yc rev eremothecium: 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 (13542 sequences in 4999 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 2026-10-24T14:56:58. Source tables: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/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 19.5%, InterPro 24.9%, GO 11.8%, any vocabulary 26.6%. 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 |
|---|---|---|---|---|---|---|---|
| Eremgoss | universe | 4758 | 91.1% | 68.8% | 94.3% | 86.5% | 94.8% |
| Eremgoss | candidates | 54 | 18.5% | 11.1% | 24.1% | 16.7% | 27.8% |
| Eremcymb | universe | 4429 | 91.7% | 68.2% | 94.4% | 88.7% | 95.1% |
| Eremcymb | candidates | 59 | 22.0% | 10.2% | 25.4% | 10.2% | 27.1% |
| Eremsine | universe | 4524 | 91.7% | 68.7% | 94.9% | 85.4% | 95.2% |
| Eremsine | candidates | 56 | 17.9% | 7.1% | 25.0% | 8.9% | 25.0% |
| ALL_IN | universe | 13711 | 91.5% | 68.6% | 94.5% | 86.8% | 95.0% |
| ALL_IN | candidates | 169 | 19.5% | 9.5% | 24.9% | 11.8% | 26.6% |
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 | 101 | 0 / 166 | 0 / 177 | 1 / 487 | 7 / 3053 |
| whole_set | protein | 169 | 2 / 929 | 2 / 324 | 5 / 2195 | 7 / 4184 |
| Eremcymb | family | 59 | 0 / 129 | 0 / 163 | 0 / 395 | 0 / 2874 |
| Eremcymb | protein | 59 | 0 / 154 | 0 / 172 | 0 / 456 | 0 / 2961 |
| Eremgoss | family | 54 | 0 / 133 | 0 / 169 | 0 / 415 | 0 / 1994 |
| Eremgoss | protein | 54 | 0 / 165 | 0 / 180 | 0 / 493 | 0 / 2089 |
| Eremsine | family | 56 | 0 / 123 | 0 / 170 | 1 / 402 | 3 / 1872 |
| Eremsine | protein | 56 | 0 / 146 | 0 / 179 | 1 / 462 | 3 / 1935 |
Top 25 Pfam terms (whole set, family level)
25 rows shown, ordered by FDR then p-value; 0 have FDR < 0.05 (bold).
| Term | Name | k / N cand. | n / M bg | Fold | FDR (BH) |
|---|---|---|---|---|---|
| PF00096 | zf-C2H2: Zinc finger, C2H2 type | 3 / 21 | 33 / 4507 | 19.511 | 0.072 |
| PF00004 | AAA: ATPase family associated with various cellular activities (AAA) | 0 / 21 | 28 / 4507 | 0.0 | 1.000 |
| PF00005 | ABC_tran: ABC transporter | 0 / 21 | 18 / 4507 | 0.0 | 1.000 |
| PF00009 | GTP_EFTU: Elongation factor Tu GTP binding domain | 0 / 21 | 11 / 4507 | 0.0 | 1.000 |
| PF00010 | HLH: Helix-loop-helix DNA-binding domain | 0 / 21 | 6 / 4507 | 0.0 | 1.000 |
| PF00018 | SH3_1: SH3 domain | 0 / 21 | 16 / 4507 | 0.0 | 1.000 |
| PF00022 | Actin: Actin | 0 / 21 | 8 / 4507 | 0.0 | 1.000 |
| PF00023 | Ank: Ankyrin repeat | 0 / 21 | 8 / 4507 | 0.0 | 1.000 |
| PF00026 | Asp: Eukaryotic aspartyl protease | 0 / 21 | 6 / 4507 | 0.0 | 1.000 |
| PF00069 | Pkinase: Protein kinase domain | 0 / 21 | 86 / 4507 | 0.0 | 1.000 |
| PF00071 | Ras: Ras family | 0 / 21 | 10 / 4507 | 0.0 | 1.000 |
| PF00076 | RRM_1: RNA recognition motif | 0 / 21 | 45 / 4507 | 0.0 | 1.000 |
| PF00083 | Sugar_tr: Sugar (and other) transporter | 0 / 21 | 13 / 4507 | 0.0 | 1.000 |
| PF00085 | Thioredoxin: Thioredoxin | 0 / 21 | 8 / 4507 | 0.0 | 1.000 |
| PF00097 | zf-C3HC4: Zinc finger, C3HC4 type (RING finger) | 0 / 21 | 6 / 4507 | 0.0 | 1.000 |
| PF00106 | adh_short: short chain dehydrogenase | 0 / 21 | 14 / 4507 | 0.0 | 1.000 |
| PF00107 | ADH_zinc_N: Zinc-binding dehydrogenase | 0 / 21 | 7 / 4507 | 0.0 | 1.000 |
| PF00117 | GATase: Glutamine amidotransferase class-I | 0 / 21 | 7 / 4507 | 0.0 | 1.000 |
| PF00118 | Cpn60_TCP1: TCP-1/cpn60 chaperonin family | 0 / 21 | 5 / 4507 | 0.0 | 1.000 |
| PF00122 | E1-E2_ATPase: P-type ATPase actuator domain | 0 / 21 | 8 / 4507 | 0.0 | 1.000 |
| PF00125 | Histone: Core histone H2A/H2B/H3/H4 domain | 0 / 21 | 5 / 4507 | 0.0 | 1.000 |
| PF00133 | tRNA-synt_1: tRNA synthetases class I (I, L, M and V) | 0 / 21 | 5 / 4507 | 0.0 | 1.000 |
| PF00134 | Cyclin_N: Cyclin, N-terminal domain | 0 / 21 | 14 / 4507 | 0.0 | 1.000 |
| PF00149 | Metallophos: Calcineurin-like phosphoesterase | 0 / 21 | 13 / 4507 | 0.0 | 1.000 |
| PF00152 | tRNA-synt_2: tRNA synthetases class II (D, K and N) | 0 / 21 | 5 / 4507 | 0.0 | 1.000 |
Top 25 InterPro terms (whole set, family level)
25 rows shown, ordered by FDR then p-value; 1 have FDR < 0.05 (bold).
