How to retrieve TSS200 and TSS1500 from DNA Methylation data?
Hello,
I'm looking for a way to retrieve the TSS200 and TSS1500 promoters regions for a set of genes from a dna methylation data,
Do you suggest any way to do so?
Cheers,
dna-methylation
• 316 views
•
link
updated
by
Ram
•
written
by
Zakaria Benmounah •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Forum: Annotation for WGBS
written by veronicoHi everyone, Does anyone have a good recommendation for annotating genes, gene bodies, enhancers, promoters, CpG islands, etc for WGBS data (just CpGs)? I want …
-
Using ATACseq to do motif analysis in the promoters of a gene set
written by dljone02 •Hi, I have ATACseq data analyzed for my cell of interest. I also have RNAseq from my cells with/without stimulus. After doing differential gene expression …
-
Combining DNA methylation scores from ensembl
written by Irene Hemel •Dear all, I'm looking into DNA methylation data in the promotor area of genes. For this I'm using ENCODE data in ensembl. In most promotor …
-
Download from TCGA
written by saswatimahapatra2015 •Hi Can any one suggest me, how to download DNA methylation and gene expression data for the same set of genes from TCGA?
-
Why is a probe annotated more than one UCSC_RefGene_Group in the same gene?
written by RC •Hi, i'm processing a data from 450K beadchip to identify differentially methylated probes(DMPs) between our case and control. And i get more than 10000 DMPs. …
-
What is the first exon in negative strand genes?
written by Zakaria Benmounah •Hello Biostars! I would like to extract locations (starting point and ending point) for some regions characterizing genes. Using Biomart, for example, I can extract …
-
Any Automatic way to get the TSS1500 and TSS200 promoter?
written by Zakaria Benmounah •Hello, I'm looking for a way to retrieve the TSS200 and TSS1500 promoters regions for a set of genes, Cheers
-
is there any databse that provides the promoter of a specific gene?
written by Zakaria Benmounah •Hi, I have a list of genes and I want to know the location of the promoters of these genes ('start' and 'end' position). Are …
-
How to say that a gene is hypermethylated or hypomethylated?
written by Zakaria Benmounah •Hi, I have a set of genes and for each gene, I have a vector of methylation values per base pair, for example if a …
-
How do we browse different data from the same sample from TCGA ?
written by Zakaria Benmounah •Ni hao for everyone!, I have a computer science background and I would like to analyse different data (CNA, mRNA and miRNA) from the same …
Have you tried
bedtools flank, or thepromoter()and related functions in the R GenomicFeatures package?