Multivariate Analysis of RNA-seq Data

PAST software (V 4.07) (Hammer et al., 2001 ) was used to perform multivariate analyses. We performed the NM-MDS according to the Bray–Curtis similarity index using raw RNA-seq data with individual read values for each replicate (Figures 5A,B) transformed as log10. This analysis was also used to analyze (dis-)similarity between the different bacterial samples also in the expression of subsets of genes involved in host-pathogen interaction and toxin-antitoxin systems.

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Talà A., Calcagnile M., Resta S.C., Pennetta A., De Benedetto G.E, & Alifano P. (2023). Thiostrepton, a resurging drug inhibiting the stringent response to counteract antibiotic-resistance and expression of virulence determinants in Neisseria gonorrhoeae. Frontiers in Microbiology, 14, 1104454.

Publication 2023

Bacterial Expression genes Host pathogen interaction Replicate Rna seq Toxin antitoxin systems

Corresponding Organization :

Other organizations : University of Salento

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Variable analysis

independent variables

Bacterial samples

dependent variables

Gene expression levels (RNA-seq data)
Similarity/dissimilarity between bacterial samples based on gene expression

control variables

Individual read values for each replicate
Log10 transformation of RNA-seq data

controls

No positive or negative controls were explicitly mentioned.

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