Mammalian ncRNA-disease repository: a global view of ncRNA-mediated disease network

Wang, Y; Chen, L; Chen, B; Li, X; Kang, Jisoo; Fan, Kaili; Hu, Yongfei; Xu, Jin; Yi, Lynn; Yang, Ji-Qin; Huang, Yan; Cheng, Lixin; Li, Yan Hui; Wang, C; Li, Ke-ying; Wang, D

doi:10.1038/cddis.2013.292

Cited by 84 publications

(54 citation statements)

References 8 publications

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“…The relevant hits were downloaded and prepared systematically for further manual data curation. Second, RAID v2.0 integrated diverse RNA-associated interactions from other 18 databases, including ChIPBase (10), LncRNA2Target (11), LncRNAdisease (7), miR2Disease (12), miRTarBase (13), MNDR (14), ncRDeathDB (8), NPInter (15), OncomiRDB (16), sRNATarBase (17), StarBase (6), TransmiR (18) and ViRBase (19) as well as five computational prediction databases (DroID (20), EIMMo (21), miRanda (22), miRDB (23) and TargetScan (9)).…”

Section: Data Collectionmentioning

confidence: 99%

RAID v2.0: an updated resource of RNA-associated interactions across organisms

et al. 2016

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With the development of biotechnologies and computational prediction algorithms, the number of experimental and computational prediction RNA-associated interactions has grown rapidly in recent years. However, diverse RNA-associated interactions are scattered over a wide variety of resources and organisms, whereas a fully comprehensive view of diverse RNA-associated interactions is still not available for any species. Hence, we have updated the RAID database to version 2.0 (RAID v2.0, www.rna-society.org/raid/) by integrating experimental and computational prediction interactions from manually reading literature and other database resources under one common framework. The new developments in RAID v2.0 include (i) over 850-fold RNA-associated interactions, an enhancement compared to the previous version; (ii) numerous resources integrated with experimental or computational prediction evidence for each RNA-associated interaction; (iii) a reliability assessment for each RNA-associated interaction based on an integrative confidence score; and (iv) an increase of species coverage to 60. Consequently, RAID v2.0 recruits more than 5.27 million RNA-associated interactions, including more than 4 million RNA–RNA interactions and more than 1.2 million RNA–protein interactions, referring to nearly 130 000 RNA/protein symbols across 60 species.

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Section: Data Collectionmentioning

confidence: 99%

RAID v2.0: an updated resource of RNA-associated interactions across organisms

et al. 2016

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“…In this work, we explored the known lncRNA-disease associations stored in the manually crated diverse ncRNA-disease repository (MNDR) [66] and LncRNADisease [12] database by adopting two validation frameworks of global LOOCV and 5-fold cross validation. Specifically, for the framework of global LOOCV, each known lncRNA-disease association was left out in turn for testing and other samples were used for training, and all the lncRNA-diseases without recorded association evidence were considered as candidate samples.…”

Section: Resultsmentioning

confidence: 99%

FMLNCSIM: fuzzy measure-based lncRNA functional similarity calculation model

et al. 2016

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Accumulating experimental studies have indicated the influence of lncRNAs on various critical biological processes as well as disease development and progression. Calculating lncRNA functional similarity is of high value in inferring lncRNA functions and identifying potential lncRNA-disease associations. However, little effort has been attempt to measure the functional similarity among lncRNAs on a large scale. In this study, we developed a Fuzzy Measure-based LNCRNA functional SIMilarity calculation model (FMLNCSIM) based on the assumption that functionally similar lncRNAs tend to be associated with similar diseases. The performance improvement of FMLNCSIM mainly comes from the combination of information content and the concept of fuzzy measure, which was applied to the directed acyclic graphs of disease MeSH descriptors. To evaluate the effectiveness of FMLNCSIM, we further combined it with the previously proposed model of Laplacian Regularized Least Squares for lncRNA-Disease Association (LRLSLDA). As a result, the integrated model, LRLSLDA-FMLNCSIM, achieve good performance in the frameworks of global LOOCV (AUCs of 0.8266 and 0.9338 based on LncRNADisease and MNDR database) and 5-fold cross validation (average AUCs of 0.7979 and 0.9237 based on LncRNADisease and MNDR database), which significantly improve the performance of previous classical models. It is anticipated that FMLNCSIM could be used for searching functionally similar lncRNAs and inferring lncRNA functions in the future researches.

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“…1 Currently, microRNAs (miRNAs) are the most studied type of ncRNAs, but novel classes of ncRNAs, such as long noncoding RNAs (lncRNAs) and snoRNAs, continue to be identified, and many studies have begun to focus on the role of ncRNA in programmed cell death. [2][3][4][5] Convincing evidence has been found for the involvement of microRNA, 6, 7 lncRNA 8 and snoRNA 3 in common cell death subroutines such as apoptosis and autophagy. Despite this progress, unsolved questions remain; for example, while the outline of protein crosstalk between different PCD subroutines is relatively well characterized, 9,10 To address these issues, we collected a large amount of published data describing the roles of diverse ncRNAs in PCD to develop and update the database ncRDeathDB (www.rna-society.org/ncrdeathdb) according to our previous miRDeathDB 11 Furthermore, based on this comprehensive repository, we implemented several bioinformatics network techniques to systematically analyze the hierarchical and topologic characteristics of the ncRNA-mediated cell death system (Fig.…”

Section: Introductionmentioning

confidence: 98%

ncRDeathDB: A comprehensive bioinformatics resource for deciphering network organization of the ncRNA-mediated cell death system

Huang

Kang

et al. 2015

Autophagy

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Programmed cell death (PCD) is a critical biological process involved in many important processes, and defects in PCD have been linked with numerous human diseases. In recent years, the protein architecture in different PCD subroutines has been explored, but our understanding of the global network organization of the noncoding RNA (ncRNA)-mediated cell death system is limited and ambiguous. Hence, we developed the comprehensive bioinformatics resource (ncRDeathDB, www.rna-society.org/ncrdeathdb ) to archive ncRNA-associated cell death interactions. The current version of ncRDeathDB documents a total of more than 4600 ncRNA-mediated PCD entries in 12 species. ncRDeathDB provides a user-friendly interface to query, browse and manipulate these ncRNA-associated cell death interactions. Furthermore, this resource will help to visualize and navigate current knowledge of the noncoding RNA component of cell death and autophagy, to uncover the generic organizing principles of ncRNA-associated cell death systems, and to generate valuable biological hypotheses.

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Mammalian ncRNA-disease repository: a global view of ncRNA-mediated disease network

Cited by 84 publications

References 8 publications

RAID v2.0: an updated resource of RNA-associated interactions across organisms

RAID v2.0: an updated resource of RNA-associated interactions across organisms

FMLNCSIM: fuzzy measure-based lncRNA functional similarity calculation model

ncRDeathDB: A comprehensive bioinformatics resource for deciphering network organization of the ncRNA-mediated cell death system

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