yc ustilaginomycotina: 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 (20411 sequences in 10919 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 2026-10-24T14:40:05. Source tables: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_ustilaginomycotina/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 40.0%, GO 30.0%. 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 |
|---|---|---|---|---|---|---|---|
| Malaglob | universe | 4270 | 83.8% | 67.5% | 90.2% | 82.3% | 90.5% |
| Malaglob | candidates | 6 | 50.0% | 0.0% | 66.7% | 50.0% | 66.7% |
| Malasymp | universe | 4490 | 85.7% | 68.1% | 90.4% | 82.7% | 90.6% |
| Malasymp | candidates | 4 | 25.0% | 0.0% | 50.0% | 0.0% | 50.0% |
| Moesaphi | universe | 6011 | 76.6% | 62.7% | 81.8% | 72.4% | 81.9% |
| Moesaphi | candidates | 0 | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% |
| Kalmbras | universe | 5650 | 82.9% | 67.8% | 88.0% | 78.7% | 88.3% |
| Kalmbras | candidates | 0 | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% |
| ALL_IN | universe | 20421 | 81.8% | 66.3% | 87.2% | 78.5% | 87.4% |
| ALL_IN | candidates | 10 | 40.0% | 0.0% | 60.0% | 30.0% | 60.0% |
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 | 9 | 0 / 502 | 0 / 0 (skipped_no_annotated_candidates) | 0 / 1204 | 0 / 2872 |
| whole_set | protein | 10 | 0 / 1157 | 0 / 0 (skipped_no_annotated_candidates) | 0 / 2629 | 0 / 3910 |
| Kalmbras | family | 0 | 0 / 0 (skipped_no_annotated_candidates) | 0 / 0 (skipped_no_annotated_candidates) | 0 / 0 (skipped_no_annotated_candidates) | 0 / 0 (skipped_no_annotated_candidates) |
| Kalmbras | protein | 0 | 0 / 0 (skipped_no_annotated_candidates) | 0 / 0 (skipped_no_annotated_candidates) | 0 / 0 (skipped_no_annotated_candidates) | 0 / 0 (skipped_no_annotated_candidates) |
| Malaglob | family | 6 | 0 / 131 | 0 / 0 (skipped_no_annotated_candidates) | 0 / 411 | 0 / 1645 |
| Malaglob | protein | 6 | 0 / 149 | 0 / 0 (skipped_no_annotated_candidates) | 0 / 463 | 0 / 1678 |
| Malasymp | family | 4 | 0 / 138 | 0 / 0 (skipped_no_annotated_candidates) | 0 / 419 | 0 / 0 (skipped_no_annotated_candidates) |
| Malasymp | protein | 4 | 0 / 159 | 0 / 0 (skipped_no_annotated_candidates) | 0 / 488 | 0 / 0 (skipped_no_annotated_candidates) |
| Moesaphi | family | 0 | 0 / 0 (skipped_no_annotated_candidates) | 0 / 0 (skipped_no_annotated_candidates) | 0 / 0 (skipped_no_annotated_candidates) | 0 / 0 (skipped_no_annotated_candidates) |
| Moesaphi | protein | 0 | 0 / 0 (skipped_no_annotated_candidates) | 0 / 0 (skipped_no_annotated_candidates) | 0 / 0 (skipped_no_annotated_candidates) | 0 / 0 (skipped_no_annotated_candidates) |
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) |
|---|---|---|---|---|---|
| PF04000 | Sas10_Utp3: Sas10/Utp3/C1D family | 1 / 4 | 6 / 8159 | 339.958 | 1.000 |
| PF00173 | Cyt-b5: Cytochrome b5-like Heme/Steroid binding domain | 1 / 4 | 22 / 8159 | 92.716 | 1.000 |
| PF00004 | AAA: ATPase family associated with various cellular activities (AAA) | 0 / 4 | 37 / 8159 | 0.0 | 1.000 |
| PF00005 | ABC_tran: ABC transporter | 0 / 4 | 30 / 8159 | 0.0 | 1.000 |
| PF00006 | ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain | 0 / 4 | 5 / 8159 | 0.0 | 1.000 |
| PF00009 | GTP_EFTU: Elongation factor Tu GTP binding domain | 0 / 4 | 21 / 8159 | 0.0 | 1.000 |
| PF00010 | HLH: Helix-loop-helix DNA-binding domain | 0 / 4 | 22 / 8159 | 0.0 | 1.000 |
| PF00012 | HSP70: Hsp70 protein | 0 / 4 | 8 / 8159 | 0.0 | 1.000 |
| PF00013 | KH_1: KH domain | 0 / 4 | 8 / 8159 | 0.0 | 1.000 |
