LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments | Zendy

Peng Wang | Zendy; Xin Li | Zendy; Yue Gao | Zendy; Qiuyan Guo | Zendy; Yanxia Wang | Zendy; Ying Fang | Zendy; Xueyan Ma | Zendy; Hui Zhi | Zendy; Dianshuang Zhou | Zendy; Weitao Shen | Zendy; Weisha Liu | Zendy; Lihua Wang | Zendy; Yunpeng Zhang | Zendy; Shangwei Ning | Zendy; Xia Li | Zendy

Open Access

LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments

Author(s) -

Peng Wang,

Xin Li,

Yue Gao,

Qiuyan Guo,

Yanxia Wang,

Ying Fang,

Xueyan Ma,

Hui Zhi,

Dianshuang Zhou,

Weitao Shen,

Weisha Liu,

Lihua Wang,

Yunpeng Zhang,

Shangwei Ning,

Xia Li

Publication year - 2018

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gky1144

Subject(s) - competing endogenous rna , biology , interface (matter) , computational biology , database , computer science , bioinformatics , gene , genetics , pulmonary surfactant , rna , biochemistry , gibbs isotherm , long non coding rna

We describe LncACTdb 2.0 (http://www.bio-bigdata.net/LncACTdb/), an updated and significantly expanded database which provides comprehensive information of competing endogenous RNAs (ceRNAs) in different species and diseases. We have updated LncACTdb 2.0 with more data and several new features, including (i) manually curating 2663 experimentally supported ceRNA interactions from >5000 published literatures; (ii) expanding the scope of the database up to 23 species and 213 diseases/phenotypes; (iii) curating more ceRNA types such as circular RNAs and pseudogenes; (iv) identifying and scoring candidate lncRNA-associated ceRNA interactions across 33 cancer types from TCGA data; (v) providing illustration of survival, network and cancer hallmark information for ceRNAs. Furthermore, several flexible online tools including LncACT-Get, LncACT-Function, LncACT-Survival, LncACT-Network and LncACTBrowser have been developed to perform customized analysis, functional analysis, survival analysis, network illustration and genomic visualization. LncACTdb 2.0 also provides newly designed, user-friendly web interfaces to search, browse and download all the data. The BLAST interface is convenient for users to query dataset by inputting custom sequences. The Hot points interface provides users the most studied items by others. LncACTdb 2.0 is a continually updated database and will serve as an important resource to explore ceRNAs in physiological and pathological processes.

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