yc pseudo ectomycorrhizal: 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 (69378 sequences in 39108 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 2026-10-24T14:49:35. Source tables: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/analysis/enrichment/outputs/proteome_clustered.
Full record: PROVENANCE. Run report: report.html.
Related: yeast_convergence: comparison across contrasts
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 Pfam 20.0%, InterPro 30.9%, GO 11.0%, any vocabulary 31.2%. Enrichment for these vocabularies has low power.
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 |
|---|---|---|---|---|---|---|---|
| Laccbico | universe | 17895 | 43.8% | 35.1% | 50.9% | 36.0% | 51.1% |
| Laccbico | candidates | 832 | 17.5% | 10.3% | 25.5% | 9.4% | 25.8% |
| Laccamet | universe | 20880 | 40.5% | 32.8% | 47.0% | 33.1% | 47.3% |
| Laccamet | candidates | 967 | 17.9% | 13.7% | 30.6% | 9.4% | 30.9% |
| Hebecyli | universe | 15324 | 51.4% | 41.4% | 58.7% | 42.2% | 58.8% |
| Hebecyli | candidates | 492 | 23.0% | 17.1% | 33.7% | 12.6% | 34.2% |
| Amanmusc | universe | 17947 | 46.1% | 37.4% | 52.5% | 37.3% | 52.6% |
| Amanmusc | candidates | 377 | 26.8% | 21.8% | 40.1% | 16.7% | 40.1% |
| ALL_IN | universe | 72046 | 45.0% | 36.4% | 51.8% | 36.8% | 52.0% |
| ALL_IN | candidates | 2668 | 20.0% | 14.4% | 30.9% | 11.0% | 31.2% |
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 | 1708 | 17 / 676 | 6 / 287 | 23 / 1492 | 8 / 2900 |
| whole_set | protein | 2668 | 35 / 1903 | 16 / 418 | 61 / 4099 | 24 / 4612 |
| Amanmusc | family | 275 | 4 / 313 | 3 / 218 | 9 / 757 | 4 / 2256 |
| Amanmusc | protein | 377 | 6 / 427 | 4 / 237 | 13 / 1010 | 9 / 2419 |
| Hebecyli | family | 412 | 5 / 310 | 1 / 222 | 6 / 774 | 1 / 2289 |
| Hebecyli | protein | 492 | 9 / 442 | 7 / 242 | 16 / 1045 | 5 / 2470 |
| Laccamet | family | 705 | 12 / 360 | 4 / 219 | 14 / 848 | 5 / 2365 |
| Laccamet | protein | 967 | 17 / 498 | 8 / 246 | 23 / 1118 | 19 / 2505 |
| Laccbico | family | 693 | 6 / 316 | 2 / 213 | 9 / 766 | 4 / 2007 |
| Laccbico | protein | 832 | 8 / 450 | 5 / 240 | 12 / 1060 | 6 / 2210 |
Top 25 Pfam terms (whole set, family level)
25 rows shown, ordered by FDR then p-value; 17 have FDR < 0.05 (bold). 6 are tagged TE: transposable-element families, flagged by name (heuristic, not a test).