| PF00018 | SH3_1: SH3 domain | 0 / 4 | 31 / 8159 | 0.0 | 1.000 |
| PF00022 | Actin: Actin | 0 / 4 | 14 / 8159 | 0.0 | 1.000 |
| PF00023 | Ank: Ankyrin repeat | 0 / 4 | 9 / 8159 | 0.0 | 1.000 |
| PF00025 | Arf: ADP-ribosylation factor family | 0 / 4 | 8 / 8159 | 0.0 | 1.000 |
| PF00026 | Asp: Eukaryotic aspartyl protease | 0 / 4 | 13 / 8159 | 0.0 | 1.000 |
| PF00027 | cNMP_binding: Cyclic nucleotide-binding domain | 0 / 4 | 6 / 8159 | 0.0 | 1.000 |
| PF00043 | GST_C: Glutathione S-transferase, C-terminal domain | 0 / 4 | 7 / 8159 | 0.0 | 1.000 |
| PF00046 | Homeodomain: Homeodomain | 0 / 4 | 8 / 8159 | 0.0 | 1.000 |
| PF00063 | Myosin_head: Myosin head (motor domain) | 0 / 4 | 6 / 8159 | 0.0 | 1.000 |
| PF00067 | p450: Cytochrome P450 | 0 / 4 | 18 / 8159 | 0.0 | 1.000 |
| PF00069 | Pkinase: Protein kinase domain | 0 / 4 | 175 / 8159 | 0.0 | 1.000 |
| PF00071 | Ras: Ras family | 0 / 4 | 24 / 8159 | 0.0 | 1.000 |
| PF00072 | Response_reg: Response regulator receiver domain | 0 / 4 | 15 / 8159 | 0.0 | 1.000 |
| PF00076 | RRM_1: RNA recognition motif | 0 / 4 | 113 / 8159 | 0.0 | 1.000 |
| PF00082 | Peptidase_S8: Subtilase family | 0 / 4 | 5 / 8159 | 0.0 | 1.000 |
| PF00083 | Sugar_tr: Sugar (and other) transporter | 0 / 4 | 35 / 8159 | 0.0 | 1.000 |
Top 25 InterPro 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) |
|---|---|---|---|---|---|
| IPR012340 | Homologous_superfamily:Nucleic acid-binding, OB-fold | 2 / 6 | 91 / 8810 | 32.271 | 1.000 |
| IPR007146 | Family:Sas10/Utp3/C1D | 1 / 6 | 6 / 8810 | 244.722 | 1.000 |
| IPR001199 | Domain:Cytochrome b5-like heme/steroid binding domain | 1 / 6 | 22 / 8810 | 66.742 | 1.000 |
| IPR036400 | Homologous_superfamily:Cytochrome b5-like heme/steroid binding domain superfamily | 1 / 6 | 23 / 8810 | 63.841 | 1.000 |
| IPR000008 | Domain:C2 domain | 0 / 6 | 16 / 8810 | 0.0 | 1.000 |
| IPR000014 | Domain:PAS domain | 0 / 6 | 11 / 8810 | 0.0 | 1.000 |
| IPR000058 | Domain:Zinc finger, AN1-type | 0 / 6 | 5 / 8810 | 0.0 | 1.000 |
| IPR000073 | Domain:Alpha/beta hydrolase fold-1 | 0 / 6 | 39 / 8810 | 0.0 | 1.000 |
| IPR000086 | Domain:NUDIX hydrolase domain | 0 / 6 | 16 / 8810 | 0.0 | 1.000 |
| IPR000089 | Domain:Biotin/lipoyl attachment | 0 / 6 | 11 / 8810 | 0.0 | 1.000 |
| IPR000095 | Domain:CRIB domain | 0 / 6 | 7 / 8810 | 0.0 | 1.000 |
| IPR000156 | Domain:Ran binding domain | 0 / 6 | 7 / 8810 | 0.0 | 1.000 |
| IPR000159 | Domain:Ras-associating domain | 0 / 6 | 6 / 8810 | 0.0 | 1.000 |
| IPR000164 | Family:Histone H3/CENP-A | 0 / 6 | 5 / 8810 | 0.0 | 1.000 |
| IPR000172 | Domain:Glucose-methanol-choline oxidoreductase, N-terminal | 0 / 6 | 6 / 8810 | 0.0 | 1.000 |
| IPR000182 | Domain:GNAT domain | 0 / 6 | 34 / 8810 | 0.0 | 1.000 |
| IPR000192 | Domain:Aminotransferase class V domain | 0 / 6 | 10 / 8810 | 0.0 | 1.000 |
| IPR000194 | Domain:ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain | 0 / 6 | 5 / 8810 | 0.0 | 1.000 |
| IPR000195 | Domain:Rab-GAP-TBC domain | 0 / 6 | 31 / 8810 | 0.0 | 1.000 |
| IPR000198 | Domain:Rho GTPase-activating protein domain | 0 / 6 | 24 / 8810 | 0.0 | 1.000 |
| IPR000209 | Domain:Peptidase S8/S53 domain | 0 / 6 | 5 / 8810 | 0.0 | 1.000 |
| IPR000210 | Domain:BTB/POZ domain | 0 / 6 | 10 / 8810 | 0.0 | 1.000 |
| IPR000219 | Domain:Dbl homology domain | 0 / 6 | 28 / 8810 | 0.0 | 1.000 |
| IPR000225 | Repeat:Armadillo | 0 / 6 | 9 / 8810 | 0.0 | 1.000 |
| IPR000232 | Domain:Heat shock factor (HSF)-type, DNA-binding | 0 / 6 | 10 / 8810 | 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; 0 have FDR < 0.05 (bold).
