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. 2019 Jan 8;47(D1):D121-D127.
doi: 10.1093/nar/gky1144.

LncACTdb 2.0: An Updated Database of Experimentally Supported ceRNA Interactions Curated From Low- And High-Throughput Experiments

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Free PMC article

LncACTdb 2.0: An Updated Database of Experimentally Supported ceRNA Interactions Curated From Low- And High-Throughput Experiments

Peng Wang et al. Nucleic Acids Res. .
Free PMC article

Abstract

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.

Figures

Figure 1.
Figure 1.
Content and interface of LncACTdb 2.0. The left panel is the database content which including ceRNA information identified from low- and high-throughput experiments. The right panel is the user interface of LncACTdb 2.0. In this panel, the Search, Browse, Blast and LncACTBrowser models provide flexible ways to access the dataset. The online tools including LncACT-Function, LncACT-Survival, LncACT-Network and LncACT-Get have been developed to perform customized analysis and data visualization.
Figure 2.
Figure 2.
Case study and workflow of using LncACTdb 2.0. (A) The interface of the search module with an example of MALAT1. (B) The search results of MALAT1, including both predicted and experimentally supported dataset. (C) Search result page with detail information. (D) The browse interface of LncACTdb 2.0. (E) Functional analysis of MALAT1 based on context of GO terms, pathways and cancer hallmarks. (F) Survival analysis and Kaplan–Meier survival curves for MALAT1-associating ceRNAs. (G) A global view of all possible related ceRNA interactions for MALAT1. (H) The LncACT-Get tool implements an integrated pipeline to identify functional ceRNA interactions according to customized data. (I) The Hot points page provides a human body map and the most studied items by other researchers. (J) The BLAST interface implements a customized sequencing search to identify related ceRNAs. (K) The LncACTBrowser which provides comprehensive genomic information of MALAT1, including reference sequence, transcripts, miRNA-binding sites and CLIP-seq peaks.

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