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Final DMSO fraction and SD-versus-SEM definition for ±13 nM are not explicit in the inspected assay-specific text.", "replicates": "3 independent experiments; each 10-point curve in duplicate", "target_scope": "domain_specific", "temperature_C": 23, "uncertainty": 13.0, "uncertainty_type": null, "units": "nM", "value": 104.0, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0006", "assay_type": "NanoBRET PPI half-response", "buffer": "DMEM/F12 without phenol red; 4% FBS; 100 U/mL penicillin; 100 ug/mL streptomycin", "compound_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "compound_name": "UNC6934", "conditions": "{\"cell_line\": \"U2OS\", \"readout\": \"NSD2 PWWP1–histone H3.3 interaction\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Unstandardized half-response concentration", "evidence_class": "cellular_interaction_response", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "is_negative": false, "method": "NanoBRET PPI half-response", "pH": null, "preparation_id": "PREP:UNC6934", "publication_year": 2022, "remaining_uncertainty": "NanoLuc construct boundaries, readout temperature and SD-versus-SEM are not explicit in the inspected source. 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Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. 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Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. 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The SPR Methods paragraph explicitly names 3f, so its conditions are not copied to compound 1.", "replicates": null, "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 8, "uncertainty_type": null, "units": "µM", "value": 41, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP5:ASSAY:0034", "assay_type": "Reverse ITC Kd", "buffer": null, "compound_id": "PREP:DEFREITAS2021_1", "compound_name": "compound 1 (de Freitas 2021)", "conditions": { "compound_cell_concentration_uM": 40, "protein_syringe_concentration_mM": 1, "reverse_titration_reason": "Limited compound solubility", "titration_direction": "Protein into compound" }, "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8130708/", "is_negative": false, "method": "Reverse ITC", "pH": null, "preparation_id": "PREP:DEFREITAS2021_1", "publication_year": 2021, "remaining_uncertainty": "No uncertainty, replicate count or exact stereochemical assignment inferred from the primary Results value. A distinct reverse-ITC experiment is retained separately from SPR.", "replicates": null, "target_scope": "domain_specific", "temperature_C": null, "uncertainty": null, "uncertainty_type": null, "units": "µM", "value": 8.9, "value_operator": "=" }, { "DMSO_percent": 0.3, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0018", "assay_type": "SPR Kd", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_11", "compound_name": "compound 11 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_11", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. 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Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.19, "uncertainty_type": "SD", "units": "µM", "value": 1.02, "value_operator": "=" }, { "DMSO_percent": 0.3, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0025", "assay_type": "SPR Kd", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_11", "compound_name": "compound 11 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_11", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.31, "uncertainty_type": "SD", "units": "µM", "value": 2.3, "value_operator": "=" }, { "DMSO_percent": 0.3, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0019", "assay_type": "SPR Kd", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_12", "compound_name": "compound 12 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_12", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.13, "uncertainty_type": "SD", "units": "µM", "value": 1.47, "value_operator": "=" }, { "DMSO_percent": 0.3, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0026", "assay_type": "SPR Kd", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_12", "compound_name": "compound 12 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_12", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.31, "uncertainty_type": "SD", "units": "µM", "value": 2.8, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0030", "assay_type": "HTRF displacement IC50", "buffer": null, "compound_id": "PREP:COLLIE2025_12", "compound_name": "compound 12 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": 2, \"uncertainty_type\": \"SEM\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "IC50", "evidence_class": "biochemical_interaction_inhibition", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "HTRF displacement", "pH": null, "preparation_id": "PREP:COLLIE2025_12", "publication_year": 2025, "remaining_uncertainty": "HTRF full conditions are referenced to Carlino et al. 2024 DOI 