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Table 4 Pfam domains enriched in up- and down-regulated genes

From: The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation

Pfam domain IDa Pfam domain description Domains in genomeb Domains in subsetc P-valued
Up-regulated at 8 h encystation (compared to trophozoite)
PF00962 Adenosine/AMP deaminase 10 4 1.00 × 10-4
PF01370 NAD dependent epimerase/dehydratase family 7 3 6.45 × 10-4
PF01380 Sugar isomerase domain 3 2 2.20 × 10-3
PF01416 tRNA pseudouridine synthase 5 2 6.92 × 10-3
PF06978 Ribonucleases P/MRP protein subunit POP1 2 2 7.52 × 10-4
PF02463 Structural maintenance of chromosomes superfamily 9 3 1.46 × 10-3
PF08221 RNA polymerase III subunit RPC82 helix-turn-helix domain 3 2 2.20 × 10-3
PF00620 RhoGAP domain 97 10 2.61 × 10-4
PF00566 Rab-GTPase-TBC domain 62 6 5.48 × 10-3
PF08743 DNA repair 3 2 2.20 × 10-3
PF03114 Protein dimerisation domain 12 3 3.53 × 10-3
PF09777 Osteopetrosis-associated transmembrane protein 1 precursor 2 2 7.52 × 10-4
PF00888 Cullin family ubiquitin ligase scaffold protein 11 3 2.72 × 10-3
PF10557 Cullin protein neddylation domain 12 3 3.53 × 10-3
PF00643 B-box zinc finger 15 3 6.72 × 10-3
PF00578 Alkyl hydroperoxide reductase and thiol specific antioxidant 17 3 9.50 × 10-3
PF12796 Ankyrin repeats 87 9 5.03 × 10-4
PF03197 Bacteriophage FRD2 protein 3 2 2.20 × 10-3
PF07534 unknown function 210 19 4.34 × 10-6
Up-regulated at 24 h encystation (compared to trophozoite)
PF06045 Rhamnogalacturonate lyase family 6 5 2.74 × 10-6
PF00704 Glycosyl hydrolases family 18 7 5 9.07 × 10-6
PF07651 Phosphatidylinositol 4,5-bisphosphate binding 8 4 4.96 × 10-4
PF07653 Variant SH3 domain 21 6 6.16 × 10-4
PF00018 SH3 domain: protein-protein interaction 32 7 1.19 × 10-3
PF00614 Phospholipase D active site motif 2 2 2.98 × 10-3
PF00069 Protein kinase domain 510 41 3.42 × 10-3
PF00806 Pumilio-family RNA binding repeat 60 12 6.48 × 10-5
PF06978 Ribonucleases P/MRP protein subunit POP1 2 2 2.98 × 10-3
PF00352 Transcription factor TFIID (or TATA-binding protein, TBP) 11 4 1.98 × 10-3
PF00620 RhoGAP domain 97 18 3.50 × 10-6
PF00225 Kinesin motor domain 6 3 2.75 × 10-3
PF03953 Tubulin C-terminal domain 6 3 2.75 × 10-3
PF00443 Ubiquitin carboxyl-terminal hydrolase 29 6 3.45 × 10-3
PF13476 ATPase domain 10 4 1.33 × 10-3
PF04506 Integral membrane protein, possible sugar transporter 2 2 2.98 × 10-3
PF12796 Ankyrin repeats 87 13 6.03 × 10-4
PF07534 Unknown function 210 31 3.07 × 10-7
Up-regulated at 72 h encystation (compared to trophozoite)
PF00128 Alpha amylase, catalytic domain 24 7 5.95 × 10-5
PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain 5 3 8.37 × 10-4
PF12697 Alpha/beta hydrolase family 8 3 4.08 × 10-3
PF00614 Phospholipase D active site motif 2 2 2.04 × 10-3
PF00806 Pumilio-family RNA binding repeat 60 12 1.05 × 10-5
PF00773 Catalytic domain of ribonuclease II 10 4 6.58 × 10-4
PF01885 RNA 2'-phosphotransferase, Tpt1/KptA family 3 2 5.83 × 10-3
PF06978 Ribonucleases P/MRP protein subunit POP1 2 2 2.04 × 10-3
PF04054 CCR4-Not complex component - global regulator of transcription 5 3 8.37 × 10-4
PF00145 C-5 cytosine-specific DNA methylase 2 2 2.04 × 10-3
PF08221 RNA polymerase III subunit RPC82 helix-turn-helix domain 3 2 5.83 × 10-3
PF08743 DNA repair 3 2 5.83 × 10-3
PF02144 Repair protein Rad1/Rec1/Rad17 3 2 5.83 × 10-3
