I work with a protein that has 2 different common SNP variants in the population, and we discovered that only one form can bind a protein required for degradation. Is there a resource that links cancer panel genome wide SNP (DNA sequence) with genome wide protein expression level (eg mass spec, protein or IHC microarray) from the same samples? Or do I have to find a patient/control set and do it myself?!
DNA Data Bank of Japan (National Institute of Genetics) EMBL (European Bioinformatics Institute) GenBank (National Center for Biotechnology Information), ArrayExpress (European Bioinformatics Institute), Gene Expression Omnibus (National Center for Biotechnology information), GPX(Scottish Centre for Genomic Technology and Informatics),maxd (Univ. of Manchester) Stanford Microarray Database (SMD) (Stanford University) Genevestigator - Expression Search Engine (Nebion AG), Swiss-model[6] Server and Repository for Protein Structure Models. PMPs and SAGE, dbERGE II -- Database of Experimental Results on Gene Expression
This might not be exactly what you're after, but worth a look as a good place to start. http://www.proteomicsdb.org/
On cBioPortal you can look up mutations, copy number alterations (from GISTIC analysis) and mRNA expression z-scores from various TCGA publications on many cancers. Here is the link: http://www.cbioportal.org/public-portal/
Thanks for the links but none of these correlate *protein* expression with SNP sequence in the same sample. Perhaps there is set of cancer cell lines that has been analysed in both proteomics and high throughput/SNP DNA sequencing, where I could manually cross-correlate?
Hi Andrew,
An association between protein abundance and SNP can possibly be extracted from the data presented in the following paper:
"Proteogenomic characterization of human colon and rectal cancer"
http://www.nature.com/nature/journal/v513/n7518/full/nature13438.html.
They used large scale LC-MS/MS analyses and looked for SNPs. If the SNPs you are interested in are within those identified by RNA-seq, then you can follow up on protein abundances in the analyzed tumor samples.
Hope this helps.
Ilian
Thanks Ilian - that paper is a good resource but unfortunately my protein is not in the list of 3200 or so that they have reliable data for. Javier- I was not aware that TCGA had proteomics attached but now see that they have recently started to. I shall peruse! The issue will be *finding* data that is matched to SNP sequences, amongst the huge repository!
@AJD
Have you tried
1. Chemical Abstracts Database - CAS/SciFinder?
2. http://isciencesearch.com/iss/
3......4. 5. 6.
6...
(ther could be many data bases (paid and free) including patents databases
This will give you bottom-up approach
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cancer panel genome wide SNP (DNA sequence with protein expression levels)
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If you can share your exact query, may be i can provide you required information
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