10.1021/acs.jmedchem.4c00215. Its main protocol remains inaccessible after official repository checks. The actual supplement was inspected but contains no HTRF protocol. Table 1 reports SEM; independence level of HTRF replicates is not specified.", "replicates": "2", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 0.06, "uncertainty_type": "SEM", "units": "µM", "value": 2.49, "value_operator": "=" }, { "DMSO_percent": 0.3, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0020", "assay_type": "SPR Kd", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_13", "compound_name": "compound 13 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_13", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.04, "uncertainty_type": "SD", "units": "µM", "value": 0.75, "value_operator": "=" }, { "DMSO_percent": 0.3, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0027", "assay_type": "SPR Kd", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_13", "compound_name": "compound 13 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_13", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.05, "uncertainty_type": "SD", "units": "µM", "value": 1.52, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0031", "assay_type": "HTRF displacement IC50", "buffer": null, "compound_id": "PREP:COLLIE2025_13", "compound_name": "compound 13 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SEM\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "IC50", "evidence_class": "biochemical_interaction_inhibition", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "HTRF displacement", "pH": null, "preparation_id": "PREP:COLLIE2025_13", "publication_year": 2025, "remaining_uncertainty": "HTRF full conditions are referenced to Carlino et al. 2024 DOI 10.1021/acs.jmedchem.4c00215. Its main protocol remains inaccessible after official repository checks. The actual supplement was inspected but contains no HTRF protocol. Table 1 reports SEM; independence level of HTRF replicates is not specified.", "replicates": "at least 3", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 0.06, "uncertainty_type": "SEM", "units": "µM", "value": 1.31, "value_operator": "=" }, { "DMSO_percent": 0.3, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0015", "assay_type": "SPR Kd", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_5", "compound_name": "compound 5 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_5", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.03, "uncertainty_type": "SD", "units": "µM", "value": 0.16, "value_operator": "=" }, { "DMSO_percent": 0.3, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0022", "assay_type": "SPR Kd", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_5", "compound_name": "compound 5 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_5", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.03, "uncertainty_type": "SD", "units": "µM", "value": 0.92, "value_operator": "=" }, { "DMSO_percent": 0.3, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0016", "assay_type": "SPR Kd", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_6", "compound_name": "compound 6 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_6", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.09, "uncertainty_type": "SD", "units": "µM", "value": 0.71, "value_operator": "=" }, { "DMSO_percent": 0.3, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0023", "assay_type": "SPR Kd", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_6", "compound_name": "compound 6 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_6", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.64, "uncertainty_type": "SD", "units": "µM", "value": 5.83, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0028", "assay_type": "HTRF displacement IC50", "buffer": null, "compound_id": "PREP:COLLIE2025_6", "compound_name": "compound 6 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": 2, \"uncertainty_type\": \"SEM\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "IC50", "evidence_class": "biochemical_interaction_inhibition", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "HTRF displacement", "pH": null, "preparation_id": "PREP:COLLIE2025_6", "publication_year": 2025, "remaining_uncertainty": "HTRF full conditions are referenced to Carlino et al. 2024 DOI 10.1021/acs.jmedchem.4c00215. Its main protocol remains inaccessible after official repository checks. The actual supplement was inspected but contains no HTRF protocol. Table 1 reports SEM; independence level of HTRF replicates is not specified.", "replicates": "2", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 0.08, "uncertainty_type": "SEM", "units": "µM", "value": 1.24, "value_operator": "=" }, { "DMSO_percent": 0.3, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0017", "assay_type": "SPR Kd", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_7", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.02, "uncertainty_type": "SD", "units": "µM", "value": 