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Welcome to LncRNAWiki 105,824 human long non-coding RNAs inside

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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 Featured lncRNAs: 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 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). Newly featured lncRNA:AATBC,ABALON, APOA1-AS, APTR, BANCR, BDNF-AS, BLACAT1, BPESC1, CAHM, CASC8, CCAT1, CCAT2,CISTR, CRNDE, CYYR1-AS1, DALIR, DANCR, DBET, DHRS4-AS1, DLEU1, DLEU2, ERICD, ESRG, FENDRR, FIRRE,FOXCUT, FTX, GHET1, GHRLOS, GPR1-AS, HAGLR, HEIH, JADRR, KANTR, LINC-PINT, LINC00163, LINC00312, LINC00850, LINC01191, LSINCT5, LUCAT1, MIR22HG, MIR31HG, MIR99AHG, MIR100HG, MIR155HG, MIR222HG, MIR503HG, MYCNUT, NAMA, NRIR, OVAAL, PACERR, PART-1, PAUPAR, PCA3, PCAT1, PCAT4, PCAT7, PRNCR1, PTCSC2, PTCSC3, PVT1, PWRN1, PWRN2, RASSF1-AS1, SCAANT1, SCHLAP1, SENCR, TARID, WFDC21P (see more) Small proteins:Considering the potential functional significance of lncRNA-encoded small proteins (Anderson, D.M. et al. Cell, 2015; 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 (lncRNAs and small proteins, 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) and also publicly available at Downloads. Expanding LncRNAWiki by this information provides a very new quality for lncRNA researchers. 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 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. 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. The majority of the lncRNA information was initially seeded with a subset of information from GENCODE, NONCODE, LNCipedia, and lncRNAdb.

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

How to Cite If you use any data or information in your work, please cite the following primary publication: Lina Ma, Ang Li, Dong Zou, Xingjian Xu, Lin Xia, Jun Yu, Vladimir B. Bajic and Zhang Zhang. LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. (2015) Nucleic Acids Research, 43:D187-92. Related publication: Lina Ma, Vladimir B. Bajic, Zhang Zhang. On the classification of long non-coding RNAs. (2013) RNA Biology, 10(6),924-933.

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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