pezizo set1: functional enrichment (novelty)
One-sided hypergeometric test per term; Benjamini-Hochberg FDR within each scope, level and vocabulary. Candidates are the novelty candidates: gene families present in the IN group and absent from the OUT group. Universe: proteome. Background clustered: True (48610 sequences in 26964 clusters, mmseqs easy-cluster --min-seq-id 0.3 -c 0.8). Family level: one unit per candidate family and per background cluster.
Sources: Pfam: 2026-01-27-Pfam38.2; InterPro entries: 110.0; GO: releases/2026-07-26; analysis generated 2026-10-14T21:57:46. Source tables: studies/fungi/pezizo_set1/analysis/enrichment/outputs/proteome_clustered.
Full record: PROVENANCE. Run report: report.html.
Caveats
- Annotation provenance is not fully recorded: PROVENANCE.yaml lists the per-species annotation files and their checksums, but not the UniProt release they come from.
- GO results are secondary. GO annotations include computational evidence (IEA, IBA); the GO evidence column shows if a term has non-IEA support.
- Candidate families (pipeline clustering of candidates) and background clusters (mmseqs clustering of the background proteome) are made by different runs, so family-level counts are not fully comparable.
- Low annotation: the candidate set has less than 50% annotation for GO 39.0%. Enrichment for these vocabularies has low power.
- GO and InterPro cover only 4 of 5 species: Ncra, Afum, Ztri, Cimm. No GO and InterPro annotation for Amega; this species adds no units to the GO and InterPro tests, so those results describe the covered species only.
Summary figure
Annotation coverage
Fraction of proteins with at least one term per vocabulary. Universe = all proteins of the species; candidates = the candidate set.
| Species | Set | Proteins | Pfam | Pfam clan | InterPro | GO | Any |
|---|---|---|---|---|---|---|---|
| Amega | universe | 11859 | 63.1% | 51.0% | 0.0% | 0.0% | 63.1% |
| Amega | candidates | 574 | 67.1% | 44.8% | 0.0% | 0.0% | 67.1% |
| Ncra | universe | 9759 | 68.5% | 54.6% | 73.4% | 64.3% | 74.1% |
| Ncra | candidates | 641 | 62.3% | 39.2% | 73.3% | 48.7% | 75.2% |
| Afum | universe | 9647 | 79.8% | 65.9% | 85.1% | 76.1% | 85.8% |
| Afum | candidates | 708 | 63.1% | 42.9% | 75.6% | 53.5% | 77.8% |
| Ztri | universe | 10951 | 68.1% | 56.0% | 73.3% | 61.6% | 73.5% |
| Ztri | candidates | 684 | 63.0% | 41.2% | 75.4% | 45.6% | 76.0% |
| Cimm | universe | 9587 | 64.1% | 51.6% | 68.6% | 58.6% | 68.9% |
| Cimm | candidates | 586 | 61.3% | 39.1% | 70.0% | 41.1% | 71.3% |
| ALL_IN | universe | 51803 | 68.5% | 55.6% | 57.9% | 50.2% | 72.7% |
| ALL_IN | candidates | 3193 | 63.3% | 41.4% | 60.5% | 39.0% | 73.8% |
Tests summary
Per vocabulary: terms with FDR < 0.05 / terms tested. Protein level counts proteins; family level counts candidate families and background clusters.
| Scope | Level | Cand. units | Pfam sig / tested | Pfam clan sig / tested | InterPro sig / tested | GO sig / tested |
|---|---|---|---|---|---|---|
| whole_set | family | 2209 | 46 / 1015 | 8 / 339 | 29 / 1654 | 18 / 3464 |
| whole_set | protein | 3193 | 160 / 3994 | 36 / 493 | 103 / 3953 | 93 / 5193 |
| Afum | family | 684 | 3 / 328 | 3 / 237 | 9 / 822 | 4 / 2757 |
| Afum | protein | 708 | 9 / 438 | 5 / 253 | 16 / 1068 | 15 / 2954 |
| Amega | family | 526 | 9 / 438 | 2 / 237 | 0 / 0 (not_available_no_annotated_units) | 0 / 0 (not_available_no_annotated_units) |
| Amega | protein | 574 | 14 / 510 | 4 / 244 | 0 / 0 (not_available_no_annotated_units) | 0 / 0 (not_available_no_annotated_units) |
| Cimm | family | 570 | 4 / 269 | 2 / 213 | 6 / 691 | 4 / 2045 |
| Cimm | protein | 586 | 4 / 304 | 4 / 223 | 6 / 803 | 4 / 2120 |
| Ncra | family | 628 | 3 / 305 | 1 / 238 | 6 / 769 | 5 / 2604 |
| Ncra | protein | 641 | 4 / 368 | 2 / 244 | 11 / 914 | 5 / 2700 |
| Ztri | family | 654 | 6 / 332 | 3 / 239 | 10 / 833 | 2 / 2508 |
| Ztri | protein | 684 | 7 / 406 | 3 / 248 | 13 / 1014 | 6 / 2636 |
Top 25 Pfam terms (whole set, family level)
25 rows shown, ordered by FDR then p-value; 25 have FDR < 0.05 (bold).