0.15, "value_operator": "=" }, { "DMSO_percent": 0.3, "assay_construct_end": 350, "assay_construct_start": 211, "assay_record_id": "PWWP:ASSAY:0024", "assay_type": "SPR Kd", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 211–350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_7", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": 0.01, "uncertainty_type": "SD", "units": "µM", "value": 0.76, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0029", "assay_type": "HTRF displacement IC50", "buffer": null, "compound_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N", "compound_name": "compound 7 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD2 208–368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SEM\"}", "domain_id": "UP:O96028:PWWP1", "endpoint": "IC50", "evidence_class": "biochemical_interaction_inhibition", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": false, "method": "HTRF displacement", "pH": null, "preparation_id": "PREP:COLLIE2025_7", "publication_year": 2025, "remaining_uncertainty": "HTRF full conditions are referenced to Carlino et al. 2024 DOI 10.1021/acs.jmedchem.4c00215. Its main protocol remains inaccessible after official repository checks. The actual supplement was inspected but contains no HTRF protocol. Table 1 reports SEM; independence level of HTRF replicates is not specified.", "replicates": "at least 3", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 0.01, "uncertainty_type": "SEM", "units": "µM", "value": 0.21, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0035", "assay_type": "Quantitative assay verification pending", "buffer": null, "compound_id": "PREP:HS13", "compound_name": "HS13", "conditions": "{}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Qualitative / association", "evidence_class": "abstract_reported_covalent_association", "evidence_url": "https://doi.org/10.1016/j.bmc.2026.118751", "is_negative": false, "method": "Quantitative assay verification pending", "pH": null, "preparation_id": "PREP:HS13", "publication_year": 2026, "remaining_uncertainty": "Primary abstract reports Kd 8.33 µM and C294 covalency; full assay method, construct, uncertainty and exact chemical identity not verified. Main value remains null.", "replicates": null, "target_scope": "domain_specific", "temperature_C": null, "uncertainty": null, "uncertainty_type": null, "units": null, "value": null, "value_operator": null }, { "DMSO_percent": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0001", "assay_type": "SPR Kd", "buffer": null, "compound_id": "INCHIKEY:WYAGGMZTARRIDX-UHFFFAOYSA-N", "compound_name": "MR837 (3f)", "conditions": "{}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8130708/", "is_negative": false, "method": "SPR", "pH": null, "preparation_id": "PREP:MR837", "publication_year": 2021, "remaining_uncertainty": "Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent.", "replicates": null, "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 3.0, "uncertainty_type": null, "units": "µM", "value": 7.0, "value_operator": "=" }, { "DMSO_percent": 0.5, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0002", "assay_type": "SPR Kd", "buffer": null, "compound_id": "INCHIKEY:WYAGGMZTARRIDX-UHFFFAOYSA-N", "compound_name": "MR837 (3f)", "conditions": "{\"DMSO_percent\": 0.5}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8130708/", "is_negative": false, "method": "SPR", "pH": null, "preparation_id": "PREP:MR837", "publication_year": 2021, "remaining_uncertainty": "Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent.", "replicates": null, "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 0.4, "uncertainty_type": null, "units": "µM", "value": 3.4, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0003", "assay_type": "SPR Kd", "buffer": null, "compound_id": "INCHIKEY:XPHOPAPMJBSLFN-UHFFFAOYSA-N", "compound_name": "MRT866", "conditions": "{}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "is_negative": false, "method": "SPR", "pH": null, "preparation_id": "PREP:MRT866", "publication_year": 2022, "remaining_uncertainty": "349 ± 19 nM verified in Results; MRT866-specific SPR construct/protocol, replicate definition and uncertainty statistic remain unresolved. Crystallography 211–350 is not assigned as the binding-assay construct.", "replicates": null, "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 19.0, "uncertainty_type": null, "units": "nM", "value": 349.0, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP5:ASSAY:0007", "assay_type": "SPR Kd", "buffer": null, "compound_id": "INCHIKEY:JXTDBIVBSAFNBJ-PLCURSASSA-N", "compound_name": "UNC7096", "conditions": {}, "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "is_negative": false, "method": "SPR", "pH": null, "preparation_id": "PREP:UNC7096", "publication_year": 2022, "remaining_uncertainty": "UNC7096-specific construct, buffer, uncertainty and replicate definition were not independently verified; the general UNC6934/UNC7145 SPR protocol is not