This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Protein Expression Data For Liver Cancer

Hello,

I'm looking for liver protein expression data for both normal liver and cancer liver. I was able to find normal liver protein expression data for thousands of proteins (http://pax-db.org/#!species/9606) but wasn't not successful for cancer liver. I was wondering if anybody knows any experiments for protein expression data for liver cancer.

thanks

protein
• 5,121 views • link
updated by Malachi Griffith Malachi Griffith • written by ftp ftp

3 answers

Probably you need to search in PubMed for articles like this http://www.molbiolcell.org/content/13/6/1929.full.pdf and their respective data or if you are OK with using transcript expression as evidence of protein expression, you can take a look to TCGA data sets: https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm?mode=ApplyFilter&showMatrix=true&diseaseType=LIHC&tumorNormal=TN&tumorNormal=T&tumorNormal=NT

• 106 views • link
written by JC JC

I actually look at transcript expression from TCGA... however, since a gene can be post-transcriptionally/translationally modified i need to look at protein expression data. thanks.

• 0 views • link
written by ftp ftp

Gene expression is easy to find in transcript level, protein level is hard to find.

• 0 views • link
written by JC JC

Finding protein expression from mass spec data can be tricky, but here are two resources that at least have some metadata associated with specific datasets:

http://www.ebi.ac.uk/pride/

http://www.peptideatlas.org/

You may be able to find some protein microarray data in GEO or ArrayExpress, but it isn't very common.

Sorry that I can't be much more help - this is also a problem for me. Hope you can find something interesting in one of these databases!

• 101 views • link
written by Charles Warden Charles Warden

Did you check IntoGen?

You can find genes that are over- or under-expressed in different cancer types.

• 0 views • link
written by miquelduranfrigola miquelduranfrigola

IntOGen seems like an interesting resource, but the main and supplemental text only mention proteomics as a potential additional data type that IntOGen is capable of handling. I can currently only find CGH and RNA expression experiments and searching for "protein" experiments doesn't yield any protein data.

Are you aware of any proteomics data in IntOGen?

• 0 views • link
written by Charles Warden Charles Warden

I agree... I didn't find any proteomics data using IntOGen

• 0 views • link
written by ftp ftp

Log in to answer this question.

More posts like this