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Protocols

NPInter specifications

Information


Unique identifier OMICS_02786
Name NPInter
Alternative name Noncoding RNAs and Protein related biomacromolecules Interaction
Restrictions to use None
Database management system MySQL
Data access File download, Browse
User data submission Allowed
Version 3.0
Maintained No

Taxon


  • Bacteria
    • Escherichia coli
  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainers


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Publications for Noncoding RNAs and Protein related biomacromolecules Interaction

NPInter citations

 (9)
library_books

LPI NRLMF: lncRNA protein interaction prediction by neighborhood regularized logistic matrix factorization

2017
Oncotarget
PMCID: 5732780
PMID: 29262614
DOI: 10.18632/oncotarget.21934

[…] in interactions by using interaction data between RNAs and proteins instead of using ncRNA-protein interaction data, which would bias the predictions. (2) Most of the experimental data comes from the NPInter database, which is currently the best database for storing lncRNA and protein data, but the latest NPInter only provides gene-protein interactions corresponding to relevant lncRNAs rather than […]

library_books

Non Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non Invasive Diagnostic Tools

2016
Genes
PMCID: 5295003
PMID: 28035947
DOI: 10.3390/genes8010008

[…] nting out the importance of an integrated bioinformatics analysis of potential interaction partners for a tissue and disease-specific functional characterization of lncRNAs. Popular databases such as NPInter [], the Protein Data Bank (PDB) [] and Nucleic Acid Database (NDB) [] include information about the experimental determined structure of proteins and nucleic acids as well as RNA-protein compl […]

call_split

A childhood acute lymphoblastic leukemia genome wide association study identifies novel sex specific risk variants

2016
PMCID: 5120913
PMID: 27861356
DOI: 10.1097/MD.0000000000005300
call_split See protocol

[…] ined the Swiss Regulon browser.[] Gene set enrichment analysis (GSEA) was performed using DAVID v6.7.[] The interactions of candidate genes with other genes and noncoding RNAs were investigated using NPinter v3.0,[] which provides experimental data. Computational miRNA targets on protein-coding genes were explored using TargetScan.[] To map the HLA-DQA1 SNPs to HLA-DQA1 types, we examined complete […]

library_books

Long non coding RNA Databases in Cardiovascular Research

2016
PMCID: 4996844
PMID: 27049585
DOI: 10.1016/j.gpb.2016.03.001

[…] n, ChIPBase contains information on TFs that regulate the expression of non-coding genes. In the next step, the interactions of lncRNAs with other biomolecules may be examined by using starBase and NPInter . These databases provide experimentally-validated data on interactions with proteins, DNA, and other RNA types, especially miRNAs. Finally, genomic variations within the lncRNA gene sequence […]

library_books

A Bipartite Network based Method for Prediction of Long Non coding RNA–protein Interactions

2016
PMCID: 4792848
PMID: 26917505
DOI: 10.1016/j.gpb.2016.01.004

[…] ithms, similar to the item-based collaborative filtering method . The performance evaluation is based on leave-one-out cross validation (LOOCV) of the known lncRNA–protein interactions extracted from NPInter . To further demonstrate the effectiveness of lncRNA–protein bipartite network, six lncRNAs were used to evaluate the performance of LPBNI in comparison with the existing methods, lncPro and […]

library_books

Impact of microRNA 130a on the neutrophil proteome

2015
BMC Immunol
PMCID: 4659159
PMID: 26608132
DOI: 10.1186/s12865-015-0134-8

[…] n probability by mapping to RAIN [http://rth.dk/resources/rain/] via the STRING 10 alias file. For miRNA target identification, RAIN incorporates experimentally supported interactions (miRTarBase [], NPInter [], StarBase []), miRNA and mRNA co-occurrence-based text mining of Medline abstracts [], as well as processed miRNA target predictions from the prediction algorithms TargetScan [], PicTar [], […]

Citations

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NPInter institution(s)
Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computing Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
NPInter funding source(s)
Supported by National Natural Science Foundation of China (No. 31520103905, 31371320, 31401119) and National High Technology Research and Development Program (‘863’ Program) of China (No. 2015AA020108, 2014AA021103, 2014AA021502); Training Program of the Major Research Plan of the National Natural Science Foundation of China (No. 91229120); Chinese Academy of Science Strategic Project of Leading Science and Technology (No. XDA01020402).

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