I would like to compile a list of proteins highly expressed in a given tissue. What would be the best and most complete resource for this purpose? I'm mostly interested in human/mice/pig, and preferably healthy tissue.
Thanks in advance! /F
Besides Protein Atlas, if you are ok with transcript expression from microarrays and RNAseq for tissue enrichment, you can use BioGPS, GeneCards, RNAseq atlas, AlexaSeq, EMBL GXA and VeryGene. Many of these sites have the data available for download.
www.gtexportal.org/
Nice graphically pleasing RNAseq data
The human protein atlas has pretty comprehensive coverage for human proteins in a variety of tissues: http://www.proteinatlas.org/
Though its more of a qualitative resource and therefore may not satisfy your need to identify only highly expressed (assuming you mean high abundance) proteins.
If you are working with humans the bodymap dataset may interest you. I attach you the link to download the raw RNA-seq data from the 16 different tissues generated in the project.
Hope it helps!
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One comment: there can be many different cell types in a tissue. If one of them is of particular interest to you, try to look if someone did a microarray/RNASeq experiment on FACS sorted cells, using a marker of your cell type coupled to GFP.
For example, you can use OMP-GFP mice (OMP = olfactory marker proteins) to extract olfactory sensory neurons from their surrounding tissue, and find proteins they express specifically.