| Term | Name | k / N cand. | n / M bg | Fold | FDR (BH) |
|---|---|---|---|---|---|
| PF28437 | DUF8397: Domain of unknown function (DUF8397) | 15 / 329 | 30 / 11894 | 18.076 | 2.23e-13 |
| PF13358 | DDE_3: DDE superfamily endonuclease TE | 12 / 329 | 17 / 11894 | 25.519 | 3.04e-13 |
| PF05699 | Dimer_Tnp_hAT: hAT family C-terminal dimerisation region TE | 19 / 329 | 64 / 11894 | 10.733 | 9.42e-13 |
| PF03184 | DDE_1: DDE superfamily endonuclease TE | 14 / 329 | 35 / 11894 | 14.461 | 2.71e-11 |
| PF20681 | DUF6818: Domain of unknown function (DUF6818) | 8 / 329 | 8 / 11894 | 36.152 | 4.26e-11 |
| PF13391 | HNH_2: HNH endonuclease | 15 / 329 | 48 / 11894 | 11.297 | 1.67e-10 |
| PF20147 | Crinkler: Crinkler effector protein N-terminal domain | 17 / 329 | 73 / 11894 | 8.419 | 9.02e-10 |
| PF01400 | Astacin: Astacin (Peptidase family M12A) | 7 / 329 | 9 / 11894 | 28.118 | 3.37e-08 |
| PF20149 | DUF6532: Domain of unknown function (DUF6532) | 13 / 329 | 57 / 11894 | 8.245 | 2.69e-07 |
| PF03221 | HTH_Tnp_Tc5: Tc5 transposase DNA-binding domain TE | 7 / 329 | 14 / 11894 | 18.076 | 2.28e-06 |
| PF27039 | ZBED1_RNase-like_helical: ZBED1 RNase-like helical domain TE | 8 / 329 | 28 / 11894 | 10.329 | 3.71e-05 |
| PF13384 | HTH_23: Homeodomain-like domain | 5 / 329 | 8 / 11894 | 22.595 | 4.63e-05 |
| PF01728 | FtsJ: FtsJ-like methyltransferase | 3 / 329 | 5 / 11894 | 21.691 | 0.009 |
| PF04937 | DUF659: Domain of unknown function (DUF659) | 3 / 329 | 5 / 11894 | 21.691 | 0.009 |
| PF19193 | Tectonin: Tectonin domain | 3 / 329 | 5 / 11894 | 21.691 | 0.009 |
| PF20415 | DUF6699: Family of unknown function (DUF6699) | 8 / 329 | 61 / 11894 | 4.741 | 0.011 |
| PF02661 | Fic: Fic/DOC family | 3 / 329 | 8 / 11894 | 13.557 | 0.042 |
| PF06094 | GGACT: Gamma-glutamyl cyclotransferase, AIG2-like | 3 / 329 | 9 / 11894 | 12.051 | 0.055 |
| PF12776 | Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain | 3 / 329 | 9 / 11894 | 12.051 | 0.055 |
| PF01693 | Cauli_VI: Ribonuclease H1 N-terminal domain | 5 / 329 | 39 / 11894 | 4.635 | 0.141 |
| PF08593 | Mug135_C: Mug135-like, C-terminal domain | 3 / 329 | 13 / 11894 | 8.343 | 0.157 |
| PF05730 | CFEM: CFEM domain | 3 / 329 | 15 / 11894 | 7.23 | 0.229 |
| PF00646 | F-box: F-box domain | 7 / 329 | 86 / 11894 | 2.943 | 0.284 |
| PF14441 | OTT_1508_deam: OTT_1508-like deaminase | 3 / 329 | 17 / 11894 | 6.38 | 0.301 |
| PF00078 | RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase) TE | 2 / 329 | 7 / 11894 | 10.329 | 0.395 |
Top 25 InterPro terms (whole set, family level)
25 rows shown, ordered by FDR then p-value; 23 have FDR < 0.05 (bold).
