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1. lncRNA information in TCGA2. Understanding annotation of lncRNAfunc
Search page, example: MAGI2-AS3
lncRNA search result page
lncRNA annotation result page
1) lncRNA summary
2) lncRNA structure and expression level
3) lncRNA-Protein interaction
4) lncRNA-DNA interaction
5) lncRNA-RNA interaction
6) Variants in lncRNA
7) lncRNAs regulate the target genes through functioning as enhancers
8) lncRNAs regulate the target genes through recruiting transcript factors
9) lncRNAs regulate the alternative splicing events through interacting with splicing factor
10) lncRNAs regulate mRNA through targeting the 3'-UTR region
11) lncRNAs regulate mRNA by competing with miRNA
12) lncRNA coding potential
3. Download data and contact us
1. lncRNA information in TCGA We analyzed 15900 lncRNA across 33 cancer types from TCGA (The Cancer Genome Atlas) which included 33 types lncRNA in cancer. Form the differential expresision for each cancer we found 2528 cancer-associated lncRNA.
2. Understanding annotation of lncRNAfunc Search page, example: MAGI2-AS3- Input query: Gene symbol or Ensembl gene ID.
lncRNA search result pageSelect your lncRNA from the lncRNA list.
lncRNA annotation result pageThese are lncRNA's annotation categories for your query with links to their corresponding annotation parts.
1) lncRNA summary categoryThis category shows the information of the lncRNA. It shows each lncRNA's overall information from basic information such as symbol, name, and Entrez ID.
2) 'lncRNA structure and expression level' categoryThis category provides the known gene isoform models based on GENCODE basic v.19 with expression levels in cancer (TCGA) and normal tissues (GTEx).
3) 'lncRNA-Protein interaction' categoryThis category provides the interaction between the known lncRNA and transcript factor/RNA binding protein/Epi factor.
4) 'lncRNA-DNA interaction' categoryThis category provides the prediction of lncRNA's target region in DNA.
5) 'lncRNA-RNA interaction' categoryThis category provides the prediction of the lncRNA-RNA interaction.
6) 'Variants in lncRNA' categoryThis category provides the variants in lncRNA including RNA editing in lncRNA, tumor specific RNA editing in lncRNA, and cis-eQTL of lncRNA.
Note: There is no result of MAGI2-AS3 in this category. Here is the result of RP13-104F24.2 (ENSG00000215769) as an example.
7) 'lncRNAs regulate the target genes through functioning as enhancers' categoryThis category provides lncRNA regulates protein-coding genes by function as enhancer.
8) 'lncRNAs regulate the target genes through recruiting transcript factors' categoryThis category provides lncRNA regulates protein-coding through transcript factor.
9) 'lncRNAs regulate the alternative splicing events through interacting with splicing factor' categoryThis category provides lncRNA regulates alternative splicing events through splicing factor.
10) 'lncRNAs regulate mRNA through targeting the 3'-UTR region' categoryThis category provides lncRNA regulates mRNA by directly targeting 3'UTR region.
11) 'lncRNAs regulate mRNA by competing with miRNA' categoryThis category provides lncRNA regulates mRNA by competing with miRNA.
12) 'lncRNA coding potential' categoryThis category provides ORFfinder result for the gencode.v22.lncRNA.transcript.fa.
3. Download data and contact usPlease go to download page and contact page.