| Term | Name | k / N cand. | n / M bg | Fold | FDR (BH) |
|---|---|---|---|---|---|
| PF20684 | Fung_rhodopsin: Fungal rhodopsin domain | 109 / 1433 | 198 / 14763 | 5.671 | 1.68e-55 |
| PF06985 | HET: Heterokaryon incompatibility protein (HET) | 48 / 1433 | 107 / 14763 | 4.622 | 1.40e-18 |
| PF01048 | PNP_UDP_1: Phosphorylase superfamily | 15 / 1433 | 25 / 14763 | 6.181 | 2.58e-07 |
| PF01757 | Acyl_transf_3: Acyltransferase domain | 8 / 1433 | 9 / 14763 | 9.157 | 1.62e-05 |
| PF26639 | Het-6_barrel: Het-6 beta-barrel domain | 9 / 1433 | 12 / 14763 | 7.727 | 2.54e-05 |
| PF26118 | DUF8035: Family of unknown function (DUF8035) | 9 / 1433 | 13 / 14763 | 7.132 | 6.29e-05 |
| PF11951 | Fungal_trans_2: Fungal specific transcription factor domain | 29 / 1433 | 114 / 14763 | 2.621 | 1.34e-04 |
| PF02434 | Fringe: Fringe-like | 7 / 1433 | 9 / 14763 | 8.013 | 3.07e-04 |
| PF07814 | WAPL: Wings apart-like protein regulation of heterochromatin | 5 / 1433 | 5 / 14763 | 10.302 | 5.79e-04 |
| PF15341 | SLX9: Ribosome biogenesis protein SLX9 | 5 / 1433 | 5 / 14763 | 10.302 | 5.79e-04 |
| PF16679 | CDT1_C: DNA replication factor Cdt1 C-terminal domain | 5 / 1433 | 5 / 14763 | 10.302 | 5.79e-04 |
| PF23394 | DUF7102: Domain of unknown function (DUF7102) | 5 / 1433 | 5 / 14763 | 10.302 | 5.79e-04 |
| PF23395 | SAM_6: SAM-like domain | 5 / 1433 | 5 / 14763 | 10.302 | 5.79e-04 |
| PF26121 | HTH_CDT1: Cell division cycle protein CDT1-like, helix-turn-helix domain | 5 / 1433 | 5 / 14763 | 10.302 | 5.79e-04 |
| PF28272 | AIM11_N: AIM11 N-terminal domain | 5 / 1433 | 5 / 14763 | 10.302 | 5.79e-04 |
| PF24476 | DUF7580: Domain of unknown function (DUF7580) | 10 / 1433 | 21 / 14763 | 4.906 | 5.91e-04 |
| PF05368 | NmrA: NmrA-like family | 14 / 1433 | 41 / 14763 | 3.518 | 0.001 |
| PF11913 | DUF3431: Protein of unknown function (DUF3431) | 6 / 1433 | 8 / 14763 | 7.727 | 0.001 |
| PF26176 | zf_C2H2_17_2: C2H2-domain containing protein second zinc finger domain | 6 / 1433 | 8 / 14763 | 7.727 | 0.001 |
| PF20255 | DUF6606: Family of unknown function (DUF6606) | 5 / 1433 | 6 / 14763 | 8.585 | 0.002 |
| PF26177 | zf_C2H2_17_1st: C2H2-domain containing protein first zinc finger domain | 5 / 1433 | 6 / 14763 | 8.585 | 0.002 |
| PF11885 | DUF3405: Protein of unknown function (DUF3405) | 6 / 1433 | 9 / 14763 | 6.868 | 0.002 |
| PF13424 | TPR_12: Tetratricopeptide repeat | 10 / 1433 | 25 / 14763 | 4.121 | 0.003 |
| PF11915 | DUF3433: Protein of unknown function (DUF3433) | 7 / 1433 | 13 / 14763 | 5.547 | 0.003 |
| PF13374 | TPR_10: Tetratricopeptide repeat | 8 / 1433 | 17 / 14763 | 4.848 | 0.003 |
Top 25 InterPro terms (whole set, family level)
25 rows shown, ordered by FDR then p-value; 25 have FDR < 0.05 (bold).
