EEEC_landscape

This repository contains metadata and codes necessary for analysis of the proteogenomics data of Endometrial Carcinoma presented in Hu et al. Nature Genetics (2024).

Data availability

• Raw sequencing data generated in this study are deposited in Genome Sequence Archive for Human (https://ngdc.cncb.ac.cn/gsa-human/) with accession number HRA003319.
• The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD046507.
• TCGA-UCEC and CPTAC-UCEC data was obtained from Cbioportal (https://www.cbioportal.org/) with the dataset identifier ucec_tcga_pan_can_atlas_2018 and ucec_cptac_2020.
• Panel sequencing of genomic data from AACR GENIE Project was obtained from Synapse (https://www.synapse.org/) with the dataset identifier syn7222066.
• RNA-seq data from six public datasets (GSE1378, GSE1379, GSE6532, GSE9195, GSE12093, GSE17705) of patients with breast cancer treated with endocrine therapy was obtrained from GEO.

Data visualization

Requirements

Tested on macOS Ventura and CentOS

1. R version: 4.1.2
2. R packages
   • ggplot2
   • data.table
   • maftools
   • dplyr
   • tidyr
   • ggpubr
   • RColorBrewer
   • pheatmap
   • ggsignif
   • ComplexHeatmap