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Fig. 4 | Microbiome

Fig. 4

From: Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data

Fig. 4

The log10-transformed ratios of bacterial read pairs from a specific taxon to the total number of bacterial read pairs from that patient were calculated for all AML samples as described in Fig. 3. Ratios where the numerator was 0 were assigned an arbitrary value of −7, ratios where both the numerator and denominator were 0 were assigned an arbitrary value of 0, and comparisons where the denominator was 0 were assigned an arbitrary value of 7. Counts for the number of patients where one of these arbitrary values were assigned are shown below the x-axis. When >5 points are at a given value, some data points may overlap each other making it impossible for all data points to be seen. The samples were all collected and sequenced at the same locations, and the data are color-coded by plate. The samples on plate 735 and 736 have a higher abundance of Ralstonia spp., suggesting that these samples may have been contaminated and this may be responsible for the bimodal distribution of samples in those comparisons. As was seen with the plot of all the cancer types, there is very little variation for the comparison of Staphylococcus spp. to Propionibacterium spp

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