PF02145 Rap/ran-GAP 33 6 2.67 × 10-3
PF00620 RhoGAP domain 97 11 2.92 × 10-3
PF04506 Integral membrane protein, possible sugar transporter 2 2 2.04 × 10-3
PF01436 NHL repeat 8 3 4.08 × 10-3
PF05237 MoeZ/MoeB domain: unknown function 3 2 5.83 × 10-3
PF07534 Unknown function 210 20 8.17 × 10-4
Up-regulated at 2 h excystation (compared to 72 h cyst)
PF00723 Glycosyl hydrolases family 15 6 4 4.71 × 10-4
PF00534 Glycosyl transferases group 1 4 3 1.75 × 10-3
PF01592 Iron-sulfur cluster assembly 148 24 2.86 × 10-4
PF00076 RNA recognition motif (aka RRM, RBD, or RNP domain) 36 9 1.11 × 10-3
PF00270 DEAD/DEAH box helicase 12 5 1.29 × 10-3
PF00565 Staphylococcal nuclease homolog 5 3 4.03 × 10-3
PF01416 Pseudouridine synthesis 4 3 1.75 × 10-3
PF04719 hTAFII28-like protein conserved region 9 4 3.10 × 10-3
PF01926 50S ribosome-binding GTPase 2 2 6.08 × 10-3
PF02270 Transcription initiation factor IIF (TFIIF) 22 7 8.81 × 10-4
PF00226 DnaJ domain 4 3 1.75 × 10-3
PF08423 DNA repair and recombination 19 6 2.12 × 10-3
PF02450 Lecithin:cholesterol acyltransferase 2 2 6.08 × 10-3
PF06728 GPI transamidase subunit 2 2 6.08 × 10-3
PF01238 Phosphomannose isomerase type I 46 10 1.81 × 10-3
PF00112 Papain family cysteine protease 6 3 7.44 × 10-3
PF01067 Calpain large subunit, domain III (protease) 28 20 1.03 × 10-16
PF00630 Filamin/ABP280 repeat 24 9 4.09 × 10-5
PF01602 Adaptin N-terminal region 9 6 1.47 × 10-5
PF04324 BFD-like [2Fe-2S] binding domain 4 3 1.75 × 10-3
PF02777 Iron/manganese superoxide dismutases, C-terminal domain 8 4 1.87 × 10-3
PF00400 WD domain, G-beta repeat 263 51 7.47 × 10-10
PF13115 YtkA-like: unknown function 12 7 9.20 × 10-6
PF06229 FRG1-like family: unknown function 4 3 1.75 × 10-3
PF08238 Sel1 repeat 21 6 3.60 × 10-3
Down-regulated at 72 h encystation (compared to trophozoite)
PF00723 Glycosyl hydrolases family 15 6 4 5.42 × 10-4
PF00106 Short chain dehydrogenase 12 6 1.55 × 10-4
PF01663 Type I phosphodiesterase/nucleotide pyrophosphatase 19 7 4.13 × 10-4
PF02878 Phosphoglucomutase/phosphomannomutase domain I 3 3 5.29 × 10-4
PF02880 Phosphoglucomutase/phosphomannomutase domain III 3 3 5.29 × 10-4
PF00408 Phosphoglucomutase/phosphomannomutase, C-terminal domain 3 3 5.29 × 10-4
PF00349 Phosphorylates hexoses 2 2 6.54 × 10-3
PF01467 Cytidylyltransferase 9 6 1.82 × 10-5
PF09334 tRNA synthetases class I (M) 3 3 5.29 × 10-4
PF00432 Prenyltransferase and squalene oxidase repeat 4 4 4.27 × 10-5
PF00630 Filamin/ABP280 repeat 28 25 1.10 × 10-24
PF00307 Calponin homology (CH) domain 50 13 9.75 × 10-5
PF06268 Actin cross-linking 6 5 1.90 × 10-5
PF01602 Adaptin N-terminal region 24 9 5.41 × 10-5
PF04324 BFD-like [2Fe-2S] binding domain 9 6 1.82 × 10-5
PF00248 Aldo/keto reductase family 4 4 4.27 × 10-5
PF02777 Iron/manganese superoxide dismutases, C-terminal domain 4 4 4.27 × 10-5
PF00081 Iron/manganese superoxide dismutases, alpha-hairpin domain 5 4 1.96 × 10-4
PF13115 YtkA-like: unknown function 12 8 6.40 × 10-7
PF00501 AMP-binding enzyme 26 11 2.08 × 10-6
PF12796 Ankyrin repeats 87 20 1.15 × 10-5
  1. aSelected Pfam domains that were significantly enriched (P <0.05) in genes up- or down-regulated at 8 h, 24 h and 72 h post-encystation, and at 2 h post-excystation. bNumber of a Pfam domain in the whole E. invadens genome. cNumber of a Pfam domain among the subset of regulated genes. dP-value for Pfam domain enrichment.