*[[:Category:Transcripts|Transcripts]]
+*[[:Category:Genes|Genes]]
 *[[LncRNAWiki:Classification|Classification]]
-|style="width:18%;|
+|style="width:15%;|
-*[[:Category:Genes|Genes]]
+*[[LncRNAWiki:Featured|Featured LncRNAs]]
-*[[Special:BLAST|BLAST]]
+*[https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&biological_context=Disease Disease]
-|style="width:18%;|
+*[https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism= Function]
-*[[LncRNAWiki:Download|Downloads]]
+|style="width:15%;|
-*[[LncRNAWiki:FAQ|FAQ]]
+*[[LncRNAWiki:Small_proteins|Small Proteins]]
-|style="width:18%;|
+*[http://bigd.big.ac.cn/lgc Prediction]
-*[[File:New5.png]][[LncRNAWiki:Featured|Featured LncRNAs]]
+*[http://bigd.big.ac.cn/lncbook/blast BLAST]
-*[[File:New5.png]][[LncRNAWiki:Small_proteins|Small Proteins]]
+|style="width:15%;|
+<div style="padding:0.5em 0.5em;">[[File:News2.png|center|150px|link=https://ngdc.cncb.ac.cn/lncrnawiki/]]</div>
 |}
 <!---------------welcome Box----------------->
 {|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"
@@ Line 28: / Line 30: @@
 <div style="padding:1em 0.5em;">
 {{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>
+<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>
-----
+|}
-*<span style="color: red;">Featured lncRNAs</span>: 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, as of 28 June 2016, a total of 719 lncRNAs that are community-curated (the detailed list is available at [[LncRNAWiki:Featured|Featured LncRNAs]]). Moreover, among these 719 lncRNAs, 633 are newly reported in recent publications, while 289 have been experimentally proved to be associated with cancer and other diseases (e.g., [[BANCR|''BANCR'']]). Newly featured lncRNA:[[AATBC|''AATBC'']],[[ABALON|''ABALON'']], [[ENST00000444200.1|''APOA1-AS'']], [[NONHSAT121673|''APTR'']], [[BANCR|''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]])
+<!--------------main part one---------------->
+{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"
+|-
+<!-----------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:Homepage-2020.png|center|500px|link=LncRNAWiki:Featured]]</div>
+|style="padding:0px 4px;"|
+<!-----------Top 10 lncRNA-associated diseases------------>
+|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;">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
+* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&context_detail=oral%20squamous%20cell%20cancer Oral squamous cell cancer]: 234
+* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&context_detail=Gastric%20cancer Gastric cancer]: 233
+* [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
-*<span style="color: red;">Small proteins</span>:Considering the potential functional significance of lncRNA-encoded small proteins ([http://www.ncbi.nlm.nih.gov/pubmed/25640239 Anderson, D.M. et al. Cell, 2015]; [http://www.ncbi.nlm.nih.gov/pubmed/26816378 Nelson, B.R. et al. Science, 2016]), we developed computational approaches for identification of small proteins in 105,823 human lncRNAs. 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]]). 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.
+* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&context_detail=obesity Obesity]: 151
-*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.
+</div>
 |}
-<!--------------main part one---------------->
+<!--------------main part two---------------->
 {|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"
 |-
-<!-----------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]] <span style="color: red;">In the updated version, 633 lncRNAs reported by recent publications were added and curated. These lncRNAs are mainly obtained from HGNC. In total, there are 719 new featured lncRNAs in LncRNAWiki.</span>
+<!-----------------Extensively curated---------------------->
+|valign="top" style="border:1px solid #66B3FF; background-color:transparent;width:50%;"|
+{|style="width:100%;"
+<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%;|
+* [[NONHSAT028508|''HOTAIR'']]
+* [[ENST00000534336.1|''MALAT-1'']]
+* [[NONHSAT017465|''H19'']]
+* [[NONHSAT039745|''MEG3'']]
+* [[ENST00000501122.2|''NEAT1'']]
+* [[ENST00000513868.2|''PVT1'']]
+* [[NONHSAT007663|''GAS5'']]
+* [[Lnc-C9orf53-2:1|''CDKN2B-AS1'']]
+* [[NONHSAT119717|''HOTTIP'']]
+* [[NONHSAT113149|''7SK'']]
+|style="width:33%;|
+* [[BANCR|''BANCR'']]
+* [[BTG3-AS1|''BTG3-AS1'']]
+* [[CERNA2|''CERNA2'']]
+* [[FLICR|''FLICR'']]
+* [[GUARDIN|''GUARDIN'']]
+* [[LINC-ROR|''LINC-ROR'']]
+* [[PINCR|''PINCR'']]
+* [[PLUT|''PLUT'']]
+* [[LUNAR1|''LUNAR1'']]
+* [[Lnc-SRA1-1:1|''SRA'']]
+|style="width:34%;|
+* [[NONHSAT017524|''KCNQ1OT1'']]
+* [[NONHSAT076153|''PCGEM1'']]
+* [[NONHSAT137541|''XIST'']]
+* [[Lnc-EPCAM-1:2|''BCYRN1'']]
+* [[NONHSAT084827|''TUG1'']]
+* [[Lnc-OR10H5-1:1|''UCA1'']]
+* [[NONHSAT107640|''HULC'']]
+* [[NONHSAT129019|''PRNCR1'']]
+* [[TP53COR1|''TP53COR1'']]
+* [[Lnc-CDKN1A-1:1|''PANDAR'']]
+|}
-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.
+|style="padding:0px 4px;"|
-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].
+<!-----------------Function---------------------->
-<br /></div>
+|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;">[https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism= Functional mechanism]</div>
-<!-----------------Classification---------------------->
-|style="padding:0px 5px;"|
-|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="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 />
+''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 />
+* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism=ceRNA ceRNA]:	194
+* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism=Transcriptional%20regulation Transcriptional regulation]:	85
+* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism=Epigenetic%20regulation Epigenetic regulation]:	84
+* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism=Post-transcriptional%20regulation Post-transcriptional regulation]:	12
+* [https://ngdc.cncb.ac.cn/lncrnawiki/browse?flag=True&functional_mechanism=Translational%20regulation Translational regulation]:	2
-<br />
-[[File:web2a.png|center|400px]]
 </div>
 |}
-<!--------------main part two---------------->
+<!--------------main part three---------------->
 {|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"
 <!------------- Participating---------------->
-|valign="top" style="border:1px solid #66B3FF; background-color:transparent; width:42%"|
+|valign="top" style="border:1px solid #66B3FF; background-color:transparent; width:75%"|
-<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</div>
+<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;">
-* 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.（''If you use any data or information of LncRNAWiki in your work, please cite this paper.''）
+If you use any data or information in your work, please cite the following publications.
-* 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>
+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-------------->
+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>

Difference between revisions of "Main Page"

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