Table 1 Transcriptional differences in HP compared to the WT strain at the level of biological processes
Gene sets | HP vs WT | ||||||
|---|---|---|---|---|---|---|---|
Ontology | Name | Code | Size | t1 | t2 | t3 | t4 |
KEGG Pathway | Translation | 145 | + | + | |||
Ribosome | sen03010 | 64 | + | + | |||
Metabolism of terpenoids and polyketides | 128 | + | + | + | |||
Biosynthesis of ansamycins | sen01051 | 13 | + | + | + | ||
Biosynthesis of 12-, 14- and 16-membered macrolides | sen00522 | 8 | + | + | + | ||
Type I polyketide structures | sen01052 | 9 | + | + | + | ||
Nitrogen metabolism | sen00910 | 56 | − | ||||
C5-branched dibasic acid metabolism | sen00660 | 10 | + | ||||
Valine, leucine and isoleucine biosynthesis | sen00290 | 23 | + | ||||
Tyrosine metabolism | sen00350 | 38 | − | ||||
Tryptophan metabolism | sen00380 | 39 | + | + | |||
Glycolysis/gluconeogenesis | sen00010 | 74 | − | ||||
Citrate cycle (TCA cycle) | sen00020 | 48 | − | ||||
Pyruvate metabolism | sen00620 | 73 | − | ||||
Metabolism of cofactors and vitamins | 192 | + | |||||
Lipid metabolism | 169 | − | |||||
Fatty acid biosynthesis | sen00061 | 29 | − | ||||
Xenobiotics biodegradation and metabolism | 175 | − | |||||
Styrene degradation | sen00643 | 13 | + | ||||
Atrazine degradation | sen01052 | 9 | − | − | |||
Purine metabolism | sen00230 | 88 | − | − | |||
Nucleotide metabolism | 118 | − | − | − | |||
Oxidative phosphorylation | sen00190 | 49 | + | ||||
Inositol phosphate metabolism | sen00562 | 20 | + | ||||
Membrane transport | 138 | − | |||||
ABC transporters | sen02010 | 117 | − | ||||
GO biological process | DNA biosynthetic process | GO:0071897 | 18 | − | − | ||
DNA replication | GO:0006260 | 29 | − | − | |||
DNA integration | GO:0015074 | 48 | − | ||||
DNA recombination | GO:0006310 | 44 | + | − | |||
DNA repair | GO:0006281 | 45 | − | ||||
Transposition, DNA-mediated | GO:0006313 | 62 | − | − | − | ||
DNA-templated transcription, initiation | GO:0006352 | 36 | − | − | − | ||
Negative regulation of transcription, DNA-templated | GO:0045892 | 19 | − | − | |||
Translation | GO:0006412 | 68 | + | + | + | ||
Methylation | GO:0032259 | 126 | + | ||||
Dephosphorylation | GO:0016311 | 26 | + | ||||
Biosynthetic process | GO:0009058 | 59 | + | + | |||
Fatty acid biosynthetic process | GO:0006633 | 23 | − | ||||
Antibiotic biosynthetic process | GO:0017000 | 16 | + | + | + | ||
Proteolysis | GO:0006508 | 152 | + | + | + | ||
Amino acid transmembrane transport | GO:0003333 | 33 | − | ||||
Carbohydrate transport | GO:0008643 | 25 | − | ||||