Members: Mani Hema Prashaad, Wang Yiteng, Wong Jun Hong, Yang Xinyi.

• Isolation of Breast Cancer Related Genes' Expression
• Cibersort
• Cox Analysis
• Random Survival Forest (RSF)
• Generation of Means Comparison Graphs

• Isolation of prognostic gene expression.ipynb

  • Extracts the FPKM values for the genes-of-interest after filtering for the primary tumour samples' RNAseq data files for each case.

• Datasets

  • FPKM data of the patients, pulled from GDC.

• CibersortProcess.java

  • Executed to generate the mixture file to be sent to CIBERSORT.
  • Also determines the cases without FPKM data (GDC does not have FPKM records of these patients).

• filtered_cases.txt

  • Contains the 967 cases-of-interest after dropping cases or imputation (from 1098 cases).

• Manifest

  • Contains the file IDs of all files pulled from GDC.

• File to case ID mapping

  • MANIFEST.txt file does not include the case ID of each dataset.
  • Using a scrapped JSON, these file IDs were mapped to their respective Case IDs.

• Gene mapping

  • GDC FPKM files uses the ENSEMBL gene symbols which were incompatible with CIBERSORT's LM22 signature matrix, which required HUGO symbols.
  • Maps the ENSEMBL symbols to HUGO symbols.

• Mixture file

  • The output mixture file after executing CibersortProcess.java.
  • Uploaded to CIBERSORT.

• Cibersort Output file

  • Output from CIBERSORT after 100 permutations were ran, using LM22 and mixture file.
  • Contains the cellular proportion of each case. This was used as a feature for predicting survival.

• CG_COX

  • Cox and penalized Cox model for a combination of clinical and gene expression data after feature selection.

• CL_COX

  • Data processing including trimming and imputation for clinical data.
  • Cox and penalized Cox model for only clinical features.

• CT_COX

  • Cox and penalized Cox model for a combination of clinical and TIIC data after feature selection.

• Clinical features

  • Contains the 962 patients' clinical data and survival status.

• Expression profile of Prognostic genes

  • Contains the gene expression data of 962 patients with regards to the prognostic genes.

• Random Survival Forest model

  • Contains the code for Random Survival Forest model.

• Graphing.ipynb
  • Plots barplots overlaid with scatters of datapoints for the testing and training accuracy metrics for the survival analysis models utilised.