Circadian Rhythm Genes in Cancer Transcriptome Analysis

A total of 48 CRGs, including 13 clock control genes and 35 core clock genes, were obtained when we used the keywords ((((circadian clock gene) OR (circadian rhythm gene) OR (clock control gene) OR (core clock gene)) AND (cancer)) in PubMed (https://pubmed.ncbi.nlm.nih.gov/) (Additional file 4: Table S1).
In the Cancer Genome Atlas data portal (TCGA, https://portal.gdc.cancer.gov/), 18 cancer types (Additional file 4: Table S2) were filtered based on the presence of at least 5 normal samples. We downloaded RNA-Seq data expressed as fragments per kilobase per million (FPKM) from the UCSC Xena browser (GDC Center, https://gdc.xenahubs.net). The gene-expression profiles of TCGA in the Fragments Per Kilobase per Million (FPKM) format were transformed into TPMs (transcripts per kilobase million) by using R version 4.2.0 software. Additionally downloaded for analysis were clinical data, copy number variation data, and single nucleotide variation data.
Microarray datasets including gene expression profiles and corresponding clinical information data of GSE42568, GSE14333, and GSE31908 were employed from the Gene Expression Omnibus database (GEO, https://www.ncbi.nlm.nih.gov/geo/). We downloaded the chemotherapy and immunotherapy response datasets from the GEO database (GSE25055, GSE20194, GSE42127, GSE14814, GSE146163, GSE78220, and GSE174570). Moreover, we acquired four sets of mice's expression profile data from the GEO database that had circadian rhythm genes knocked out (GSE134333, GSE188688, GSE134333, and GSE143524). For microarray data, we performed log2 conversion of the normalized expression profile data. The list of these datasets was displayed in Additional file 4: Table S3.