06/08/17

I used the Enrichment tool and entered in the total list of detected proteins for each of the 22 samples. I selected biological processes and a P-value cutoff of 1E-1 and downloaded all 22 reports.

Here are the text files:

We decided to track one silo through development and try to hone in on key differences in GO terms observed through development. I copied and pasted the GO terms from Silo 2 here. They are listed in order of decreasing statistical significance. Here is an excel worksheet that makes it easier to see everything at once.

Pooled larvae Day 1 (Sample 1)
mRNA processing RNA splicing mRNA metabolic process nitrogen compound metabolic process heterocycle metabolic process cellular aromatic compound metabolic process cellular nitrogen compound metabolic process organic cyclic compound metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile mRNA splicing, via spliceosome RNA splicing, via transesterification reactions RNA processing nucleobase-containing compound metabolic process small molecule metabolic process organonitrogen compound metabolic process generation of precursor metabolites and energy metabolic process cellular metabolic process energy derivation by oxidation of organic compounds purine ribonucleoside monophosphate metabolic process purine nucleoside monophosphate metabolic process organic substance catabolic process ribonucleoside monophosphate metabolic process regulation of translation nucleobase-containing small molecule metabolic process gene expression cofactor metabolic process regulation of cellular amide metabolic process small molecule catabolic process nucleoside monophosphate metabolic process oxidation-reduction process cilium morphogenesis organic acid metabolic process regulation of mRNA metabolic process

Silo 2-23C Day 3 (Sample 3)
mRNA metabolic process mRNA processing RNA splicing nitrogen compound metabolic process cellular nitrogen compound metabolic process small molecule metabolic process heterocycle metabolic process organonitrogen compound metabolic process cellular aromatic compound metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile mRNA splicing, via spliceosome purine ribonucleoside monophosphate metabolic process purine nucleoside monophosphate metabolic process RNA splicing, via transesterification reactions organic cyclic compound metabolic process generation of precursor metabolites and energy nucleobase-containing compound metabolic process organic acid metabolic process ribonucleoside monophosphate metabolic process oxoacid metabolic process carboxylic acid metabolic process cellular amino acid metabolic process nucleoside monophosphate metabolic process ribonucleoside triphosphate metabolic process nucleoside triphosphate metabolic process ATP metabolic process gene expression purine ribonucleoside triphosphate metabolic process nicotinamide nucleotide metabolic process oxidation-reduction process RNA processing organic substance catabolic process oxidoreduction coenzyme metabolic process small molecule catabolic process energy derivation by oxidation of organic compounds pyridine nucleotide metabolic process ribonucleoside diphosphate metabolic process peptidyl-proline modification

Silo 2-23C Day 5 (Sample 11)
small molecule metabolic process organonitrogen compound metabolic process purine ribonucleoside monophosphate metabolic process purine nucleoside monophosphate metabolic process organic acid metabolic process ribonucleoside metabolic process purine ribonucleoside metabolic process oxoacid metabolic process purine nucleoside metabolic process nucleoside monophosphate metabolic process ribonucleoside monophosphate metabolic process single-organism metabolic process carboxylic acid metabolic process generation of precursor metabolites and energy nucleoside metabolic process glycosyl compound metabolic process oxidation-reduction process organic substance catabolic process nucleobase-containing small molecule metabolic process small molecule catabolic process catabolic process single-organism catabolic process energy derivation by oxidation of organic compounds nucleoside triphosphate metabolic process ribonucleoside triphosphate metabolic process nucleoside phosphate metabolic process purine ribonucleoside triphosphate metabolic process nucleoside diphosphate metabolic process nucleotide metabolic process regulation of translation regulation of cellular amide metabolic process mRNA metabolic process ATP metabolic process posttranscriptional regulation of gene expression cellular catabolic process purine-containing compound metabolic process organonitrogen compound biosynthetic process RNA splicing cellular amino acid metabolic process mRNA processing ribose phosphate metabolic process single-organism carbohydrate catabolic process purine ribonucleotide metabolic process

