Computational Biology / Bioinformatics/cancer databases

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Question
hi dear Sridhar
i'm student in tehran university (in iran / ms course) and i'm working on cancer prediction using machine learning and data mining approach ...
so i need to a complete gene database for my work
can u introduce me a perfect one ?

Answer
Hi Behzad,

I apologize for the delay, I was on travel to a conference.

I can suggest a couple of options rather than the perfect single one.

The first thing that comes to my mind is searching and retrieving data from the GEO and SRA databases, which are one of the most comprehensive gene expression database. Many of the tumor specific databases actually contain links to these databases.

Other than that I would suggest to see the 'Cancer Genome Anatomy Project' of the National Cancer Institute, which has a comphrehensive information on human transcriptome and expression data. It has several data related to tumors.  For example you can retrieve expression data from normal vs tumor types (http://cgap.nci.nih.gov/Tissues/xProfiler).
Also the NCI's Cancer Genome Atlas provides another portal for bulk download of gene expression data.
https://tcga-data.nci.nih.gov/tcga/findArchives.htm

I would also see the data at Jackson's laboratory's Mouse Tumor Biology Database (http://tumor.informatics.jax.org/mtbwi/geneExpressionSearch.do)

There is cBioPortal for Cancer Genomics http://www.cbioportal.org/index.do

All the above have bulk download options.

Hope it helps,

Sridhar

Computational Biology / Bioinformatics

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Sridhar Acharya Malkaram

Expertise

Sequence and Structural Analysis, Next generation sequencing, Illumina, SOLiD, CHiP-sequencing, RNA sequencing, miRNA sequencing analysis, Molecular Dynamics, Protein and Nucleic acid simulations, computational methods, Bioinformatics tools, Biological Databases, Search techniques, Protein comparative modelling, Mutation analysis

Experience

about fifteen (15) years

Education/Credentials
Bachelor of Science in Agriculture Master of Science in Biotechnology Ph.D in computational Biology

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