Data set repositories

5. Training_TCGA_203samples.txt

There are 15 files in this data repository. The descriptions for each file are as follows:

1. tcga_tumor.exp.txt

The processed TCGA-CESC RNA-Seq data, which was normalized as fragments per kilobase of transcript per million mapped reads (FPKM) and then log2-transformed.

2.CGCI.tumor.exp.tsv

The processed CGCI-HTMCP-CC RNA-Seq data, which was normalized as fragments per kilobase of transcript per million mapped reads (FPKM) and then log2-transformed.

3. GSE72723_GPL6884_data.txt

The gene expression data in GSE72723, which was downloaded using R library ‘GEOquery’ and annotated according to GPL6884 platform.

4. GSE72723_GPL10558_data.txt

The gene expression data in GSE72723, which was downloaded using R library ‘GEOquery’ and annotated according to GPL10558 platform.

This is the training dataset for developing ccHPS model using 70% of TCGA-CESC cohort samples.

6. Test1_TCGA_86samples.txt

This is the first validation dataset of ccHPS model using the rest of 30% of TCGA-CESC cohort samples.

7. Test2_CGCI-HTMCP-CC_117samples.txt

This is an independent validation dataset using CGCI-HTMCP-CC cohort samples.

8. ccHPS_score_GPL10558.tsv

ccHPS score calculated for each sample in GSE72723 with array platform GPL10558.

9. ccHPS_score_GPL6884.tsv

ccHPS score calculated for each sample in GSE72723 with array platform GPL6884.

10.ccHPS_score_TCGA.tsv

ccHPS score calculated for TCGA samples.

11.ccHPS_score_CGCI-HTMCP-CC.txt

ccHPS score calculated for CGCI-HTMCP-CC samples.

12. ccHPS score for cervical cancer cell lines.txt

ccHPS score calculated for eight cervical cancer cell lines treated in hypoxic and normoxic conditions.

13.Differential_gene_analysis_rank_between_high_low_risk.txt

The different gene analysis result using 'limma' package between high-risk and low-risk samples.

14.ESTIMATEscore.txt

The ESTIMATE score for each TCGA-CESC sample.

15. tcga.drug_sensitivity_predicted_allSolidTumor.txt

Drug estimated IC50 of each sample.

16.scripts.zip

This zip folder includes four R scripts used in data analysis (calculate_CIBERSORT.R, calculate_MCPcounter.R, GSEA analysis.R and ccHPS.R)