GFRN_signatures

This repository presents all analyses done for the paper "Discrete growth and survival phenotypes link to apoptotic mechanism and drug response in breast cancer." ASSIGN folder describes pathway prediction generation in cell lines and in patient samples.GFRN_characterization_in_breast_cancer_Final.Rmdscript has code for all the results described in the paper.

Datasets

You will need the following datasets for running the GFRN_characterization_in_breast_cancer_Final.Rmd script:

1. ICBP breast cancer cell line gene expression dataset: icbp_Rsubread_tpmlog.txt
2. ICBP breast cancer cell line drug response dataset: ICBP_drugs.txt
3. TCGA cancer tumor gene expression dataset: GSM1536837_06_01_15_TCGA_24.tumor_Rsubread_TPM.txt.gz
4. TCGA PAM50 classification of tumor samples: BRCA.547.PAM50.SigClust.Subtypes.txt
5. TCGA clinical dataset: GSE62944_06_01_15_TCGA_24_548_Clinical_Variables_9264_Samples.txt.gz
6. ICBP cell line single pathway optimized predictionL:optimized_single_pathway_icbp.txt (in Datasets downloadable directory below)
7. TCGA cell line single pathway optimized prediction: optimized_single_pathway_tcga.txt (in Datasets downloadable directory below)
8. Drug response assay: Drug_response_assay.txt (in Datasets downloadable directory below)
9. Gene Expression Data for GFRN Signatures (AKT, BAD, HER2, IGF1R, and RAF): [GSE83083_GFP18_AKT_BAD_HER2_IGF1R_RAF_GFP30_KRAS-G12V_tpmlog.txt.gz] (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=avanmkmqrnmrdwn&acc=GSE83083)
10. Gene Expression Data for GFRN Signatures (EGFR): GSE59765_RAW.tar

To download all the required files click Datasets.

Required R packages

1. gplots
2. RColorBrewer
3. data.table
4. mclust
5. ggplot2
6. gridExtra
7. ComplexHeatmap
8. Cluster

Other Required Files:

Key_ASSIGN_functions_balancedsig.R - This file is available in this repository.