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Fig. 2 | Genome Medicine

Fig. 2

From: Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data

Fig. 2

Validation of the reconstructed microbiome profiles from The Cancer Genome Atlas (TCGA) with the European Institute of Oncology (IEO) cohort. a Principal component analysis of microbiome profiles from the TCGA (primary tumour and non-pathological solid tissue normal samples) and the IEO cohort shows cross-cohort clustering of colon adenocarcinoma samples. b Total number of normal and tumour samples. c Density plot of the Spearman coefficients describing the correlation between the 76 most abundant bacterial genera (present in more than 20% of the samples) profiled in both RNA sequencing (RNA-Seq) and ribosomal RNA 16S gene (16S) sequencing data. The majority of correlation coefficients are significantly larger than zero (p < 0.005, one-sample Wilcoxon test), meaning a similar tendency of detecting bacteria by the two approaches. d Correlation between the reconstructed microbiome (RNA-Seq bacterial relative abundances) and fluorescence in situ hybridisation (FISH) quantification of two bacteria, Faecalibacterium prausnitzii and Akkermansia muciniphila. Pearson (rp) and Spearman (rs) coefficients are indicated. e Representative FISH images of A. muciniphila and F. prausnitzii. GBM, glioblastoma multiforme; LUAD, lung adenocarcinoma; LUSC, lung squamous cell carcinoma; HNSC, head and neck squamous cell carcinoma; OV, ovarian serous cystadenocarcinoma; READ, rectum adenocarcinoma; SKCM, skin cutaneous melanoma, BRCA, breast invasive carcinoma. Number of samples analysed in brackets

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