automatically transferred.", "replicates": null, "target_scope": "domain_specific", "temperature_C": null, "uncertainty": null, "uncertainty_type": null, "units": "nM", "value": 46, "value_operator": "=" }, { "DMSO_percent": 0.5, "assay_construct_end": 368, "assay_construct_start": 208, "assay_record_id": "PWWP:ASSAY:0007", "assay_type": "SPR no appreciable binding", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.05% Tween-20; 0.5% DMSO", "compound_id": "INCHIKEY:HUIINGSTUYTZJL-UHFFFAOYSA-N", "compound_name": "UNC7145", "conditions": "{\"highest_tested_concentration_uM\": 20, \"phase3_verification\": \"SV02A\", \"purified_tags\": \"AviTag/NSD2(208–368)/polyhistidine; biotinylated\", \"source_protocol_highest_concentration_uM\": 2}", "domain_id": "UP:O96028:PWWP1", "endpoint": "Qualitative / association", "evidence_class": "negative_binding_test", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "is_negative": true, "method": "SPR no appreciable binding", "pH": 7.4, "preparation_id": "PREP:UNC7145", "publication_year": 2022, "remaining_uncertainty": "Primary-source concentration discrepancy: Results report no appreciable binding up to 20 uM, but SPR Methods state 2 uM as highest concentration. Neither is converted into a Kd bound; human source review required.", "replicates": null, "target_scope": "domain_specific", "temperature_C": null, "uncertainty": null, "uncertainty_type": null, "units": "µM", "value": null, "value_operator": null }, { "DMSO_percent": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP5:ASSAY:0009", "assay_type": "SPR Kd", "buffer": null, "compound_id": "INCHIKEY:MDIKJIFCQAJLPD-UHFFFAOYSA-N", "compound_name": "UNC8153", "conditions": {}, "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10116495/", "is_negative": false, "method": "SPR", "pH": null, "preparation_id": "PREP:UNC8153", "publication_year": 2023, "remaining_uncertainty": "Original value and uncertainty preserved from later primary-table reprint; original Figure 3 numeric image not separately opened. Original experiment replicate/statistic assignment and construct remain uncurated; this is not a second 2024 experiment.", "replicates": null, "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 7, "uncertainty_type": null, "units": "nM", "value": 24, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP5:ASSAY:0015", "assay_type": "SPR Kd", "buffer": null, "compound_id": "PREP:UNC8269", "compound_name": "UNC8269", "conditions": {}, "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://www.nature.com/articles/s41589-024-01660-y", "is_negative": false, "method": "SPR", "pH": null, "preparation_id": "PREP:UNC8269", "publication_year": 2024, "remaining_uncertainty": "Exact domain is stated; assay construct boundaries and full buffer were not independently recovered. Original table image and supporting SPR panel inspected.", "replicates": "3 independent experiments", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 21, "uncertainty_type": "SD", "units": "nM", "value": 36, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP5:ASSAY:0018", "assay_type": "SPR Kd", "buffer": null, "compound_id": "PREP:UNC8325", "compound_name": "UNC8325", "conditions": {}, "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://www.nature.com/articles/s41589-024-01660-y", "is_negative": false, "method": "SPR", "pH": null, "preparation_id": "PREP:UNC8325", "publication_year": 2024, "remaining_uncertainty": "Exact domain is stated; assay construct boundaries and full buffer were not independently recovered. Original table image and supporting SPR panel inspected.", "replicates": "3 independent experiments", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 19, "uncertainty_type": "SD", "units": "nM", "value": 41, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP5:ASSAY:0021", "assay_type": "SPR Kd", "buffer": null, "compound_id": "INCHIKEY:CSTHTJLTORVUST-UHFFFAOYSA-N", "compound_name": "UNC8732", "conditions": {}, "domain_id": "UP:O96028:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://www.nature.com/articles/s41589-024-01660-y", "is_negative": false, "method": "SPR", "pH": null, "preparation_id": "PREP:UNC8732", "publication_year": 2024, "remaining_uncertainty": "Exact domain is stated; assay construct boundaries and full buffer were not independently recovered. Original table image and supporting SPR panel inspected.", "replicates": "3 independent experiments", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 4, "uncertainty_type": "SD", "units": "nM", "value": 76, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP5:ASSAY:0024", "assay_type": "SPR qualitative no binding", "buffer": null, "compound_id": "PREP:UNC8884", "compound_name": "UNC8884", "conditions": {}, "domain_id": "UP:O96028:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_control", "evidence_url": "https://www.nature.com/articles/s41589-024-01660-y", "is_negative": true, "method": "SPR qualitative no