1. Intraset concordancy and transcriptome-proteome discordancy of gene products related to protein translation, OxP, and chaperone proteins.
Intraset concordancy and transcriptome-proteome discordancy of gene products related to protein translation, OxP, and chaperone proteins. (A) The eIF and RP complexes displayed significant intraset concordancy (Pc [transcriptome] = 8.9E−16) and transcriptome-proteome discordancy (cyan outlines). (B) The OxP pathway also displayed significant intraset concordancy [qe (transcriptome, up) = 3.4E−6, Pc[transcriptome] = 9.3E−10] and transcriptome-proteome discordancy (cyan outlines). (C) All of the following categories of transcriptome and proteome data related to the four annotations were analyzed: eIFs, the 40S ribosomal complex (RPS), the 60S ribosomal complex (RPL), and the OxP pathway. Each triangle depicts a microarray probe (transcriptome [Trans.] data subset) or a protein group (quantified nonredundantly; proteome [Prot.] data subset). Red and blue triangles depict significantly increased and decreased gene products, respectively (gray triangles = not significantly affected). The lines indicate each median and interquartile range. Each binomial test either used all of the data or was restricted to just the significantly affected data, as indicated. n/a, not applicable. (D) A protein-protein interaction network was prepared using all of the chaperones (rectangles) and cochaperones (ovals) that were significantly affected by germ status within the proteome data subset, and the intraset concordance was significant (Pc = 6.1E−5). Also included are the E3 ubiquitin ligases (yellow hexagons) that have been reported to associate with chaperones and typically target misfolded/unfolded proteins. Edge weight data depict the protein-protein interaction confidence (increasing weight values depict low, medium, high, and very high confidence). (E) Summary of the effects on the GF mouse intestine. The decrease in immune cell populations was reported previously by Morgun et al. (14).
Nathan P. Manes et al. mSystems 2017; doi: /mSystems