Silo 2-23C Day 7 (Sample 19)
organonitrogen compound metabolic process oxidation-reduction process purine ribonucleoside monophosphate metabolic process purine nucleoside monophosphate metabolic process ribonucleoside monophosphate metabolic process nucleoside monophosphate metabolic process small molecule metabolic process mRNA metabolic process RNA splicing generation of precursor metabolites and energy energy derivation by oxidation of organic compounds ribonucleoside triphosphate metabolic process mRNA processing ATP metabolic process single-organism metabolic process purine ribonucleoside triphosphate metabolic process carboxylic acid metabolic process ribonucleoside metabolic process organic acid metabolic process oxoacid metabolic process purine ribonucleoside metabolic process nucleoside metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile mRNA splicing, via spliceosome purine nucleoside metabolic process cellular respiration organonitrogen compound biosynthetic process glycosyl compound metabolic process nucleoside triphosphate metabolic process peptide metabolic process RNA splicing, via transesterification reactions intracellular transport organic substance catabolic process

Silo 2-23C Day 9 (Sample 27)
nucleoside triphosphate metabolic process purine nucleoside monophosphate metabolic process purine ribonucleoside monophosphate metabolic process organonitrogen compound metabolic process ribonucleoside triphosphate metabolic process nucleoside monophosphate metabolic process ATP metabolic process ribonucleoside monophosphate metabolic process purine ribonucleoside triphosphate metabolic process generation of precursor metabolites and energy purine nucleoside triphosphate metabolic process RNA splicing small molecule metabolic process organic substance catabolic process catabolic process purine ribonucleoside metabolic process ribonucleoside metabolic process organonitrogen compound biosynthetic process purine nucleoside metabolic process organic acid metabolic process mRNA metabolic process oxoacid metabolic process carboxylic acid metabolic process glycosyl compound metabolic process energy derivation by oxidation of organic compounds nucleoside metabolic process nucleobase-containing small molecule metabolic process purine nucleoside diphosphate metabolic process purine ribonucleoside diphosphate metabolic process nucleoside phosphate metabolic process nucleoside diphosphate metabolic process mRNA processing protein folding nucleotide metabolic process ADP metabolic process cellular catabolic process nucleoside diphosphate phosphorylation ribonucleoside diphosphate metabolic process single-organism catabolic process nitrogen compound metabolic process ATP generation from ADP glycolytic process ribose phosphate metabolic process purine-containing compound metabolic process protein peptidyl-prolyl isomerization pyruvate metabolic process purine ribonucleotide metabolic process nicotinamide nucleotide metabolic process ribonucleotide metabolic process small molecule catabolic process nucleotide phosphorylation RNA splicing, via transesterification reactions with bulged adenosine as nucleophile mRNA splicing, via spliceosome cellular nitrogen compound metabolic process purine nucleotide metabolic process chaperone-mediated protein folding nucleoside triphosphate biosynthetic process pyridine nucleotide metabolic process organophosphate metabolic process cellular metabolic process carbohydrate derivative metabolic process oxidation-reduction process cellular respiration RNA splicing, via transesterification reactions

Silo 2-23C Day 11 (Sample 35)
organonitrogen compound metabolic process small molecule metabolic process organic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process organonitrogen compound biosynthetic process single-organism catabolic process generation of precursor metabolites and energy small molecule catabolic process purine nucleoside monophosphate metabolic process purine ribonucleoside monophosphate metabolic process translation peptide biosynthetic process purine ribonucleoside triphosphate metabolic process catabolic process ATP metabolic process organic substance catabolic process purine ribonucleoside metabolic process purine nucleoside metabolic process organic acid catabolic process carboxylic acid catabolic process cellular amino acid metabolic process ribonucleoside monophosphate metabolic process purine nucleoside triphosphate metabolic process nucleoside diphosphate phosphorylation ribonucleoside triphosphate metabolic process nucleoside triphosphate metabolic process glycosyl compound metabolic process purine ribonucleotide metabolic process purine-containing compound metabolic process nucleoside metabolic process amide biosynthetic process purine nucleotide metabolic process nucleoside monophosphate metabolic process monocarboxylic acid metabolic process ribose phosphate metabolic process ribonucleoside metabolic process peptide metabolic process carbohydrate derivative metabolic process nucleotide phosphorylation nucleoside diphosphate metabolic process energy derivation by oxidation of organic compounds ribonucleotide metabolic process oxidation-reduction process nucleobase-containing small molecule metabolic process cellular amide metabolic process nucleoside phosphate metabolic process fatty acid oxidation lipid oxidation nucleotide metabolic process protein folding ADP metabolic process nicotinamide nucleotide metabolic process purine nucleoside diphosphate metabolic process purine ribonucleoside diphosphate metabolic process fatty acid beta-oxidation pyridine nucleotide metabolic process monocarboxylic acid catabolic process ATP generation from ADP glycolytic process cellular amino acid catabolic process carbohydrate catabolic process cellular catabolic process ribonucleoside diphosphate metabolic process cellular respiration fatty acid beta-oxidation using acyl-CoA dehydrogenase single-organism metabolic process alpha-amino acid catabolic process fatty acid catabolic process pyruvate metabolic process alpha-amino acid metabolic process oxidoreduction coenzyme metabolic process formation of translation preinitiation complex organonitrogen compound catabolic process coenzyme metabolic process pyridine-containing compound metabolic process

