Kaitlyn’s notebook: Enrichment and Protein abundance heatmaps

These heatmaps were created by using the BP-FAT file created by DAVID when I entered my uniquely clustered proteins with a background of all detected proteins (in silos 3 and 9).

  • Enriched processes merged back to a protein based on Uniprot Accession IDs
  • Protein abundances are values in heatmap
  • merged-test-table

These heatmaps show how the protein abundances change over time for proteins whose Uniprot accession codes are associated with enriched BPs represented by parent terms which were given by DAVID during enrichment analysis.

I also included the heatmaps clustered by time below the first pair of plots.

The patterns of abundance seem to be very similar between the two silos, but silo 3 tends to have higher abundances than silo 9 except with platelet degranulation.

heatmap-silo3.jpeg

heatmap-silo9


 

The days are clustered in the plots below. If we look only until the second node, we see  three main groups for Silo 3:

  1. Day 13
  2. Days 7, 5, 11, 9 
  3. Days 15, 0, 3

and two main groups for Silo 9:

  1. Days 0, 3, 9   
  2. Days 15, 13, 11, 7, 5

Based on this, we can see that protein abundance patterns are different between the silos, but we knew this already since these proteins were selected based on differential clustering before. The new information we can see is how the processes the proteins are linked to shift based on time.

heatmap-silo3-clus

heatmap-silo9-clus

This was done with the BP-FAT file because it had the fewest enriched processes and would be the easiest to work with and view as a test attempt. Here is the code I made.