Here we provide supplemental data for our publication

Hadzega, D.; Minarik, G.; Karaba, M.; Kalavska, K.; Benca, J.; Ciernikova, S.; Sedlackova, T.; Nemcova, P.; Bohac, M.; Pindak, D.; Klucar, L; Mego, M.
Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq.
Int. J. Mol. Sci. 2021, 22, 9058.
https://doi.org/10.3390/ijms22169058

There are two directories on this website (http://www.embnet.sk/supp/BC_metatranscriptomics/) :

1. LefSe_plot_differential_features/

   For every comparison (from the next directory) transcript profile for every single called microbe or virus was plotted.

2. complete_plots_plotLefSeResults/

   All plots for LefSe results are presented here. Two or more groups were compared to find out overrepresented or underrepresented microbes in one of them. While in the figures in the publication graphs contain only results with stricter conditions (specified there), here the graphs have been made under default LefSe parameters (LDA>2, Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05).

   Files:

   • LefSe_CTC.png - comparison between  breast cancer (BC) patients with circulating tumour cells (CTC) detected in their blood and those negative on CTC detectection
   • LefSe_HER2.png - comparison between BC patients positive on HER2 marker (HER2+) and HER2-patients
   • LefSe_HR.png - comparison between BC patients positive on hormonal receptor markers (HR+) and HR- patients
   • LefSe_Ki64.png - comparison between patients  with proliferation index (Ki67) <20% and those with Ki67 >20%
   • LefSe_Nstage.png - comparison between patients with higher and lower Nstage
   • LefSe_SRA_ChineseSamples_BreastTumour_vs_Nomaltissue.png - comparison between primary breast tumour tissue microbiome of 73 Chinese women and normal breast tissue of 18 healthy women
   • LefSe_SlovakSamples_BreastTumour_vs_NormalTissue.png - comparison between primary breast tumour tissue microbiome of 18 Slovak women and normal breast tissue of 5 healthy women
   • LefSe_Tstage.png - comparison between patients with higher and lower Tstage
   • LefSe_grade.png - comparison between patients according to tumour grading
   • LefSe_molecular_subtypes.png - comparison between patients with different molecular subtypes of BC - luminal A, luminal B, HER2+, triple negative breast cancer (TNBC)
   • LefSe_p53.png - comparison between patients with detected p53 protein and undetected p53 protein
   • LefSe_Nomal_age.png - comparison between healthy donors over age of 50 and healthy donors below age of 50