Secretome and membrane receptor profiles I am looking the secretome profile and the membrane receptor profile for a given cell type. 

In my specific case, this should be the secretome and outer membrane receptor profiles of dorsal root ganglion. 

What I've done in the past is taken proteomics datasets or RNAseq datasets and used this as a reference cell surface proteome or secretome. 

I wasn't sure what the best way to filter secreted proteins or membrane receptors were, so I used the Human Protein Atlas and this turned out to be a big headache. A possible alternative method might be to use DAVID, but there must be a more efficient method via the command line.

My questions are these:


Is there a "consensus" database containing protein expression
profiles for different tissue types in human?
If not, what is the best way to filter out the secreted and transmembrane proteins by gene symbol?
I don't think there is a database with expression data for your particular cell type. I am afraid your "headache" approach doesn't sound so bad...

So get expression data e.g., from GEO for your cell type, and define which genes/proteins you consider as "expressed" (e.g., minimal RPKM value).

Then, you can use GO annotation to find your genes involved with membrane or secretion (or what ever). You can use biomaRt in R for this.

For example, you want to know all "membrane" genes.

&gt; library(biomaRt)
&gt; 
&gt; ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
&gt; 
&gt; membrane.genes &lt;- getBM(attributes=c('hgnc_symbol',
&gt; 'ensembl_transcript_id', 'go_id'),
&gt; filters = 'go', values = 'GO:0016020', mart = ensembl)


And now you want to know it only from genes that are expressed in your ganglion cells (with dummy example of two genes).

&gt; gene.list &lt;- c("KIR2DL3", "GPR1")
&gt; 
&gt; membrane.genes.list &lt;- membrane.genes[membrane.genes$hgnc_symbol ==
&gt; gene.list,]
&gt; 
&gt; membrane.only &lt;- membrane.genes.list[membrane.genes.list$go_id ==
&gt; 'GO:0016020',]