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

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!

genome gene
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updated by Ram Ram • written by zhangjunpeng_411 • zhangjunpeng_411

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

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written by Prakki Rama Prakki Rama

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

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written by zhangjunpeng_411 • 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.

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updated by Ram Ram • written by zhangjunpeng_411 • zhangjunpeng_411

4 answers

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

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updated by Ram Ram • written by onuralp onuralp

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.

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updated by Ram Ram • written by zhangjunpeng_411 • zhangjunpeng_411

Concerning wet bench biomarkers

NIH has small but robust markers for different tumors

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

hth

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updated by Ram Ram • written by Manvendra Singh Manvendra Singh

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

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updated by Ram Ram • written by zhangjunpeng_411 • zhangjunpeng_411

http://www.mycancergenome.org/

This might be of some help.

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updated by Ram Ram • written by Bioinformatics_NewComer Bioinformatics_NewComer

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.

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updated by Ram Ram • written by zhangjunpeng_411 • zhangjunpeng_411

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.

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updated by Ram Ram • written by Bioinformatics_NewComer Bioinformatics_NewComer

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.

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updated by Ram Ram • written by zhangjunpeng_411 • zhangjunpeng_411

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

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updated by Ram Ram • written by cdsouthan cdsouthan

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.

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updated by Ram Ram • written by zhangjunpeng_411 • zhangjunpeng_411

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