Mon. Mar 4, 2019 oyster proteomics network analysis

Network analysis on same-day temperature ChiSq pvalue 0.1 selected proteins

Conclusions:

  • Temperature seems to affect the biological processes transport, metabolism, and development
    • Regarding transport, a couple of proteins related to cytoskeleton-dependent intracellular transport are upregulated at 29C across almost all days while a few proteins related to vesicle mediated transport are downregulated especially on Day 13.
    • Regarding metabolism, over time there is a general downregulation of proteins associated with different metabolic processes at 29C.
    • Regarding development, early on at Day 3 there is an upregulation of proteins associated with cell morphogenesis and nervous system processes at 29C. Day 11 also shows more upregulated than downregulated development proteins at 29C
      • revisiting past analysis, the PCA of technical replicates showed that 29C time points sometimes clustered with the succeeding 23C time points, suggesting the increased temperature could speed up development.
      • This could be apparent in the ASCA PCA plot of the timextemperature interaction effect with most of the 23C time points being separated from most of the 29C time points along PC1. This could be more dramatic separation if I removed time point 0.
      • revisiting phenotypic data Rhonda gathered, on Day 6, 29C seed was generally larger in size
      • .

To do:

  • Need to swap CHOYP names for gene names or protein names
  • Dig into the lit about the proteins mentioned above so get a better idea of the implications of their temperature-altered abundance.
  • Probably need to threshold the uniprot mapping by e-value since I haven’t done that yet
  • Maybe try this mapping pipeline for molecular function GO terms
  • see what people think about this network analysis
  • It would be cool to visualize these networks as dynamic networks rather than each day side-by-side. And there seem to be a few Cytoscape apps for visualising dynamic networks
Written on March 4, 2019