binding", "pH": null, "preparation_id": "PREP:UNC8884", "publication_year": 2024, "remaining_uncertainty": "Table reports NB for binding and ND for degradation endpoints; ND means not determined and is not converted to zero or inactivity.", "replicates": null, "target_scope": "domain_specific", "temperature_C": null, "uncertainty": null, "uncertainty_type": null, "units": null, "value": null, "value_operator": null } ] }, "UP:Q9BZ95:PWWP1": { "counts": { "alphafold_count": 5, "assay_count": 13, "bioactivity_only_count": 10, "bound_structure_count": 9, "compound_count": 19, "domain_id": "UP:Q9BZ95:PWWP1", "domain_name": "PWWP1", "gene": "NSD3", "measured_assay_count": 13, "negative_count": 7, "preparation_count": 11, "probe_count": 1, "resolved_compound_count": 13, "unresolved_identity_count": 6 }, "observations": [ { "DMSO_percent": 2.0, "assay_construct_end": 398, "assay_construct_start": 263, "assay_record_id": "PWWP:ASSAY:0008", "assay_type": "SPR Kd", "buffer": "50 mM Tris; 150 mM NaCl; 1 mM TCEP; 0.005% Tween-20; 2% DMSO", "compound_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "compound_name": "BI-9321", "conditions": "{}", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://www.thesgc.org/chemical-probes/bi-9321", "is_negative": false, "method": "SPR", "pH": 8.0, "preparation_id": "PREP:BI-9321", "publication_year": 2019, "remaining_uncertainty": "Primary replicate conflict: Figure 3a states n=3 independent experiments, while Supplementary Table 7 states SPR n=4; both report SD. Indexed primary SPR Methods supply residues 263–398 and buffer, but the full PDF was unavailable. Exact assay temperature, mutations and per-dose contact times remain not inspected.", "replicates": "3 independent experiments (Figure 3a); 4 (Supplementary Table 7); unresolved source discrepancy", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 3.0, "uncertainty_type": "SD", "units": "nM", "value": 166.0, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0009", "assay_type": "NanoBRET IC50", "buffer": null, "compound_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "compound_name": "BI-9321", "conditions": "{\"cell_line\": \"U2OS\"}", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "IC50", "evidence_class": "cellular_interaction_response", "evidence_url": "https://www.thesgc.org/chemical-probes/bi-9321", "is_negative": false, "method": "NanoBRET", "pH": null, "preparation_id": "PREP:BI-9321", "publication_year": 2019, "remaining_uncertainty": "The value 1.2 ± 0.06 uM, SD and n=3 were verified in the actual Supplementary Table 7. Full NanoBRET construct and conditions were not inspected. The 1.4 uM direct tracer-engagement endpoint is separate from this histone PPI assay.", "replicates": "3 independent replicates (Figure 4e; also Supplementary Table 7)", "target_scope": "domain_specific", "temperature_C": null, "uncertainty": 0.06, "uncertainty_type": "SD", "units": "µM", "value": 1.2, "value_operator": "=" }, { "DMSO_percent": 1, "assay_construct_end": 402, "assay_construct_start": 247, "assay_record_id": "PWWP5:ASSAY:0001", "assay_type": "ITC Kd", "buffer": "50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP", "compound_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N", "compound_name": "BI-9321", "conditions": { "buffer": "50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP", "compound_syringe_concentration_uM": 200, "construct": "NSD3 247–402 in pNICBio2, E. coli expressed", "first_injection_removed": true, "model": "single binding site", "pH": 6.8, "protein_concentration_uM": 20, "temperature_C": 15 }, "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "evidence_class": "direct_binding_affinity", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8882712/", "is_negative": false, "method": "ITC", "pH": 6.8, "preparation_id": "PREP:BI-9321", "publication_year": 2022, "remaining_uncertainty": "Primary manuscript and Methods inspected; individual raw titration files not re-fitted. BI-9321 is a distinct study-specific ITC measurement, not the original 2019 SPR result.", "replicates": "2 independent measurements", "target_scope": "domain_specific", "temperature_C": 15, "uncertainty": 0.04, "uncertainty_type": "SD", "units": "µM", "value": 1.7, "value_operator": "=" }, { "DMSO_percent": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP5:ASSAY:0008", "assay_type": "Official SGC control activity summary", "buffer": null, "compound_id": "INCHIKEY:SFZHMKDAVPIXRB-UHFFFAOYSA-N", "compound_name": "BI-9466", "conditions": {}, "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "qualitative", "evidence_class": "qualitative_control", "evidence_url": "https://www.thesgc.org/chemical-probes/bi-9321", "is_negative": false, "method": "Official SGC control activity summary", "pH": null, "preparation_id": "PREP:BI-9466", "publication_year": null, "remaining_uncertainty": "Endpoint-specific absolute numeric value and test construct not transcribed; no numerical affinity derived from the fold