TCGA hosts a variety kind of omics data from cancer patients. Subio Platform is a software for analyzing quantitative data, while somatic mutation is qualitative data. TCGA Somatic mutation data is provided in MAF format file, and you can analyze it with Excel.
MAF contains columns of followings. (I omit latter than "R")
- A: Hugo_Symbol
- B: Entrez_Gene_Id
- C: Center
- D: Ncbi_Build
- E: Chrom
- F: Start_Position
- G: End_Position
- H: Strand
- I: Variant_Classification
- J: Variant_Type
- K: Reference_Allele
- L: Tumor_Seq_Allele1
- M: Tumor_Seq_Allele2
- N: Dbsnp_Rs
- O: Dbsnp_Val_Status
- P: Tumor_Sample_Barcode
- Q: Matched_Norm_Sample_Barcode
A-B are gene inoformation
C is resource of the data.
D-H are genomic location information.
I-J are type of mutation
K-M are actual changes on sequence
P is ID of tumor sample
Q is ID of normal sample
- separate data by "type of mutations (I-J)."
- count per locations to know if it's common or not.
- use clinical information to divide patients into some groups.
- and re-count by groups.
After these analysis on Excel, you can visualize the data on Subio Platform and combine with other data like gene expression or DNA methylation. Subio Platform is very good at this part.
We also can provide analysis service for the somatic mutations data. Please contact us for details.