_Silo 2-23C Day 13 (Sample 43)
organonitrogen compound metabolic process small molecule metabolic process organic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process organonitrogen compound biosynthetic process catabolic process organic substance catabolic process translation single-organism metabolic process purine nucleoside monophosphate metabolic process purine ribonucleoside monophosphate metabolic process peptide biosynthetic process glycosyl compound metabolic process cellular amino acid metabolic process ribonucleoside monophosphate metabolic process generation of precursor metabolites and energy cellular catabolic process nucleobase-containing small molecule metabolic process purine nucleoside metabolic process single-organism catabolic process cellular amide metabolic process nucleoside metabolic process nucleoside monophosphate metabolic process amide biosynthetic process small molecule catabolic process purine ribonucleoside metabolic process peptide metabolic process oxidation-reduction process ribonucleoside metabolic process purine ribonucleoside triphosphate metabolic process ATP metabolic process nucleoside triphosphate metabolic process protein folding organic acid catabolic process carboxylic acid catabolic process nucleoside phosphate metabolic process purine-containing compound metabolic process ribonucleoside triphosphate metabolic process nucleotide metabolic process energy derivation by oxidation of organic compounds purine nucleoside triphosphate metabolic process nucleoside diphosphate phosphorylation ribose phosphate metabolic process carbohydrate derivative metabolic process purine ribonucleotide metabolic process ribonucleotide metabolic process nucleotide phosphorylation nucleoside diphosphate metabolic process alpha-amino acid metabolic process purine nucleotide metabolic process chaperone-mediated protein folding tRNA aminoacylation for protein translation purine nucleoside diphosphate metabolic process purine ribonucleoside diphosphate metabolic process metabolic process nicotinamide nucleotide metabolic process monocarboxylic acid metabolic process amino acid activation tRNA aminoacylation

Silo 2-23C Day 15 (Sample 51)
organonitrogen compound metabolic process small molecule metabolic process organic substance catabolic process catabolic process oxidation-reduction process organic acid metabolic process cellular catabolic process oxoacid metabolic process single-organism metabolic process mRNA metabolic process carboxylic acid metabolic process purine ribonucleoside monophosphate metabolic process purine nucleoside monophosphate metabolic process organonitrogen compound biosynthetic process mRNA processing small molecule catabolic process ribonucleoside monophosphate metabolic process generation of precursor metabolites and energy protein folding single-organism catabolic process RNA splicing nitrogen compound metabolic process nucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic process nucleoside phosphate metabolic process energy derivation by oxidation of organic compounds nucleotide metabolic process cellular metabolic process metabolic process nucleoside triphosphate metabolic process intracellular protein transport intracellular transport cellular nitrogen compound metabolic process cofactor metabolic process ribonucleoside metabolic process protein transport ribonucleoside triphosphate metabolic process Golgi vesicle transport nicotinamide nucleotide metabolic process ATP metabolic process establishment of protein localization purine ribonucleoside metabolic process glycosyl compound metabolic process