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Looking someone experienced in genomics/bioinformatics to help guide me through applying AlphaGenome

am new to bioinformatics and cancer genomomics, so I apologize if I am misunderstanding some concepts.

I am unfamiliar new on a LUAD radiation-sensitivity project using TCGA-LUAD patient tumors and CCLE LUAD cell lines. Samples/cell lines have been separated into relatively radiation-sensitive and radiation-resistant groups.

Differential-expression and pathway analyses have already been performed. We obtained approximately 47 significant genes from TCGA and 92 from CCLE, with only a small number of overlapping genes, but several overlapping pathways including fatty-acid metabolism, glycolysis and oxidative phosphorylation.

My professor has asked me to investigate whether AlphaGenome could contribute to this project.

bioinformatics
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written by entrepreneurshipa • entrepreneurshipa

My main questions are:

  1. Is this an appropriate use of AlphaGenome?
  2. Which TCGA and CCLE data types should I obtain for this purpose?
  3. Would somatic mutation/MAF data be sufficient, or should I also consider CNV, germline/non-coding variants or other data?
  4. How should AlphaGenome predictions be integrated with our existing RNA-seq/DEG results?

Also where i could find someone can assist me and explain to me in simple terms and help me with the project but my budget is tight i dont have much money but i also work part time

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written by entrepreneurshipa • entrepreneurshipa

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