Tool:Pan-Cancer Analysis And Networks Of LncRNAs, MiRNAs, circRNAs, CeRNAs And RNA-Binding Proteins From TCGA 32 Cancer Types and CLIP-seq data
We had released
to decipher Pan-Cancer Interaction Networks of lncRNAs, miRNAs, circRNAs, competing endogenous RNAs (ceRNAs) and RNA-binding proteins (RBPs) by mining clinical and expression profiles of TCGA 32 cancer types ( starBase v3.0 Pan-Cancer Analysis and Networks Platform ~10,000 RNA-seq and ~9,900 miRNA-seq samples) and hundreds of CLIP-Seq (PAR-CLIP, HITS-CLIP, iCLIP, CLASH), degradome-seq, RNA-RNA interactome datasets on the starBase platform ( http://starbase.sysu.edu.cn/).
Pan-Cancer Analysis website: http://starbase.sysu.edu.cn/panCancer.php
starBase platform provides the following
Pan-Cancer and Interaction Analysis Services:
starBase generated Pan-Cancer networks of CLIP-Se q experimentally supported
and miRNA-lncRNA interactions. miRNA-mRNA starBase identified
involving lncRNAs and mRNAs. Pan-Cancer ceRNA networks starBase firstly provided Pan-Cancer maps of interactions between
and RNAs(lncRNAs, mRNAs). RNA-binding proteins (RBPs) starBase provided Pan-Cancer
. Differential Expression of lncRNAs, mRNAs, ncRNAs starBase provided Pan-Cancer
. Survival Analysis of of lncRNAs, mRNAs, ncRNAs starBase provided Pan-Cancer
. Target CoExpression of lncRNAs, mRNAs, ncRNAs starBase provided Pan-Cancer
. miRNA Differential Expression starBase provided Pan-Cancer
. miRNA Survival Analysis starBase provided Pan-Cancer
. miRNA-Target CoExpression
starBase v3.0 Pan-Cancer Analysis:
starBase paper is available at (1) and
http://nar.oxfordjournals.org/content/42/D1/D92.full (2) http://nar.oxfordjournals.org/content/39/suppl_1/D202.full
How can I download Pan-Cancer data (14 cancer types) of miRNA-lncRNA, protein-lncRNA, competing endogenous RNA (ceRNA) pairs from your website.
An invited paper described protein-lncRNA interactions has been published in
We released starBase
to decode interaction between lncRNAs and RNA-binding proteins (RBPs) by mining 111 CLIP-Seq (PAR-CLIP, HITS-CLIP, iCLIP, CLASH) datasets. RBP-lncRNA Platform
RBP-lncRNA Interaction web site: http://starbase.sysu.edu.cn/rbpLncRNA.php
Distinct features as follows:
We provide interactive web-page to display the 22,735 RBP-lncRNA regulatory relationships identified from 117 CLIP-Seq datasets generated by 50 independent studies.
We discovered hundreds of disease-related single nucleotide polymorphisms (SNP) resided in the RBP binding sites of lncRNAs.
We also revealed the expression correlation of RBP-lncRNA interaction networks by mining expression profiles of over 6000 normal and tumor samples from 14 cancer types.
We found that one single lncRNA will generally be bound and regulated by one or multiple RBPs, the combination of which may coordinately regulate gene expression.
in starBase, what methods were used to identify CLIP-Seq peaks?
in starBase download page, what a numerical value (displayed in the score column of bed files) means? Is it CLIP-Seq peak height? It can be further used to filter Protein-RNA interactions???
How can i find the lncRNAs with chromosome locations but not gene names in starBase?
what is mean for bioComplex and clipReadNum in starBase?
I am trying to using
starBase in order to look for miR-lncRNA interactions.
Is the lncRNAs list that are available on site is complete?
regarding circRNABase in Starbase I'd like to know:
in search page, which input in the field circRNA Symbol has to be inserted?
When I select a specific miRNA(
hsa-let-7a-5p) the output target is
RRP1B_hsa_circ_001854, what does the name before the circRNA name (e.g.
In the miRNA-lncRNA interactions of starBase, you mean that miRNA regulate lncRNA? In starBase, if we can obtain lncRNA-miRNA interactions, lncRNA-mRNA interactions, lncRNA-TF, and TF-lncRNA? Thanks in advance.
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