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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|105,257]] human long non-coding RNAs inside</div>
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<div style="padding:0em; font-size:100%">[[:Category:Transcripts|105,823]] human long non-coding RNAs inside</div>
  
 
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*<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;">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 105,255 human lncRNAs. As a result, we obtained '''9,304''' small proteins based on protein instability, secondary structure and transmembrane helix. Among the 9,304 small proteins, '''2,213''' 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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*<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.
 
*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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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].
 
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].
  
<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 such lncRNAs in present database.</span>
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<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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Revision as of 07:27, 29 June 2016


Welcome to LncRNAWiki
105,823 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

  • Small proteins: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 (lncRNAs and small proteins, help). We also provide download of all the information of predicted small proteins (see Downloads).
  • BLAST lncRNAs: If a lncRNA is newly reported in a published paper but is not found in LncRNAWiki after BLAST, please consider to create a new page for this lncRNA to obtain its authorship in LncRNAWiki. See 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.
Data sources
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 GENCODE, NONCODE, LNCipedia, and lncRNAdb.

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.


Classification

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).
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


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Publications
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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