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Old 07-12-2012, 11:00 AM   #1
gunbuddy
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Location: United States

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Default Cancer-Specific Gene Regulatory Networks datasets

Hi all,

I am new to Bioinformatics research.
I have developed an algorithm which can find the most important links in a given social network to maintain its robustness. I am now trying to use a different version of the same algorithm to find the most important connections in a cancer specific gene-regulatory network.
Currently I am struggling to find a good dataset with cancer specific gene regulatory data. I am looking for a dataset which contains information about source gene, target gene and the strength to the connection.

Please be kind enough to reply to this with places that I can find such datasets.

Thank you
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Old 07-12-2012, 11:57 AM   #2
Richard Finney
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Check out reactome, Nature Pathway Interaction Database, Kegg, BIND, BioGRID, HPRD, pantherdb for gene/protein interactions. Check current licensing, I know KEGG changed at some point.

Public real raw cancer data using nextgen is pretty rare. You'd be better off protoyping your "gene measurements" using the abundant array data available at NCBI GEO or EMBL-EBI Array Express.
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Old 07-14-2012, 05:50 AM   #3
adaptivegenome
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This sounds really cool.
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Old 08-17-2012, 09:34 AM   #4
dubayc
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Quote:
Originally Posted by gunbuddy View Post
Hi all,

I am new to Bioinformatics research.
I have developed an algorithm which can find the most important links in a given social network to maintain its robustness. I am now trying to use a different version of the same algorithm to find the most important connections in a cancer specific gene-regulatory network.
Currently I am struggling to find a good dataset with cancer specific gene regulatory data. I am looking for a dataset which contains information about source gene, target gene and the strength to the connection.

Please be kind enough to reply to this with places that I can find such datasets.

Thank you
I like your idea.

You might take a look at cBIO: www.cbioportal.org

They have a very nice portal to the TCGA data, which has patient data as well. They use the Reactome networks to create networks from user supplied gene lists, and the you can see how (if) those genes are altered in patients with different cancer types.

Also, if you have not used Cytoscape, you must check it out now (cBio will download networks into a Cytoscape compatible format: GraphML)

Good luck! I think you have an important idea.

Christopher
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