| Term | Name | k / N cand. | n / M bg | Fold | FDR (BH) |
|---|---|---|---|---|---|
| IPR052786 | Family:Outer_spore_wall_assembly | 4 / 29 | 8 / 4662 | 80.379 | 4.05e-05 |
| IPR036910 | Homologous_superfamily:High mobility group box domain superfamily | 2 / 29 | 10 / 4662 | 32.152 | 0.397 |
| IPR036236 | Homologous_superfamily:Zinc finger C2H2 superfamily | 3 / 29 | 54 / 4662 | 8.931 | 0.704 |
| IPR013087 | Domain:Zinc finger C2H2-type | 3 / 29 | 64 / 4662 | 7.536 | 0.851 |
| IPR009057 | Homologous_superfamily:Homeodomain-like superfamily | 2 / 29 | 26 / 4662 | 12.366 | 1.000 |
| IPR001356 | Domain:Homeodomain | 1 / 29 | 7 / 4662 | 22.966 | 1.000 |
| IPR060769 | Homologous_superfamily:EIF3B-like, beta-propeller domain superfamily | 1 / 29 | 10 / 4662 | 16.076 | 1.000 |
| IPR015943 | Homologous_superfamily:WD40/YVTN repeat-like-containing domain superfamily | 1 / 29 | 126 / 4662 | 1.276 | 1.000 |
| IPR000008 | Domain:C2 domain | 0 / 29 | 10 / 4662 | 0.0 | 1.000 |
| IPR000073 | Domain:Alpha/beta hydrolase fold-1 | 0 / 29 | 17 / 4662 | 0.0 | 1.000 |
| IPR000086 | Domain:NUDIX hydrolase domain | 0 / 29 | 6 / 4662 | 0.0 | 1.000 |
| IPR000089 | Domain:Biotin/lipoyl attachment | 0 / 29 | 7 / 4662 | 0.0 | 1.000 |
| IPR000182 | Domain:GNAT domain | 0 / 29 | 12 / 4662 | 0.0 | 1.000 |
| IPR000195 | Domain:Rab-GAP-TBC domain | 0 / 29 | 10 / 4662 | 0.0 | 1.000 |
| IPR000198 | Domain:Rho GTPase-activating protein domain | 0 / 29 | 8 / 4662 | 0.0 | 1.000 |
| IPR000219 | Domain:Dbl homology domain | 0 / 29 | 6 / 4662 | 0.0 | 1.000 |
| IPR000232 | Domain:Heat shock factor (HSF)-type, DNA-binding | 0 / 29 | 5 / 4662 | 0.0 | 1.000 |
| IPR000253 | Domain:Forkhead-associated (FHA) domain | 0 / 29 | 12 / 4662 | 0.0 | 1.000 |
| IPR000306 | Domain:FYVE zinc finger | 0 / 29 | 5 / 4662 | 0.0 | 1.000 |
| IPR000326 | Domain:Phosphatidic acid phosphatase type 2/haloperoxidase | 0 / 29 | 5 / 4662 | 0.0 | 1.000 |
| IPR000330 | Domain:SNF2, N-terminal domain | 0 / 29 | 16 / 4662 | 0.0 | 1.000 |
| IPR000340 | Domain:Dual specificity phosphatase, catalytic domain | 0 / 29 | 5 / 4662 | 0.0 | 1.000 |
| IPR000387 | Domain:Tyrosine-specific protein phosphatases domain | 0 / 29 | 9 / 4662 | 0.0 | 1.000 |
| IPR000403 | Domain:Phosphatidylinositol 3-/4-kinase, catalytic domain | 0 / 29 | 8 / 4662 | 0.0 | 1.000 |
| IPR000408 | Repeat:Regulator of chromosome condensation, RCC1 | 0 / 29 | 5 / 4662 | 0.0 | 1.000 |
Top 15 GO terms (whole set, family level) — secondary, computational evidence (IEA/IBA) included
15 rows shown, ordered by FDR then p-value; 7 have FDR < 0.05 (bold).
