Sam had run a series of ranks to see which one was most appropriate. Specifically he ran from 5-75.
It looks like 35 is where we go forward
- • Gene sparsity increases sharply after rank 35.
Heatmaps at 35
Figures for all ranks can be seen at https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries_molecular/M-multi-species/scripts/22-Visualizing-Rank-outs.html
Comparison of GO terms
Full report:
Key Findings The top 5 biological processes across all rank 35 components are:
- Innate immune response - 80 occurrences across 27 components.
- Proteolysis - 79 occurrences across 25 components.
- Positive regulation of gene expression - 78 occurrences across 27 components.
- Defense response to Gram-negative bacterium - 76 occurrences across 30 components.
- Positive regulation of transcription by RNA polymerase II - 76 occurrences across 21 components.
Some of this is part is driven by Group IDs in multiple components
