Difference between revisions of "Main Page"

From LncRNAWiki
Jump to: navigation, search
 
(177 intermediate revisions by 2 users not shown)
Line 2: Line 2:
 
__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
 +
 
<!-----------------title--------------------->
 
<!-----------------title--------------------->
 
{|style="width:100%; margin-top:10px; background-color:#f6f6f6; border:1px solid #d2d2d2; margin-bottom: 10px;"
 
{|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:50%; 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</div>
<div style="padding:0em; font-size:100%">[[Special:Categories|105,256]] 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:18%;|
*<span class=plainlinks>[[:Category:Genes|Genes]]</span>
+
*[[:Category:Transcripts|Transcripts]]
*[[RiceWiki:GeneFamilies|Gene Families]]
+
*[[:Category:Genes|Genes]]
 +
*[[LncRNAWiki:Classification|Classification]]
 
|style="width:18%;|
 
|style="width:18%;|
*[[RiceWiki:Databases|Databases]]
+
*[[LncRNAWiki:Featured|Featured LncRNAs]]
*[[Special:ListUsers|Registered Users]]
+
*[http://bigd.big.ac.cn/lncbook/disease Disease]
 +
*[http://bigd.big.ac.cn/lncbook/function Function]
 
|style="width:18%;|
 
|style="width:18%;|
*[[RiceWiki:Templates|Templates]]
+
*[[LncRNAWiki:Small_proteins|Small Proteins]]
--->
+
*[http://bigd.big.ac.cn/lgc Prediction]
 +
*[http://bigd.big.ac.cn/lncbook/blast BLAST]
 
|}
 
|}
 
 
<!---------------welcome Box----------------->
 
<!---------------welcome Box----------------->
 
{|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%;"
 
|valign="top" style="border:1px solid #c6c6c6; background-color:transparent; width:100%;"|
 
|valign="top" style="border:1px solid #c6c6c6; background-color:transparent; width:100%;"|
 
<div style="background:#f1f1f1; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Introduction</div>
 
<div style="background:#f1f1f1; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Introduction</div>
<div style="padding:0.5em 0.5em;">LncRNAWiki is a wiki-based database for management of human lncRNAs, aiming to harness collective intelligence to collect, edit, and annotate information about human lncRNAs. This database is a publicly editable and open-content platform for community curation of human lncRNAs, bearing the potential to become a comprehensive and up-to-date knowledgebase for human lncRNAs.
+
<div style="padding:1em 0.5em;">
 +
{{LncRNAWiki:Summary}}
 +
<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>
 +
|}
 +
 
 +
<!--------------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:Featured-2019-3.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  [http://bigd.big.ac.cn/lncbook/disease lncRNA-associated diseases]</div>
  
A featured lncRNA, [[ENST00000534336.1]], that is overexpressed in many kinds of cancers and is closely associated with tumor growth and metastasis, is community-curated.
 
</div>
 
----
 
 
<div style="padding:0.5em 0.5em;">
 
<div style="padding:0.5em 0.5em;">
{|
+
''Diseases and their associated lncRNAs' counts are listed below.''
|
+
 
If a lncRNA is newly reported in a published paper or is annotated in a lncRNA database and this lncRNA is found not to be included by the present LncRNAWiki dataset after search, users can create a new page for this lncRNA.[[LncRNAWiki:FAQ#Curation|'''''Help''''']]  
+
* [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
  
For example, [[LUNAR1]], the recently discovered lncRNA, which is Notch-regulated and functions to enhance IGF1R (insulin-like growth factor receptor 1) mRNA expression to maintain human T cell acute lymphoblastic leukemia (T-ALL), has been added to LncRNAWiki.
+
* [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>
 
</div>
 
|}
 
|}
  
<!--------------main part one---------------->
+
<!--------------main part two---------------->
 
{|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%;"
 
|-
 
|-
<!-----------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]] 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 at most 103 lncRNAs have been functionally annotated to date, indicating a long-term process of human lncRNA annotation.
 
<br /></div>
 
  
<!-----------------Classification---------------------->
+
<!-----------------Extensively curated---------------------->
|style="padding:0px 5px;"|
+
|valign="top" style="border:1px solid #66B3FF; background-color:transparent;width:50%;"|
|valign="top" style="border:1px solid #66B3FF; background-color:transparent;width:40%;"|
+
{|style="width:100%;"
<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;">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'']]
 +
|}
 +
 
 +
|style="padding:0px 4px;"|
 +
 
 +
<!-----------------Function---------------------->
 +
|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;">[http://bigd.big.ac.cn/lncbook/function Function]</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 />
+
''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>
 
|}
 
|}
  
<!--------------main part two---------------->
+
<!--------------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---------------->
|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;">
 
<div style="padding:0.5em 1em;">
* [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.
</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>
 
</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:

Visitor Statistics