Kaitlyn’s notebook: Enrichment on all proteins in each silo

I used DAVID to run gene enrichment on each silo. The input was Uniprot accession codes. Significance cutoffs were at 0.05 for Benjamini corrected p-values (false discovery rate). I’m going to look at the clusters for each silo next.

Pathways:

Biosynthesis of antibiotics and the spliceosome were enriched in all silos, and the spliceosome was enriched in the same place for each silo. Antibiotic synthesis suggests that all of the larvae needed to dedicate large amounts of energy into preventing or fighting infection, possibly suggesting an increased vulnerability, contagion or vial survival or proliferation. This is consistent with mass mortality events commonly seen in hatcheries. An enriched spliceosome could suggest that editing mRNA for translation is occurring at a high rate at this point in development. Could this be because of the larva’s need to produce higher amounts of protein, or could this be the beginning of increased protein synthesis for growth?

Biological Processes:

Protein folding was the most enriched for every silo. Silo 2 and Silo 3 were almost identical except that Silo 3 lacked enriched oxidation-reduction processes. Silo 9 did have enriched oxidation-reduction pathways as well as intra-golgi vesicle mediated transport which was not enriched in any other silo. I’m not sure how increased intra-golgi vesicle mediated transport might affect the organism. The golgi is responsible for post-translational modification and distribution of proteins. It produces proteoglycans, plays a role in lipid metabolism, and lysosome production. Also, silo 9 lacked enriched viral processes which was enriched in silos 3 and 9 suggesting increased viral influences at cooler silos.

The overall trend is increases in protein production, modification and transport. Silos 2 and 3 have viral processes enriched in addition to those. However, silo 9 has the greatest p-value associated with biosynthesis of antibiotics (9.9E-4 compared to 3.7E-3 for Silo 3 and 1.1E-3 for Silo 2).

Process #
S2 Process #
S3 Process #
S9
1 protein folding 1 protein folding 1 protein folding
2 RNA splicing 2 RNA splicing 6 ER to Golgi vesicle-mediated transport
3 mRNA processing 3 mRNA processing 5 cell-cell adhesion
4 intracellular protein transport 4 intracellular protein transport 3 mRNA processing
5 cell-cell adhesion 6 ER to Golgi vesicle-mediated transport 7 protein transport
6 ER to Golgi vesicle-mediated transport 7 protein transport 4 intracellular protein transport
7 protein transport 5 cell-cell adhesion 2 RNA splicing
8 oxidation-reduction process 9 viral process 8
oxidation-reduction process
9 viral process 10 mRNA splicing, via spliceosome 10 mRNA splicing, via spliceosome
10 mRNA splicing, via spliceosome       intra-Golgi vesicle-mediated transport

 

Silo 9(29C):

Silo 3(23C):

Silo 2(23C):