| Term | Name | k / N cand. | n / M bg | Fold | FDR (BH) |
|---|---|---|---|---|---|
| IPR049326 | Domain:Rhodopsin domain, fungi | 78 / 1382 | 135 / 13480 | 5.636 | 2.89e-39 |
| IPR052337 | Family:Satratoxin biosynthesis SC1 cluster protein 4-like | 70 / 1382 | 120 / 13480 | 5.69 | 1.09e-35 |
| IPR010730 | Domain:Heterokaryon incompatibility | 46 / 1382 | 100 / 13480 | 4.487 | 2.55e-17 |
| IPR052895 | Family:Heterokaryon incompatibility protein 6 | 25 / 1382 | 37 / 13480 | 6.591 | 3.45e-14 |
| IPR002656 | Domain:Acyltransferase 3 domain | 8 / 1382 | 9 / 13480 | 8.67 | 2.70e-05 |
| IPR050879 | Family:Acyltransferase 3 | 8 / 1382 | 9 / 13480 | 8.67 | 2.70e-05 |
| IPR058348 | Domain:Domain of unknown function DUF8035 | 8 / 1382 | 10 / 13480 | 7.803 | 1.05e-04 |
| IPR045312 | Domain:Phenylcoumaran benzylic ether reductase-like | 9 / 1382 | 13 / 13480 | 6.753 | 1.23e-04 |
| IPR003378 | Domain:Fringe-like, glycosyltransferase domain | 7 / 1382 | 9 / 13480 | 7.586 | 6.44e-04 |
| IPR008030 | Domain:NmrA-like domain | 13 / 1382 | 31 / 13480 | 4.09 | 7.24e-04 |
| IPR051609 | Family:NmrA-type/Isoflavone reductase-like domain-containing protein | 10 / 1382 | 19 / 13480 | 5.134 | 7.24e-04 |
| IPR021838 | Family:Protein of unknown function DUF3431 | 6 / 1382 | 7 / 13480 | 8.361 | 9.34e-04 |
| IPR059095 | Domain:C2H2-domain containing protein, second zinc finger domain | 6 / 1382 | 7 / 13480 | 8.361 | 9.34e-04 |
| IPR021822 | Family:Protein of unknown function DUF3405 | 5 / 1382 | 5 / 13480 | 9.754 | 0.001 |
| IPR046347 | Homologous_superfamily:Basic-leucine zipper domain superfamily | 18 / 1382 | 58 / 13480 | 3.027 | 0.001 |
| IPR053137 | Family:Nucleotide-binding leucine-rich repeat (NLR)-like | 9 / 1382 | 18 / 13480 | 4.877 | 0.003 |
| IPR021858 | Family:Fungal transcription factor | 24 / 1382 | 100 / 13480 | 2.341 | 0.005 |
| IPR059009 | Domain:C2H2-domain containing protein, first zinc finger domain | 5 / 1382 | 6 / 13480 | 8.128 | 0.006 |
| IPR053029 | Family:Transcription initiation factor Rrn11 | 5 / 1382 | 7 / 13480 | 6.967 | 0.017 |
| IPR030456 | Conserved_site:Fork head domain conserved site 2 | 5 / 1382 | 8 / 13480 | 6.096 | 0.031 |
| IPR021460 | Family:Protein of unknown function DUF3112 | 4 / 1382 | 5 / 13480 | 7.803 | 0.031 |
| IPR039970 | Family:Transcription factor Grauzone-like | 4 / 1382 | 5 / 13480 | 7.803 | 0.031 |
| IPR046541 | Domain:Domain of unknown function DUF6606 | 4 / 1382 | 5 / 13480 | 7.803 | 0.031 |
| IPR051478 | 4 / 1382 | 5 / 13480 | 7.803 | 0.031 | |
| IPR055915 | Domain:Domain of unknown function DUF7492 | 4 / 1382 | 5 / 13480 | 7.803 | 0.031 |
Top 15 GO terms (whole set, family level) — secondary, computational evidence (IEA/IBA) included
15 rows shown, ordered by FDR then p-value; 15 have FDR < 0.05 (bold).