statement.", "replicates": null, "target_scope": "domain_specific", "temperature_C": null, "uncertainty": null, "uncertainty_type": null, "units": null, "value": null, "value_operator": null }, { "DMSO_percent": 0.3, "assay_construct_end": 398, "assay_construct_start": 263, "assay_record_id": "PWWP11:ASSAY:0005", "assay_type": "SPR Kd counter-screen", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_11", "compound_name": "compound 11 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263–398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "evidence_class": "negative_binding_test", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": true, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_11", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": null, "uncertainty_type": null, "units": null, "value": null, "value_operator": null }, { "DMSO_percent": 0.3, "assay_construct_end": 398, "assay_construct_start": 263, "assay_record_id": "PWWP11:ASSAY:0006", "assay_type": "SPR Kd counter-screen", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_12", "compound_name": "compound 12 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263–398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "evidence_class": "negative_binding_test", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": true, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_12", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": null, "uncertainty_type": null, "units": null, "value": null, "value_operator": null }, { "DMSO_percent": 0.3, "assay_construct_end": 398, "assay_construct_start": 263, "assay_record_id": "PWWP11:ASSAY:0007", "assay_type": "SPR Kd counter-screen", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_13", "compound_name": "compound 13 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263–398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "evidence_class": "negative_binding_test", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": true, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_13", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": null, "uncertainty_type": null, "units": null, "value": null, "value_operator": null }, { "DMSO_percent": 0.3, "assay_construct_end": 398, "assay_construct_start": 263, "assay_record_id": "PWWP11:ASSAY:0002", "assay_type": "SPR Kd counter-screen", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_5", "compound_name": "compound 5 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263–398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "evidence_class": "censored_binding_limit", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": true, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_5", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.", "replicates": "at least 3 independent replicates (Table 1 general SPR definition)", "target_scope": "domain_specific", "temperature_C": 25, "uncertainty": null, "uncertainty_type": null, "units": "µM", "value": 30.0, "value_operator": ">" }, { "DMSO_percent": 0.3, "assay_construct_end": 398, "assay_construct_start": 263, "assay_record_id": "PWWP11:ASSAY:0003", "assay_type": "SPR Kd counter-screen", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO", "compound_id": "PREP:COLLIE2025_6", "compound_name": "compound 6 (Collie 2025)", "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263–398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}", "domain_id": "UP:Q9BZ95:PWWP1", "endpoint": "Kd", "evidence_class": "censored_binding_limit", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/", "is_negative": true, "method": "SPR", "pH": 7.5, "preparation_id": "PREP:COLLIE2025_6", "publication_year": 2025, "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. 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Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. 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"feature_id": "Q9Y6K1:UPFEATURE:5", "lane": 1, "name": "PHD-type; atypical", "source": "UniProtKB canonical feature", "source_index": 5, "source_url": "https://rest.uniprot.org/uniprotkb/Q9Y6K1.json", "start": 534, "type": "Zinc finger" }, { "end": 912, "evidence": [ { "evidenceCode": "ECO:0000255", "id": "PRU01016", "source": "PROSITE-ProRule" } ], "feature_id": "Q9Y6K1:UPFEATURE:3", "lane": 0, "name": "SAM-dependent MTase C5-type", "source": "UniProtKB canonical feature", "source_index": 3, "source_url": "https://rest.uniprot.org/uniprotkb/Q9Y6K1.json", "start": 634, "type": "Domain" } ], "protein_id": "UP:Q9Y6K1", "sequence_sha256": "52ea10c47364c98bc0b066941229148e42ad779b70b1b8569855db412b95cacd", "source_status": "UniProt feature coordinates accepted after exact canonical sequence identity check against the frozen Atlas.", "uniprot": "Q9Y6K1", "uniprot_source": { "accession": "Q9Y6K1", "annotation_usage": "eligible: exact canonical sequence match", "bytes": 115767, "entry_audit": 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"/evolution/download/METHODS.md" } ], "limitations": [ "Only 78 conservatively