| Term | Name | k / N cand. | n / M bg | Fold | FDR (BH) |
|---|---|---|---|---|---|
| IPR012337 | Homologous_superfamily:Ribonuclease H-like superfamily | 37 / 518 | 210 / 14367 | 4.887 | 1.10e-12 |
| IPR059441 | Domain:Domain of unknown function DUF8397 | 15 / 518 | 30 / 14367 | 13.868 | 1.11e-11 |
| IPR038717 | Domain:Tc1-like transposase, DDE domain | 12 / 518 | 17 / 14367 | 19.578 | 1.11e-11 |
| IPR008906 | Domain:HAT, C-terminal dimerisation domain | 19 / 518 | 64 / 14367 | 8.234 | 1.99e-10 |
| IPR049203 | Domain:Domain of unknown function DUF6818 | 8 / 518 | 8 / 14367 | 27.736 | 8.09e-10 |
| IPR004875 | Domain:DDE superfamily endonuclease domain | 14 / 518 | 35 / 14367 | 11.094 | 1.52e-09 |
| IPR003615 | Domain:HNH nuclease | 15 / 518 | 50 / 14367 | 8.321 | 2.77e-08 |
| IPR045379 | Domain:Crinkler effector protein, N-terminal | 17 / 518 | 73 / 14367 | 6.459 | 1.15e-07 |
| IPR024079 | Homologous_superfamily:Metallopeptidase, catalytic domain superfamily | 11 / 518 | 29 / 14367 | 10.52 | 3.83e-07 |
| IPR001506 | Domain:Peptidase M12A | 7 / 518 | 9 / 14367 | 21.572 | 3.84e-07 |
| IPR009057 | Homologous_superfamily:Homeodomain-like superfamily | 18 / 518 | 94 / 14367 | 5.311 | 7.60e-07 |
| IPR006600 | Domain:HTH CenpB-type DNA-binding domain | 9 / 518 | 22 / 14367 | 11.346 | 3.91e-06 |
| IPR006026 | Domain:Peptidase, metallopeptidase | 6 / 518 | 8 / 14367 | 20.802 | 6.45e-06 |
| IPR045341 | Domain:Domain of unknown function DUF6532 | 13 / 518 | 57 / 14367 | 6.326 | 9.13e-06 |
| IPR038279 | Homologous_superfamily:Ndc10, domain 2 superfamily | 5 / 518 | 6 / 14367 | 23.113 | 3.46e-05 |
| IPR050863 | Family:Centromere and Transposable Element-Derived Protein | 8 / 518 | 25 / 14367 | 8.875 | 1.59e-04 |
| IPR036397 | Homologous_superfamily:Ribonuclease H superfamily | 17 / 518 | 128 / 14367 | 3.684 | 3.01e-04 |
| IPR052980 | Family:Crinkler effector family | 8 / 518 | 38 / 14367 | 5.839 | 0.004 |
| IPR029047 | Homologous_superfamily:Heat shock protein 70kD, peptide-binding domain superfamily | 5 / 518 | 16 / 14367 | 8.667 | 0.015 |
| IPR032675 | Homologous_superfamily:Leucine-rich repeat domain superfamily | 33 / 518 | 471 / 14367 | 1.943 | 0.016 |
| IPR002877 | Domain:Ribosomal RNA methyltransferase, FtsJ domain | 3 / 518 | 5 / 14367 | 16.641 | 0.029 |
| IPR006624 | Repeat:Beta-propeller repeat TECPR | 3 / 518 | 5 / 14367 | 16.641 | 0.029 |
| IPR007021 | Domain:Domain of unknown function DUF659 | 3 / 518 | 5 / 14367 | 16.641 | 0.029 |
| IPR040198 | Family:Fido domain-containing protein | 3 / 518 | 6 / 14367 | 13.868 | 0.053 |
| IPR021109 | Homologous_superfamily:Aspartic peptidase domain superfamily | 9 / 518 | 73 / 14367 | 3.419 | 0.071 |
Top 15 GO terms (whole set, family level) — secondary, computational evidence (IEA/IBA) included
15 rows shown, ordered by FDR then p-value; 8 have FDR < 0.05 (bold).