| Term | Name | k / N cand. | n / M bg | Fold | FDR (BH) | GO evidence | Families with non-IEA |
|---|---|---|---|---|---|---|---|
| GO:0140110 | molecular_function:transcription regulator activity | 127 / 903 | 842 / 10809 | 1.805 | 3.00e-08 | has_non_IEA | 46 |
| GO:0003700 | molecular_function:DNA-binding transcription factor activity | 113 / 903 | 722 / 10809 | 1.873 | 3.00e-08 | has_non_IEA | 42 |
| GO:0000976 | molecular_function:transcription cis-regulatory region binding | 63 / 903 | 341 / 10809 | 2.211 | 9.73e-07 | has_non_IEA | 37 |
| GO:0001067 | molecular_function:transcription regulatory region nucleic acid binding | 63 / 903 | 341 / 10809 | 2.211 | 9.73e-07 | has_non_IEA | 37 |
| GO:0031082 | cellular_component:BLOC complex | 8 / 903 | 8 / 10809 | 11.97 | 1.33e-06 | has_non_IEA | 6 |
| GO:0031083 | cellular_component:BLOC-1 complex | 8 / 903 | 8 / 10809 | 11.97 | 1.33e-06 | has_non_IEA | 6 |
| GO:1990837 | molecular_function:sequence-specific double-stranded DNA binding | 65 / 903 | 379 / 10809 | 2.053 | 6.67e-06 | has_non_IEA | 38 |
| GO:0000981 | molecular_function:DNA-binding transcription factor activity, RNA polymerase II-specific | 89 / 903 | 634 / 10809 | 1.68 | 2.30e-04 | has_non_IEA | 28 |
| GO:0003690 | molecular_function:double-stranded DNA binding | 66 / 903 | 430 / 10809 | 1.837 | 2.94e-04 | has_non_IEA | 38 |
| GO:0043565 | molecular_function:sequence-specific DNA binding | 71 / 903 | 490 / 10809 | 1.734 | 8.84e-04 | has_non_IEA | 41 |
| GO:0006351 | biological_process:DNA-templated transcription | 109 / 903 | 877 / 10809 | 1.488 | 0.003 | has_non_IEA | 3 |
| GO:0031070 | biological_process:intronic snoRNA processing | 5 / 903 | 6 / 10809 | 9.975 | 0.006 | has_non_IEA | 4 |
| GO:0034965 | biological_process:intronic box C/D snoRNA processing | 5 / 903 | 6 / 10809 | 9.975 | 0.006 | has_non_IEA | 4 |
| GO:0000294 | biological_process:nuclear-transcribed mRNA catabolic process, RNase MRP-dependent | 6 / 903 | 9 / 10809 | 7.98 | 0.006 | has_non_IEA | 4 |
| GO:0000172 | cellular_component:ribonuclease MRP complex | 8 / 903 | 17 / 10809 | 5.633 | 0.007 | has_non_IEA | 5 |
Actin cytoskeleton controls
Known actin-related families and how many of their proteins pass each filter. Protein ID columns are left out.
| control | pfam_ids | desc_regex | IN_universe | IN_in_matrix | IN_pass_ingroup_rule | candidates | near_miss_out1 | near_miss_out2 | n_Amega | n_Ncra | n_Afum | n_Ztri | n_Cimm | n_Nirr | n_CneoH99 | n_Ccin | n_Mcir | n_Spom | n_Scer |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Arp2/3 ARPC2 (P34-Arc) | PF04045 | 5 | 5 | 5 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Arp2/3 ARPC3 (P21-Arc) | PF04062 | 5 | 5 | 5 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | |
| Arp2/3 ARPC4 | PF05856 | 5 | 5 | 5 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Arp2/3 ARPC5 (P16-Arc) | PF04699 | 5 | 5 | 5 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Arp2/3 ARPC1 (description only) | arp2/3 complex.*(41|p41|subunit 1)|ARPC1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | |
| Arp2 / Arp3 (description only) | actin-related protein (2|3)\b|\bARP[23]\b | 32 | 32 | 31 | 0 | 0 | 0 | 4 | 6 | 8 | 7 | 7 | 6 | 5 | 5 | 6 | 7 | 7 | |
| WAVE complex NCKAP1 | PF09735 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| WAVE complex CYFIP (FragX_IP) | PF05994 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| WAVE complex ABI | PF07815|PF27594 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| SCAR/WAVE (SCAR_helical) | PF27569 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| WASP family (WH1) | PF00568 | 7 | 7 | 7 | 0 | 0 | 1 | 3 | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 3 | 1 | 1 | |
| WH2 motif (WASP, WAVE, others) | PF02205 | 11 | 11 | 11 | 0 | 0 | 0 | 2 | 1 | 3 | 3 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | |
| Formin FH2 | PF02181 | 5 | 5 | 5 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 8 | 3 | 2 | |
| Formin Drf_GBD / Drf_FH3 / Drf_DAD | PF06371|PF06367|PF06345 | 9 | 9 | 9 | 0 | 0 | 0 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | 3 | 8 | 4 | 1 | |
| Ena/VASP (VASP_tetra) | PF08776 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| Coronin (description only) | coronin | 5 | 5 | 5 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Cortactin (HS1_rep) | PF02218 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| Myosin 2 tail (Myosin_tail_1) | PF01576 | 2 | 2 | 2 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | |
| Myosin head (all myosins) | PF00063 | 21 | 21 | 21 | 0 | 0 | 0 | 4 | 4 | 4 | 5 | 4 | 5 | 4 | 5 | 17 | 5 | 5 |
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