Forum:lincRNA analysis pipeline and relevant database

Question

[Shicheng Guo]

Here, I will collect some database and pipeline which might be useful for lncRNA analysis.

1. lncMAP: http://bio-bigdata.hrbmu.edu.cn/LncMAP/index.jsp
2. LncPipe - A Nextflow-based pipeline for identification and analysis of lncRNAs from RNA-Seq data
3. Functional enrichment analysis based on long noncoding RNA associations

[Vasu]

Could you also post some databases where you can looks for lncRNA-miRNA interactions, lncRNA-protein interactions and also binding sites and motifs etc...

[sangram_keshari]

You may find some resources here - lncrnablog.com

Answer 1

[poyarkov.stanislav]

Hello, you can try to use ONCO.IO

ONCO.IO contains permanently updating manually curated direct lncRNA interactions, such as lncRNA-->miR (sponge interaction), TF-->lncRNA, miR--->lncRNa, lncRNA-->protein interaction full list is here

These interactions can use for a network creation.