Correlate Histopathological Image and Transcriptomics Data to Identify the Molecular Basis of Nuclear Morphology with Gene Co-expression Network Approach
final_script.R: R script of project
TCGA.BRCA.htseq_counts.tsv.gz: BRCA read counts from GDC
gencode.v22.annotation.gene: Gene information file
BRCA.im.select.txt: morphology features value
genecount.txt: source read counts input file of TSUNAMI
raw_genecount.RData: processed read counts file of RData
protein_coding.hg38.position:mRNA position information
coexp_modules.csv: gene sets of modules from TSUNAMI
coexp_eigengene_matrix.csv: eigengene of modules from TSUNAMI
datamatrix_2.csv: read counts filtered by TSUNAMI
TCGA-BRCA.survival.tsv: survival data of BRCA from GDC
clinical.tsv: clinical information of BRCA from GDC
basic_data.RData: RData of all basically data
expr.txt: read counts data used to calculate immune score
Estimate_gene.gct: filtered read counts data from expr.txt
Estimate_score.gct: result of immune score
c1.all.v7.4.entrez.gmt: Gene sets corresponding to each human chromosome and each cytogenetic band
cytoband.txt: cytoband enrichment result
Table_GO_result.csv: GO term enrichment result
GO_enrichment.RData: GO term enrichment result of RData file
enrich_model.RData: summary GO term enrichment result of all module
cytoband_module.RData: summary cytoband enrichment result of all module
module*.tsv: tf enrichment result of modules
module*_regulate_network_allgene.txt: TF-gene network information of modules
module*_regulate_network_type_allgene.txt: node information of TF-gene network
module*_image_gene_heatmap.pdf: correlation heatmap of morphology feature and genes
Module*_interactions_short.tsv: ppi network file from STRING database
module*_cytohubba.csv: hubgene lists from ppi network
riskscore.RData: risk score result of samples
alter_predict_final.RData: predict model process file
multi_cox_result.txt: multivariate cox regression result of risk score
ref.bib: bibtex of reference
module*_ppi.pdf: ppi network figure
module*_regulate_network.pdf: regulate network figure
univariate_cox_result.txt: univariate cox regression result of morphology features
Module*_expression.pdf: gene expression distribution of high- and low-risk score group
feature_heatmap: heatmap of morphology features in high- and low-risk score group
feature_wilcox.pdf: morphology features wilcox test of high- and low-risk score group
auc.pdf: AUC curve figure
survival.pdf: survival curve of high- and low-risk score group
riskscore.pdf: samples risk score distribution of high- and low-risk score group
feature_cor_eigengene.pdf: correlation heatmap of morphology features and eigengene
cytoband.pdf: cytobands enrichment result figure
go.pdf: go term enrichment result figure
