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How to get the phastcons score for protein coding genes and lncRNAs?

Dear All,

I'm interested in checking the conservation of lncRNAs and protein-coding genes from Gencode and similarly from my data I also have some newly assembled lncRNAs which are not found in gencode. I would like to make a plot like below:

enter image description here

The above image is taken from the paper Recurrently deregulated lncRNAs in hepatocellular carcinoma. Figure 1e

Similar to above image, I also wanted to check the conservation of known lncRNAs, protein coding genes and newly found lncRNAs.

How to calculate the phastcons score for all the genes?

rna-seq phastcons genome conservation
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updated by Biostar Biostar • written by newbie newbie

For the newly found lncRNAs, yes I will do it myself using phast. But how do I get the phastcons score for gencode protein-coding genes and known lncRNAs?

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written by newbie newbie

I found an R package GenomicScores to extract the phastcons scores.

In the tutorial of the GenomicScore I see that information can be exxtracted only by each chromosome location.

But I would like to know, whether there is any way to get the phastcons score for all protein coding genes and known lncRNAs from phastCons100way.UCSC.hg38

library(GenomicRanges)
library(phastCons100way.UCSC.hg38)
gsco <- phastCons100way.UCSC.hg38
gscores(gsco, GRanges(seqnames="chr7", IRanges(start=117232380, width=1)))

GRanges object with 1 range and 1 metadata column:
      seqnames    ranges strand |   default
         <Rle> <IRanges>  <Rle> | <numeric>
  [1]     chr7 117232380      * |       0.5
  -------
  seqinfo: 1 sequence from Genome Reference Consortium GRCh38 genome; no seqlengths

Yes from the above example I'm able to get the phastcons score for the specific chromosome location. But I'm interested in extracting the information for all protein coding genes and known lncRNAs.

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written by newbie newbie

1 answer

Hi

I found a post similar to this. I guess it'll take some work but the method should give you what you need.

Obtaining phastCons conservation score for every gene in the Human genome

I also found the link for getting PhyloP scores. http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP100way/

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written by gayachit gayachit

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