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CLIPdb specifications

Information


Unique identifier OMICS_07446
Name CLIPdb
Restrictions to use None
Database management system MySQL
Version 1.0
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainer


  • person_outline Zhi John Lu

Publication for CLIPdb

CLIPdb citations

 (5)
library_books

LncRNA OIP5 AS1 is overexpressed in undifferentiated oral tumors and integrated analysis identifies as a downstream effector of stemness associated transcription factors

2018
Sci Rep
PMCID: 5935738
PMID: 29728583
DOI: 10.1038/s41598-018-25451-3

[…] formed and retrieved from TargetScan, miRanda, miRcode, Starbase and DIANA online prediction tools. For prediction of RNA-RNA interactions and RNA-RNA binding protein (RBPs) interaction, IntaRNA, and CLIPdb online tools were employed. Individual study for assessment of the association of miRNAs in various human cancers was collected from public databases PubMed using MeSH terms such as miRNA/lncRN […]

library_books

Distinct and Modular Organization of Protein Interacting Sites in Long Non coding RNAs

2018
Front Mol Biosci
PMCID: 5893854
PMID: 29670884
DOI: 10.3389/fmolb.2018.00027

[…] T1 is highly conserved amongst mammals and is known to be localized in nucleus. We plotted the binding sites for all RBPs to the full-length of MALAT1 transcripts and the same is shown in Figure for ClipDB-CIMS, CLIPdb-CITS, and CLIPdb-Piranha-stranded datasets. We combined all the datasets for each protein within a database and divided them into three classes (Cytoplasmic, Nuclear, or Both) base […]

library_books

uvCLAP is a fast and non radioactive method to identify in vivo targets of RNA binding proteins

2018
Nat Commun
PMCID: 5861125
PMID: 29559621
DOI: 10.1038/s41467-018-03575-4

[…] ter resembled the consensus motif AYUAAY identified from highly expressed PAR-CLIP read clusters (Fig. ).We next compared uvCLAP QKI binding sites with sites derived from QKI PAR-CLIP (retrieved from CLIPdb; peaks were called by PARalyzer). JAMM produces two sets of peaks: a full set of peaks containing also small peaks and peaks with few reads, and a smaller, filtered set where these peaks are re […]

library_books

m6AVar: a database of functional variants involved in m6A modification

2017
Nucleic Acids Res
PMCID: 5753261
PMID: 29036329
DOI: 10.1093/nar/gkx895

[…] ranscriptome-wide prediction based on Random Forest algorithm. To identify the potential roles of m6A-associated variants in post-transcriptome regulation, the RBP binding sites from starBase2 () and CLIPdb () (), the miRNA–RNA interactions from starBase2 and the canonical splice sites (GT-AG) from Ensembl annotations were collected. In addition, we obtained a large number of disease-associated SN […]

library_books

LncRNA profile study reveals four lncRNA signature associated with the prognosis of patients with anaplastic gliomas

2016
Oncotarget
PMCID: 5363582
PMID: 27764782
DOI: 10.18632/oncotarget.12624

[…] GSEA showed that the differential expressed genes were enriched in hypoxia, apoptosis and p53 pathway (Figure ). We further explored the interaction properties with proteins of the four lncRNAs using CLIPdb and starBase V2.0 (Table ). AGO2 can play a role of RNA interference by encoding a member of argonaute family of proteins [] and it predictively interacted with TPT1-AS1 and MIR155HG. It is rep […]

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CLIPdb institution(s)
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China

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