| Term | Name | k / N cand. | n / M bg | Fold | FDR (BH) | GO evidence | Families with non-IEA |
|---|---|---|---|---|---|---|---|
| GO:0000460 | biological_process:maturation of 5.8S rRNA | 1 / 3 | 18 / 7761 | 143.722 | 1.000 | IEA_only | 0 |
| GO:0000178 | cellular_component:exosome (RNase complex) | 1 / 3 | 20 / 7761 | 129.35 | 1.000 | IEA_only | 0 |
| GO:1905354 | cellular_component:exoribonuclease complex | 1 / 3 | 26 / 7761 | 99.5 | 1.000 | IEA_only | 0 |
| GO:0020037 | molecular_function:heme binding | 1 / 3 | 57 / 7761 | 45.386 | 1.000 | IEA_only | 0 |
| GO:0046906 | molecular_function:tetrapyrrole binding | 1 / 3 | 57 / 7761 | 45.386 | 1.000 | IEA_only | 0 |
| GO:0005730 | cellular_component:nucleolus | 1 / 3 | 179 / 7761 | 14.453 | 1.000 | IEA_only | 0 |
| GO:0006364 | biological_process:rRNA processing | 1 / 3 | 198 / 7761 | 13.066 | 1.000 | IEA_only | 0 |
| GO:0016072 | biological_process:rRNA metabolic process | 1 / 3 | 230 / 7761 | 11.248 | 1.000 | IEA_only | 0 |
| GO:0005789 | cellular_component:endoplasmic reticulum membrane | 1 / 3 | 265 / 7761 | 9.762 | 1.000 | IEA_only | 0 |
| GO:0043228 | cellular_component:membraneless organelle | 1 / 3 | 482 / 7761 | 5.367 | 1.000 | IEA_only | 0 |
| GO:0043232 | cellular_component:intracellular membraneless organelle | 1 / 3 | 482 / 7761 | 5.367 | 1.000 | IEA_only | 0 |
| GO:0006396 | biological_process:RNA processing | 1 / 3 | 507 / 7761 | 5.103 | 1.000 | IEA_only | 0 |
| GO:0010468 | biological_process:regulation of gene expression | 1 / 3 | 513 / 7761 | 5.043 | 1.000 | IEA_only | 0 |
| GO:0010556 | biological_process:regulation of macromolecule biosynthetic process | 1 / 3 | 522 / 7761 | 4.956 | 1.000 | IEA_only | 0 |
| GO:0009889 | biological_process:regulation of biosynthetic process | 1 / 3 | 538 / 7761 | 4.809 | 1.000 | 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_Malaglob | n_Malasymp | n_Moesaphi | n_Kalmbras | n_Mycomayd | n_Sporreil | n_Ustihord | n_Cerabomb |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2 | 2 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 1 | 0 | 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 | 4 | 4 | 4 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Arp2 / Arp3 (description only) | actin-related protein (2|3)\b|\bARP[23]\b | 26 | 26 | 24 | 0 | 0 | 0 | 6 | 8 | 6 | 6 | 7 | 6 | 5 | 6 | |
| 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 | 3 | 3 | 3 | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | |
| WH2 motif (WASP, WAVE, others) | PF02205 | 5 | 5 | 4 | 0 | 0 | 0 | 1 | 2 | 1 | 1 | 2 | 2 | 2 | 2 | |
| Formin FH2 | PF02181 | 6 | 6 | 6 | 0 | 0 | 0 | 1 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | |
| Formin Drf_GBD / Drf_FH3 / Drf_DAD | PF06371|PF06367|PF06345 | 8 | 8 | 8 | 0 | 0 | 0 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | |
| Ena/VASP (VASP_tetra) | PF08776 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| Coronin (description only) | coronin | 4 | 4 | 4 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 2 | |
| 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 | 0 | 0 | 1 | |
| Myosin head (all myosins) | PF00063 | 17 | 17 | 17 | 0 | 0 | 0 | 5 | 5 | 3 | 4 | 4 | 4 | 4 | 5 |
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