Is Any Database Provide Human Genes' Conservation Scores ?

Question

[Yu]

Hi all

Recently, I deal with some human gene data and I want to know if the gene I handled is conserved gene.

Is any database provide human genes' conservation scores?

I need all human genes' conservation scores.

I know UCSC Genome Table Browser provide sequence conservation scores like phastCons and phyloP. But I can't find gene's conservation score.

Does anyone can teach me how to get it?

The format which I want is

Gene ID 1 (Ensembl ID or Refseq ID )  | conservation score
Gene ID  2 (Ensembl ID or Refseq ID )  | conservation score

Thanks

[jeff.ohana]

Hey Yu,

Did you finally obtain the phastCons conservation score for each gene? I would be interested in getting the data for a research project.

Looking forward to hearing from you soon,

All the best,
Jeff O.

[Yu]

Hi Jeff,

Sorry for the delay in replying. I downloaded the UCSC conservation scores (primates phastCons46way) and calculate the mean value of each gene. @Alex Reynolds also provide you a good way to calculate the gene conservation score. Obtaining phastCons conservation score for every gene in the Human genome

[jeff.ohana]

Thanks for your answer. But, How did you obtain the corresponding gene symbol for each gene (only the starting locate is indicated)? Further, there are more than 20,000 genes in the primates phastCons46way, meaning that you did not obtain the scores only for the coding genes (which are of interest). Right?

Looking forward to hearing from you soon,

Many thanks, Jeff O.

[Yu]

Hi,

For each gene, the gene transcription start site and transcription terminal site were defined by the ensembl annotation file(gtf). So I only calculate the mean value between transcription start site and transcription terminal site.

If memory serves me right, within the scope of my research, I only calculated no more than 2,000 genes phastCons46way score.

Answer 1

[Jelena Aleksic]

I think it depends on exactly what information you want. Is it conservation between human and a particular species? The UCSC conservation scores give you a measure of conservation based on an alignment between human and 45 other species (here is the information along with download links), which is good for a general impression of conservation levels, but less good for a specific question like "how different is this gene in the marmoset?" (for which you'd want a specific pairwise alignment). They also have a subset of scores for primates, and for placental mammals. So, one way to do it would be to download the data, then process it to extract the answer you're looking for (e.g. get the average phastCons score using the exons, or just coding sequence, of each human gene, then use that average as your gene conservation score). What you mean by "gene" would also depend on the question you were trying to answer - for example, introns may or may not be of interest to you.

[Yu]

Great! I just want a gene conservation score like phastCons. And I also can calculate a gene conservation score from UCSC conservation scores. But some people in our lab said gene conservation scores may different from sequence conservation scores ( UCSC scores ) that make me confused. So I asked the question. I think you provide me some ideas on an easy and cost effective way to find answer. Thanks for you help:)

[Jelena Aleksic]

No problem - my pleasure :)

Answer 2

[ff.cc.cc]

I suppose CANDID db does something like that, based on the conservation verified by Homologene.

This is not the only selection criterium adopted by Candid, but It's worth to have a look, maybe could help you.

[Yu]

Thanks for you help:)