Basic Info

Starting a new search ...

Basic Information for the mutation-ceRNA event

Mutation

chr11:65422866(T/G)

lncRNA

NEAT1 ( ENSG00000245532, ENST00000499732)

miRNA

hsa-miR-339-5p (MIMAT0000764)

mRNA

BCL6 (ENSG00000113916)

Disease

LIHC

FDR

1.10E-3

Reported as biomarkers
7

Circulating
6

Drug resistent
41

Survival

Binding Info

Altered binding affnity between reference and alternative allele

miRanda reference allele   (gain)
miRNA  3' gcaCUCGAGGACCUC---CUGUCCCu 5' hsa-miR-339-5p
             |:|||:| ||:|   ||||||| 
target 5' ucaGGGCUUCAGGGGACAGACAGGGa 3' NEAT1
Start: 24  End: 49
Energy: -31.53 kcal/mol
Align Score: 163
miRanda alternative allele   (loss)
                                           
                       NA                  
                                           
                         
            NA
TargetScan reference allele   (gain)
miRNA  3'   GCACUCGAGGACCUCCUGUCCCU 5' hsa-miR-339-5p
                           ||||||| 
target 5'   GGGCUUCAGGGGACAGACAGGGA NEAT1
Start: 42  End: 49
Site type: 8mer-1a
Context++ Score: -0.416
TargetScan alternative allele   (gain)
miRNA  3'   GCACUCGAGGACCUCCUGUCCCU 5' hsa-miR-339-5p
                           ||||||| 
target 5'   GGGCGUCAGGGGACAGACAGGGA NEAT1
Start: 42  End: 49
Site type: 8mer-1a
Context++ Score: -0.41
RNAhybrid reference allele   (gain)
miRNA  3' GCA       A                 5' hsa-miR-339-5p
             CUCGAGG CCUC   CUGUCCCU    
             GGGCUUC GGGG   GACAGGGA    
target 5'   A       A    ACA        G 3' NEAT1
Start: 26  End: 46
Energy: -35.7 kcal/mol
Align Score: 0.00002
RNAhybrid alternative allele   (gain)
miRNA  3' G           GA                        5' hsa-miR-339-5p
           CAC   UCGAG         CCUC   CUGUCCCU    
           GUG   AGCUC         GGGG   GACAGGGA    
target 5' A   GCU     AGGGCGUCA    ACA        G 3' NEAT1
Start: 14  End: 34
Energy: -31.7 kcal/mol
Align Score: 0.000145

Functions

Dysregulated fucntions of CNV-ceRNA event

Hallmarks

Dysregulated hallmarks of CNV-ceRNA event

Network

Related ceRNA network disturbed by CNV

Survival

Survival status of ceRNA interaction

Samples

The somatic mutation chr11:65422866 identified in the following paired samples.

TCGA-RG-A7D4-01A-12D-A33Q-10

TCGA-RG-A7D4-10A-01D-A33Q-10

Annotations

External Annotation for NEAT1

LncRNA-associated competing triplets and functions.

Comprehensive experimentally supported associations between lncRNA and human cancer.

An open-source platform for studying the RNA-RNA interactions from CLIP-seq data.

An integrated knowledge database dedicated to non-coding RNAs.

An integrated database of human annotated lncRNA transcripts.

Comprehensive annotations of eukaryotic long non-coding RNAs.



External Annotation for hsa-miR-339-5p

A high quality database of published miRNA sequences and annotation.

A curated miRNA-target database developed by DIANA LAB.

A miRNA-target database by manually filter research articles related to functional studies of miRNAs.

A comprehensive of microRNA diversity, expression profiles, target relationships, and various supporting tools.



External Annotation for BCL6

Information on all annotated and predicted human genes.

Gene nomenclature, gene families and associated resources (genomic, proteomic, phenotypic information).

Genome browser for vertebrate genomes.

An annotated collection of all publicly available DNA sequences.



External Annotation for variation: chr11:65422866

A comprehensive, authoritative compendium of human genes and genetic phenotypes.

A database of human single nucleotide variations, microsatellites, and small-scale insertions and deletions

The catalogue of somatic mutations in cancer.