Kaitlyn’s notebook: Gene enrichment

14 IDs could be mapped (out of 28) using DAVID.

Focal adhesion was enriched in the KEGG-PATHWAY with a p-value of 5.4E-2 and Benjamini 6.1E-1.

UNIPROT-ACCESSION GENE NAME Related Genes Species
A8TX70 collagen type VI alpha 5 chain(COL6A5) RG Homo sapiens
P21333 filamin A(FLNA) RG Homo sapiens

I downloaded:

  • BP_DIRECT
  • BP_FAT
  • BP_ALL
  • UP_KEYWORDS
  • the functional clustering chart for BP_FAT, BP_ALL, and BP_DIRECT

BP_DIRECT had the fewest enriched processes (and they all fit in one screenshot unlike the others that could only be accurately visualized if they were downloaded):

BP-direct

BP_DIRECT are the annotations from the source (which I believe would be considered Uniprot) without any parent terms included.

The number of enriched processes has increased quite a bit since I added in the 0 abundance proteins to even out the protein list between silos after cluster analysis. Creating a heat map with the processes doesn’t seem like it will visualize the data correctly or easily. I’m going to see what other visualization tools downstream of gene enrichment analysis exist and if any are feasible for my data that I can try.