| Term | Name | k / N cand. | n / M bg | Fold | FDR (BH) | GO evidence | Families with non-IEA |
|---|---|---|---|---|---|---|---|
| GO:0043657 | cellular_component:host cell | 17 / 181 | 73 / 9477 | 12.193 | 2.42e-11 | IEA_only | 0 |
| GO:0018995 | cellular_component:host cellular component | 17 / 181 | 74 / 9477 | 12.028 | 2.42e-11 | IEA_only | 0 |
| GO:0044217 | cellular_component:other organism part | 17 / 181 | 74 / 9477 | 12.028 | 2.42e-11 | IEA_only | 0 |
| GO:0046983 | molecular_function:protein dimerization activity | 20 / 181 | 168 / 9477 | 6.233 | 3.53e-08 | IEA_only | 0 |
| GO:0005576 | cellular_component:extracellular region | 22 / 181 | 209 / 9477 | 5.511 | 3.53e-08 | IEA_only | 0 |
| GO:0008237 | molecular_function:metallopeptidase activity | 11 / 181 | 94 / 9477 | 6.127 | 7.67e-04 | IEA_only | 0 |
| GO:0004222 | molecular_function:metalloendopeptidase activity | 7 / 181 | 41 / 9477 | 8.939 | 0.004 | IEA_only | 0 |
| GO:0003676 | molecular_function:nucleic acid binding | 55 / 181 | 1743 / 9477 | 1.652 | 0.020 | IEA_only | 0 |
| GO:0016891 | molecular_function:RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism | 6 / 181 | 52 / 9477 | 6.041 | 0.141 | IEA_only | 0 |
| GO:0008233 | molecular_function:peptidase activity | 15 / 181 | 308 / 9477 | 2.55 | 0.234 | IEA_only | 0 |
| GO:0015074 | biological_process:DNA integration | 5 / 181 | 40 / 9477 | 6.545 | 0.243 | IEA_only | 0 |
| GO:0004175 | molecular_function:endopeptidase activity | 10 / 181 | 161 / 9477 | 3.252 | 0.245 | IEA_only | 0 |
| GO:0005488 | molecular_function:binding | 104 / 181 | 4390 / 9477 | 1.24 | 0.349 | IEA_only | 0 |
| GO:0009395 | biological_process:phospholipid catabolic process | 3 / 181 | 13 / 9477 | 12.083 | 0.353 | IEA_only | 0 |
| GO:0004521 | molecular_function:RNA endonuclease activity | 6 / 181 | 70 / 9477 | 4.488 | 0.412 | IEA_only | 0 |
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_Laccbico | n_Laccamet | n_Hebecyli | n_Amanmusc | n_Amanthie | n_Ccin | n_Agbis | n_Pleuostr |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Arp2/3 ARPC2 (P34-Arc) | PF04045 | 4 | 4 | 4 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Arp2/3 ARPC3 (P21-Arc) | PF04062 | 4 | 4 | 4 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Arp2/3 ARPC4 | PF05856 | 4 | 4 | 4 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Arp2/3 ARPC5 (P16-Arc) | PF04699 | 4 | 4 | 4 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Arp2/3 ARPC1 (description only) | arp2/3 complex.*(41|p41|subunit 1)|ARPC1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | |
| Arp2 / Arp3 (description only) | actin-related protein (2|3)\b|\bARP[23]\b | 29 | 29 | 29 | 0 | 0 | 0 | 8 | 7 | 7 | 7 | 7 | 5 | 7 | 7 | |
| WAVE complex NCKAP1 | PF09735 | 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 | |
| WAVE complex ABI | PF07815|PF27594 | 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 | |
| WASP family (WH1) | PF00568 | 8 | 8 | 8 | 0 | 0 | 0 | 2 | 2 | 3 | 1 | 1 | 2 | 2 | 2 | |
| WH2 motif (WASP, WAVE, others) | PF02205 | 7 | 7 | 7 | 0 | 0 | 0 | 2 | 2 | 2 | 1 | 2 | 2 | 1 | 2 | |
| Formin FH2 | PF02181 | 8 | 8 | 8 | 0 | 0 | 0 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | |
| Formin Drf_GBD / Drf_FH3 / Drf_DAD | PF06371|PF06367|PF06345 | 12 | 12 | 12 | 0 | 0 | 0 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | |
| Ena/VASP (VASP_tetra) | PF08776 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| Coronin (description only) | coronin | 6 | 6 | 6 | 0 | 0 | 0 | 2 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | |
| Cortactin (HS1_rep) | PF02218 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| Myosin 2 tail (Myosin_tail_1) | PF01576 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | |
| Myosin head (all myosins) | PF00063 | 21 | 21 | 21 | 0 | 0 | 0 | 6 | 6 | 4 | 5 | 4 | 5 | 4 | 5 |
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