Question: Protein Expression Data For Liver Cancer
1
gravatar for ftp
6.0 years ago by
ftp120
United States
ftp120 wrote:

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 • 3.0k views
ADD COMMENTlink modified 6.0 years ago by Malachi Griffith17k • written 6.0 years ago by ftp120
1
gravatar for JC
6.0 years ago by
JC7.8k
Mexico
JC7.8k wrote:

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

ADD COMMENTlink written 6.0 years ago by JC7.8k

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.

ADD REPLYlink written 6.0 years ago by ftp120

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

ADD REPLYlink written 6.0 years ago by JC7.8k
1
gravatar for Charles Warden
6.0 years ago by
Charles Warden6.6k
Duarte, CA
Charles Warden6.6k wrote:

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!

ADD COMMENTlink written 6.0 years ago by Charles Warden6.6k
0
gravatar for miquelduranfrigola
6.0 years ago by
Barcelona
miquelduranfrigola760 wrote:

Did you check IntoGen?

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

ADD COMMENTlink written 6.0 years ago by miquelduranfrigola760

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?

ADD REPLYlink written 6.0 years ago by Charles Warden6.6k

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

ADD REPLYlink written 6.0 years ago by ftp120
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