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Pan-Cancer pattern of lncRNAs, miRNAs, mRNAs

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

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Pan-Cancer pattern of lncRNAs, miRNAs, mRNAs

Postby rnaworld2110 » Thu Feb 06, 2014 11:56 am

Dysregulation of miRNAs and lncRNAs can contribute to tumor formation and progression. Little is known about the expression profiles of lncRNAs and miRNAs across diverse cancer types.

Pan-Cancer miRNA and lncRNA resources:
(1) panCancerMine: explore Pan-Cancer pattern lncRNA, miRNA, mRNA and their regulatory networks (ceRNA, coexpression) by mining expression profiles of miRNAs, lncRNAs and mRNAs across 14 cancer types (>6000 samples) from The Cancer Genome Atlas (TCGA) Data Portal and large-scale CLIP-Seq data.

(2)cancerMiner: is a comprehensive resource for discovery and prioritization of miRNA-mRNA target interactions and relationships in human cancer using molecular datasets from The Cancer Genome Atlas.
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Re: Pan-Cancer pattern of lncRNAs, miRNAs, mRNAs

Postby rnaworld2110 » Fri May 23, 2014 8:32 am

starBase panCancerMine also provided Pan-Cancer Interactions between lncRNAs and RNA-Binding Proteins (RBPs), mRNAs and RBPs.

Correlation between RNA-Binding Proteins (RBPs) and targets across 14 cancer types (>6000 tumor and normal samples) using pearson correlation test (p-value<0.05).

For example:
(1)RBP-lncRNA: FMRP:TUG1(lncRNA) interaction with significant correlation across 14 cancer types.
(2)RBP-mRNA: TDP-43:CDK6 interaction with significant correlation across 9 cancer types.

The TDP-43(TARDBP) expression profiles across 14 cancer types:
Image
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