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. 2019 May 21;4(4):e00202-19. doi: 10.1128/mSystems.00202-19

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Copyright © 2019 Lee et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

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FIG 3 — Within-group and between-group connectivity in KlebNet for genes involved in carbapenem resistance and virulence. (A) Analysis of within-group connectivity among positive (+)-resistance genes (34 genes upregulated in K56). The null model of the within-group edge count was generated by the use of 10,000 random sets of 34 genes. The horizontal line in the violin plot indicates the median, and the red dot indicates the within-group edge count for the positive-resistance genes. The P value was determined on the basis of a permutation test. (B) Analysis of within-group connectivity among negative (−)-resistance genes (15 genes that were mutated in meropenem-resistant strain K56). A significance test was performed as described for panel A. (C) Analysis of connectivity between 15 negative-resistance genes and 34 positive-resistance genes. KlebNet edges for within-group connections are indicated by shading in the network. The null model of the between-group edge count was generated by the use of 10,000 paired random sets, one set of 15 random genes, and one set of 34 random genes. The P value was determined on the basis of a permutation test. (D) Analysis of within-group connectivity among 59 virulence genes associated with mouse lung infections. A significance test was performed as described for panel A. (E) Analysis of connectivity between 34 positive-resistance genes and 59 virulence genes. Significance testing was performed as described for panel C. (F) Analysis of connectivity between 15 negative-resistance genes and 59 virulence genes. Significance testing was performed as described for panel C.