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Pan-Cancer pattern of lncRNAs, miRNAs and their regulatory networks - (Feb/06/2014 )

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 lncRNA, miRNA 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. 


overview of panCancerMine:








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:


1. in panCancerMine, Cancer types as follows:
Urothelial bladder cancer (BLCA)
Breast cancer (BRCA)
Colon and Rectal adenocarcinoma (CRC)
Glioblastoma multiforme (GBM)
Head and neck squamous cell carcinoma (HNSC)
Chromophobe renal cell carcinoma (KICH)
Clear cell kidney carcinoma (KIRC)
Acute Myeloid Leukemia (LAML)
Lung adenocarcinoma (LUAD)
Lung squamous cell carcinoma (LUSC)
Ovarian serous cystadenocarcinoma (OV)
Cutaneous melanoma (SKCM)
Papillary thyroid carcinoma (THCA)
Uterine corpus endometrial carcinoma (UCEC)

2. in cancerMiner includes above-mentioned 12 cancer types.