Prediction of lncRNA cis regulation · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Prediction of lncRNA cis regulation

Hi, I have a set of differently expressed lncRNA and mRNA data from RNA-seq, which contains the location of each lncRNA. Based on the fact that lncRNA exerts its effect by regulating its nearby gene.. I am wondering someone could show me how to use R to build the lncRNA-mRNA based on their locations (100K)... Thanks!

rna-seq lncrna cis r

• 2,464 views • link

updated 8.7 years ago by Ben

• written 8.7 years ago by drhaoboli •

1 answer

you can see my paper titled "Functional prediction of differentially expressed lncRNAs in HSV-1 infected human foreskin fibroblasts"

• 0 views • link

written 8.7 years ago by Ben

Log in to answer this question.

More posts like this

EU-Seq Differentially expressed transcripts
written 1.8 years ago by Bruno •

Hi everyone. I'm wondering if any one can help me to stablish a correct way to find differentially expressed transcripts from nascent RNA Seq data …
Batch effect removal for RNA-seq data (single-end and pair-end)
written 3.8 years ago by hanny •

I have some RNA-seq data, in which some samples were paired-end reads, and some were single-end reads. I used Combat-seq from sva package to remove …
RNA Seq Classification
written 5.4 years ago by mosquitoking •

I have a data set of RNA-Seq stored in an excel file. The file contains gene expression values of two groups, control and disease. I …
RNA-seq Differential expression analysis show no differentially expressed genes with DEseq2
written 6.7 years ago by MoHallal •

Hello, We are investigating the knockdown effect of a specific long non-coding RNA lncRNA in cancer cell lines in an attempt to identify downstream target …
Use cmap with rna-seq results
written 9.5 years ago by bioinformatics •

Hello World, I would like to find links between drugs and the differentially expressed genes we found. I want to use cmap (https://portals.broadinstitute.org/cmap/index.jsp) with genes …
TANRIC: lncRNA and methylation interaction
written 9.8 years ago by Shicheng Guo

Hi All, I am trying to make some interaction analysis between methylation and lncRNA with TCGA dataset. However, there is no any lncRNA existed dataset …
hierarchy of gene regulation
written 9.9 years ago by yjliu1127 •

Hi everyone, I have more than 400 differentially expressed genes from RNA-seq dataset. I want to organized them in a hierarchical way based on their …
Top 20% expressed orthologus genes in two species
written 10.1 years ago by Saad Khan

Hi, I am looking at publicly available RNA-seq data and trying to see how in two species(mouse and human) the epigenomic data varies with the …
Comparing features of high expression genes vs low expression genes in two species
written 10.1 years ago by Saad Khan

Hi, I have RNA-seq data from two species (human & mouse). And I am trying to compare some features (epigenomic/genomic) and how they vary between …
Differential lncRNA-mRNA co-expression
written 10.3 years ago by hana

Hi I have 3 High-throughput RNA-Seq samples from patients with rare disease and 3 samples from healthy subjects. I have identified the differentially expressed lncRNA …