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Table 5 Domains absent in lineages under positive selection

From: Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates

Under-Represented CATH Domain Topologies in TAED
CATH domain topologyMapped Lineages Under Positive SelectionLineages Under Positive Selection MappedUncorrected P-valueFDR P-valueBonferroni P-value
Smad3 Chain A0.08%<  0.01%<  0.0001<  0.0001<  0.0001
A middle domain of Talin 10.24%<  0.01%<  0.0001<  0.0001<  0.0001
Endonuclease - Pi-scei_ Chain A domain 10.27%<  0.01%<  0.0001<  0.0001<  0.0001
Undecaprenyl pyrophosphate synthetase0.33%<  0.01%<  0.0001<  0.0001<  0.0001
Neurophysin II Chain A0.38%<  0.01%<  0.0001<  0.00010.0002
Major Prion Protein0.43%<  0.01%<  0.0001<  0.00010.0010
Archaeosine Trna-guanine Transglycosylase Chain: A domain 40.45%<  0.01%<  0.0001<  0.00010.0023
Translation Eukaryotic Peptide Chain Release Factor Subunit 1 Chain A0.52%<  0.01%<  0.00010.00020.0140
PWI domain0.53%<  0.01%<  0.00010.00030.0206
copper amine oxidase-like fold0.57%<  0.01%0.00010.00050.0472
ERH-like fold0.58%<  0.01%0.00010.00070.0608
Smad Anchor For Receptor Activation Chain B0.61%<  0.01%0.00020.00100.1011
protein kinase ck2 holoenzyme chain C domain 10.61%<  0.01%0.00020.00100.1011
Elongin C Chain C domain 10.65%<  0.01%0.00030.00170.1785
Conserved hypothetical protein from pyrococcus furiosus pfu- 392,566-001 ParB domain0.90%<  0.01%0.00420.01951.0000
titin filament fold0.92%<  0.01%0.00480.02141.0000
Transcription Regulator spoIIAA0.98%<  0.01%0.00730.03111.0000
cAMP-dependent Protein Kinase Chain A0.36%<  0.01%<  0.0001<  0.0001<  0.0001
Inorganic Pyrophosphatase0.45%<  0.01%<  0.0001<  0.0001<  0.0001
subunit c (vma5p) of the yeast v-atpase domain 20.51%<  0.01%<  0.0001<  0.0001<  0.0001
Deoxyuridine 5′-Triphosphate Nucleotidohydrolase_ Chain A0.88%<  0.01%<  0.00010.00020.0135
50s Ribosomal Protein L19e Chain O domain 10.96%<  0.01%0.00010.00050.0451
Glutathione Synthetase Chain A domain 31.15%<  0.01%0.00060.00310.3377
Deoxyhypusine Synthase1.18%<  0.01%0.00070.00370.4263
DNA Excision Repair Uvrb Chain A1.29%<  0.01%0.00170.00841.0000
  1. Enrichment analysis of CATH domain topologies in TAED showing CATH domains topologies present in lowest % of lineages under positive selection. All pathways were significant at the 0.05 level after correction with the false discovery rate (FDR). Bold numbers indicate not significant at the 0.05 level. Lineages with dN/dS > 1 considered under positive selection