| Term | Name | k / N cand. | n / M bg | Fold | FDR (BH) | GO evidence | Families with non-IEA |
|---|---|---|---|---|---|---|---|
| GO:0005619 | cellular_component:ascospore wall | 4 / 15 | 13 / 4314 | 88.492 | 1.01e-04 | has_non_IEA | 1 |
| GO:0031160 | cellular_component:spore wall | 4 / 15 | 13 / 4314 | 88.492 | 1.01e-04 | has_non_IEA | 1 |
| GO:0005628 | cellular_component:prospore membrane | 4 / 15 | 26 / 4314 | 44.246 | 0.001 | has_non_IEA | 1 |
| GO:0005811 | cellular_component:lipid droplet | 4 / 15 | 40 / 4314 | 28.76 | 0.006 | has_non_IEA | 1 |
| GO:0005618 | cellular_component:cell wall | 4 / 15 | 52 / 4314 | 22.123 | 0.012 | has_non_IEA | 1 |
| GO:0009277 | cellular_component:fungal-type cell wall | 4 / 15 | 52 / 4314 | 22.123 | 0.012 | has_non_IEA | 1 |
| GO:0030312 | cellular_component:external encapsulating structure | 4 / 15 | 54 / 4314 | 21.304 | 0.012 | has_non_IEA | 1 |
| GO:0140110 | molecular_function:transcription regulator activity | 4 / 15 | 250 / 4314 | 4.602 | 1.000 | has_non_IEA | 1 |
| GO:0003677 | molecular_function:DNA binding | 5 / 15 | 454 / 4314 | 3.167 | 1.000 | has_non_IEA | 2 |
| GO:0000981 | molecular_function:DNA-binding transcription factor activity, RNA polymerase II-specific | 3 / 15 | 158 / 4314 | 5.461 | 1.000 | has_non_IEA | 1 |
| GO:0003700 | molecular_function:DNA-binding transcription factor activity | 3 / 15 | 179 / 4314 | 4.82 | 1.000 | has_non_IEA | 1 |
| GO:0030154 | biological_process:cell differentiation | 1 / 15 | 7 / 4314 | 41.086 | 1.000 | has_non_IEA | 1 |
| GO:0043565 | molecular_function:sequence-specific DNA binding | 3 / 15 | 244 / 4314 | 3.536 | 1.000 | has_non_IEA | 1 |
| GO:0000978 | molecular_function:RNA polymerase II cis-regulatory region sequence-specific DNA binding | 2 / 15 | 104 / 4314 | 5.531 | 1.000 | has_non_IEA | 1 |
| GO:0000987 | molecular_function:cis-regulatory region sequence-specific DNA binding | 2 / 15 | 114 / 4314 | 5.046 | 1.000 | has_non_IEA | 1 |
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_Eremgoss | n_Eremcymb | n_Eremsine | n_Kluylact | n_Lachther | n_Torudelb | n_Scer |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Arp2/3 ARPC2 (P34-Arc) | PF04045 | 3 | 3 | 3 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Arp2/3 ARPC3 (P21-Arc) | PF04062 | 3 | 3 | 3 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Arp2/3 ARPC4 | PF05856 | 3 | 3 | 3 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Arp2/3 ARPC5 (P16-Arc) | PF04699 | 3 | 3 | 3 | 0 | 0 | 0 | 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 | 0 | 0 | |
| Arp2 / Arp3 (description only) | actin-related protein (2|3)\b|\bARP[23]\b | 19 | 19 | 19 | 0 | 0 | 0 | 6 | 7 | 6 | 6 | 6 | 7 | 7 | |
| WAVE complex NCKAP1 | PF09735 | 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 | |
| WAVE complex ABI | PF07815|PF27594 | 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 | |
| WASP family (WH1) | PF00568 | 3 | 3 | 3 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| WH2 motif (WASP, WAVE, others) | PF02205 | 6 | 6 | 6 | 0 | 0 | 0 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | |
| Formin FH2 | PF02181 | 9 | 9 | 9 | 0 | 0 | 0 | 3 | 3 | 3 | 2 | 2 | 2 | 2 | |
| Formin Drf_GBD / Drf_FH3 / Drf_DAD | PF06371|PF06367|PF06345 | 8 | 8 | 8 | 0 | 0 | 0 | 2 | 3 | 3 | 2 | 2 | 2 | 1 | |
| Ena/VASP (VASP_tetra) | PF08776 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| Coronin (description only) | coronin | 3 | 3 | 3 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Cortactin (HS1_rep) | PF02218 | 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 | 0 | 0 | |
| Myosin head (all myosins) | PF00063 | 9 | 9 | 9 | 0 | 0 | 0 | 3 | 3 | 3 | 3 | 3 | 3 | 5 |
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