CLIPdb

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]