Is there any database collecting proteins associated with different human cancers?

Question

[zhangjunpeng_411]

I'm looking for proteins associated with different human cancers. These proteins are also considered as bio-markers in clinical application. Recently, is there any good database collecting proteins (bio-markers) associated with different human cancers? Thanks in advance!

[Prakki Rama]

"human AND cancer" in uniprot listed quite a few proteins. Are you looking for any specific collection?

[zhangjunpeng_411]

I'm looking for all kinds of cancers not for a specific cancer. Thanks for your reply.

[Malachi Griffith]

This post may contain several relevant resources: Database Of Tumor Suppressors And/Or Oncogenes

[zhangjunpeng_411]

Thanks for the post. There are many different databases or website to search cancer or tumor genes. Most if them are predicted but not manually curated. Furthermore, proteins are different from genes to some extent.

Answer 1

[onuralp]

I am not aware of any manually-curated database of the sort you'd like to have. I bring up manual curation because you mention clinical relevance, and I'm highly skeptic of any list generated by an automatic pipeline without supervision or guidance by clinically oriented researchers.

Having said that, Lopez Bigas lab has a number of useful tools that you might like to take a look: http://bg.upf.edu/group/tools.php

[zhangjunpeng_411]

Thanks for your reply and good link. Indeed, the manually-curated database of cancer proteins is the best database for benchmark analysis. Is there sny manually-curated database collecting proteins associated with different human cancers? Thanks again.

Answer 2

[Manvendra Singh]

Concerning wet bench biomarkers

NIH has small but robust markers for different tumors

http://www.cancer.gov/cancertopics/factsheet/detection/tumor-markers

hth

[zhangjunpeng_411]

As you said, the number of biomarker is very small. It is difficult to conduct further analysis using these biomarkers as a benchmark. Thanks.

Answer 3

[Bioinformatics_NewComer]

http://www.mycancergenome.org/

This might be of some help.

[zhangjunpeng_411]

Thanks for your link. I just searched the cancer-associated genes of different cancers. The number of cancer-associated genes is very small, and far from complete. Thanks again.

[Bioinformatics_NewComer]

I'm working on a similar stuff. I started finding genes with clinical relevance or those genes which have treatment. I began from http://www.foundationone.com/genelist1.php It has a good list to start with. Then you can search each gene individually in dbSNP-NCBI, filter: clinical+ pathogen or non-synonymous, based on your needs.

[zhangjunpeng_411]

Thanks for your good advice. FoundationOne contains 315 cancer-related genes plus select introns from 28 genes often rearranged or altered in cancer, and 343 in total. However, it is just small. I found a big database (CTD). I hope it is useful for you. The database is very big, and collects gene-disease associations. However, it needs to be further processed to get what you need, such as cancer or tumor genes.

[Bioinformatics_NewComer]

Thanks for sharing link.

Answer 4

[cdsouthan]

Take a look at https://cansar.icr.ac.uk/

[zhangjunpeng_411]

Thanks for sharing link. I just had a look at canSAR, and it applies machine learning approaches to provide drug-discovery useful predictions not a manually curated database.