retained sites constrain 39 domain instances; deeper branching order is frequently unresolved.", "SH-aLRT≥80 and UFBoot≥95 are reporting thresholds, not probabilities that a relationship is true. Weak and alignment-sensitive branches must remain flagged.", "No justified outgroup is available in the structure-selected sample. Tree is unrooted; rectangular/circular layouts use an arbitrary traversal origin and do not imply direction or time.", "Comparison intervals combine deposited constructs, published structure-assisted alignments, curated CDD model spans and explicitly marked homolog transfers. They are not uniformly experimentally certified isolated folds.", "Nine nonhuman comparators are sparse and selected for structure availability; Jasper and the trypanosome entry are UniProt-unreviewed but experimentally sequence-mapped. No universal family census or species phylogeny is claimed.", "Conservation is unweighted Shannon entropy in this sampled alignment. It does not establish binding, histone specificity, pocket equivalence, chemical selectivity or therapeutic interchangeability.", "Human HDGF and rat Hdgf have identical retained sequences; their divergence and internal order cannot be inferred. The pdp2 composition test flags an uncorrected p≈0.0136 among39 sequences; this is a model diagnostic, not proof of compositional bias.", "Three predicted PWWP-like human candidates are displayed separately and excluded from alignment/tree.", "Source-deposited engineered substitutions are not substituted into the canonical sequences used for inference. Coordinate-contact observations are not affinity measurements." ], "metadata": { "alignment_length": 257, "analysis_id": "PWWP-EVO-1.0.0", "analysis_kind": "maximum_likelihood_domain_phylogeny", "branch_length_units": "expected amino-acid substitutions per retained alignment site", "candidate_count": 3, "dataset_version": "v1.2 frozen source; independently derived evolution1.0.0", "date": "2026-10-26", "display_policy": "Support-qualified unrooted inference; low-support and sensitivity-dependent branching remains unresolved.", "domain_count": 39, "excluded_columns": 179, "identical_retained_sequence_groups": [ [ "P51858_PWWP1", "Q8VHK7_PWWP1" ] ], "input_source_sha256": { "core_residue_correspondence.csv": "7bd79cc827b90bf631588f96ef3125cc778e3435202dddc1adea59c93267a384", "domains.csv": "27e4f350f4c5dc82912bb695c1f26f27840d10fe1237e47c6667d5040b0b1149", "proteins.csv": "d9143412b2fd4382cf4fa2549cc07d4bd0dd73be101f4b9d3877fb4e12a6e02d", "pwwp_atlas_public_v1.2.sqlite": "0c53107a39e222b48611302b21fda5fb4ed50b190b6b39d41423ccc5ca5958f6" }, "model": "LG+G4", "provisional": false, "retained_columns": 78, "rooting": "Unrooted. Arbitrary three-way display traversal origin only; no ancestral or time interpretation.", "sampling_scope": "Human-centered curated Atlas domain set plus nine structural comparators; no additional taxa.", "seed": 20261026, "sensitivity_seed": 20261027, "software": { "Biopython": "1.88", "IQ-TREE": "2.4.0 Linux x86_64 built Feb7 2025", "MAFFT": "7.526 (2024/Apr/26)" }, "statistics": { "internal_branches": 36, "maximum_rf_for_bifurcating_trees": 72, "note": "An identical split in the sensitivity tree is a stability check, not independent replication.", "primary_supported_branches": 13, "primary_weak_branches": 23, "robinson_foulds_distance": 0, "robust_branches_both_masks": 12, "shared_unrooted_splits": 36, "supported_and_recovered_in_sensitivity": 13 }, "status": "exploratory_unrooted_phylogeny", "support": { "bnni": true, "reporting_thresholds": { "sh_alrt": 80, "ufboot": 95 }, "sh_alrt_replicates": 1000, "ufboot_replicates": 1000 }, "supported_tree_policy": "Cladogram retaining only splits meeting SH-aLRT80 and UFBoot95 in both primary and broader masks; unsupported edges are contracted. No evolutionary length scale in this view.", "title": "PWWP domain relationships", "version": "1.0.0" }, "newick": "(P29374_PWWP1:1.0635223602,Q4LE39_PWWP1:0.0140052014,((((O95696_PWWP1:0.2264658398,Q9ULD4_PWWP1:0.1388776833)28/64:0.0391966965,P55201_PWWP1:0.2068983906)99.7/100:1.4003885110,(((((((Q9Y6K1_PWWP1:0.2486136850,(Q9UBC3_PWWP1:0.0000025823,O88509_PWWP1:0.0346957180)97.6/100:0.4268002584)91.7/69:0.5123901198,(Q96N64_PWWP1:0.3853992098,Q6NUJ5_PWWP1:0.0617308128)96.3/99:0.9033280004)64.1/62:0.5346738500,Q9P267_PWWP1:1.2146930238)82.3/50:0.3906822151,((Q49A26_PWWP1:0.7784958054,(((P51858_PWWP1:0.0000010000,Q8VHK7_PWWP1:0.0000010000)0/100:0.0000022991,(Q5TGJ6_PWWP1:0.2586620956,((Q7Z4V5_PWWP1:0.1304455355,O75475_PWWP1:0.1612071778)91.9/96:0.0981943195,(Q9Y3E1_PWWP1:0.0000010000,Q9JMG7_PWWP1:0.0000010000)74.4/98:0.0192236365)92.1/97:0.1325531540)82.9/82:0.0442354467)99.3/97:0.8309548879,Q9VAA9_PWWP1:0.2669051033)92.9/93:0.4360820842)75.6/65:0.2625303924,((Q96L73_PWWP2:0.1545860858,O96028_PWWP2:0.1875321951)86.7/95:0.1602084862,Q9BZ95_PWWP2:0.0152173772)99.8/100:1.7157268270)0/16:0.0471681552)24.7/15:0.1235380074,((Q15326_PWWP1:0.0000028522,Q8R5C8_PWWP1:0.0135763277)89.1/99:0.4678908745,Q9ULU4_PWWP1:0.7563368901)99.5/100:1.1059805370)77/41:0.1482980958,(((Q2TAK8_PWWP1:0.3658932928,Q5H9M0_PWWP1:0.1399639110)67.9/83:0.1466262746,A0A494C071_PWWP1:0.3435006546)100/100:2.0452561750,((Q9H0M4_PWWP1:0.9744708409,Q586Y0_PWWP1:1.7568776336)44.1/32:0.1243735060,Q504Y3_PWWP1:1.8185080526)73.6/32:0.1764445632)71.7/34:0.1959264517)72.1/30:0.1269719470,(P52701_PWWP1:0.8091295885,((Q96L73_PWWP1:0.7699145845,O96028_PWWP1:0.1760001724)75.3/71:0.1567025951,Q9BZ95_PWWP1:0.3507408622)97.1/99:0.6252460866)77.7/52:0.1708604459)86.4/71:0.3144622501)77.3/60:0.2302031452,((O59676_PWWP1:1.2012976942,O94312_PWWP1:0.7558833699)87.9/92:0.4439253286,Q04213_PWWP1:0.9244668427)72.9/72:0.2807254496)99.8/100:1.8369594180);", "newick_supported": "(P29374_PWWP1,Q4LE39_PWWP1,((O95696_PWWP1,Q9ULD4_PWWP1,P55201_PWWP1)99.7/100,Q9Y6K1_PWWP1,(Q9UBC3_PWWP1,O88509_PWWP1)97.6/100,(Q96N64_PWWP1,Q6NUJ5_PWWP1)96.3/99,Q9P267_PWWP1,Q49A26_PWWP1,(P51858_PWWP1,Q8VHK7_PWWP1,Q5TGJ6_PWWP1,((Q7Z4V5_PWWP1,O75475_PWWP1)91.9/96,Q9Y3E1_PWWP1,Q9JMG7_PWWP1)92.1/97)99.3/97,Q9VAA9_PWWP1,(Q96L73_PWWP2,O96028_PWWP2,Q9BZ95_PWWP2)99.8/100,((Q15326_PWWP1,Q8R5C8_PWWP1)89.1/99,Q9ULU4_PWWP1)99.5/100,(Q2TAK8_PWWP1,Q5H9M0_PWWP1,A0A494C071_PWWP1)100/100,Q9H0M4_PWWP1,Q586Y0_PWWP1,Q504Y3_PWWP1,P52701_PWWP1,(Q96L73_PWWP1,O96028_PWWP1,Q9BZ95_PWWP1)97.1/99,O59676_PWWP1,O94312_PWWP1,Q04213_PWWP1)99.8/100);", "phase5_diagnostics": { "analysis_id": "PWWP-EVO-DIAGNOSTICS-5.0.0", "architecture": { "canonical_proteins": 39, "other_source_features": 71, "rule": "Absolute scale uses canonical amino-acid positions; normalized scale divides each interval by its own protein length. No coordinate projection onto unvalidated isoforms.", "selected_constructs": 46, "validated_isoform_domain_correspondences": 103 }, "composition_flags": [ { "leaf_id": "O94312_PWWP1", "reported_p_value": 0.0136, "scope": "Uncorrected per-sequence composition chi-square diagnostic from the original IQ-TREE log, 39 tested sequences. Not a standalone model-adequacy rejection." } ], "decisions": [ "Retain all 39 original domain instances and the unrooted support-collapsed default. The 78-site primary alignment resolves selected local splits; deep relationships remain unresolved.", "Thirty human domain instances and nine structural comparators across six nonhuman species are uneven family sampling. Existing comparators are not a family-wide orthology panel or a defensible outgroup.", "Boundary evidence remains heterogeneous: 24 deposited domain constructs, eight published structure-assisted intervals, three homology-mapped intervals, three CDD homology intervals and one structure-supported subdomain. The original source-specific qualifications remain attached.", "The 108-site alternative mask recovers the same 36 best-tree splits, but only 12 pass both support thresholds in both analyses. Mask agreement is sensitivity evidence, not independent replication.", "Four pairs have at least 95% identity over at least 60 paired nongap retained positions. Preserve all tips; identical paired residues with different gap patterns are not identical complete alignment strings.", "The pdp2 composition flag has an uncorrected reported p value of 0.0136 among 39 sequences. This flag motivates assessment in a future balanced analysis; it does not by itself establish model failure.", "No new phylogeny is promoted. Balanced subgroup-specific homolog selection, independently supported folded boundaries and model adequacy tests need a separately versioned sequence set and full inference/support pipeline; graphical branch operations cannot answer those biological questions.", "Subtree conservation is descriptive unweighted 1 minus Shannon entropy divided by ln(20), excluding gaps and displaying occupancy separately. Original inference inclusion/exclusion decisions are unchanged by subgroup selection." ], "future_sampling_protocol": [ "Select a predeclared set of taxa spanning each supported human subgroup, then verify PWWP-domain homolog boundaries with UniProt/InterPro plus available deposited constructs.", "Record orthology/paralogy uncertainty and preserve PWWP1/PWWP2 as independent instances; do not select sequences to improve bootstrap values.", "Qualify alternative alignments, column masks, composition, informative sites and saturation before fitting models. Retain sequence-near-duplicate diagnostics without silently deleting tips.", "Compare unrooted split robustness under boundary, taxon and mask changes. Root or date the tree only with an independently justified biological model." ], "inference": { "formal_model_adequacy": "Not established by model selection or support alone. No new posterior-predictive or parametric adequacy test executed.", "full_alignment_columns": 257, "model": "LG+G4", "primary_internal_splits": 36, "primary_sites": 78, "robust_splits": 12, "rooting": "Unrooted. Arbitrary three-way display traversal origin only; no ancestral or time interpretation.", "sensitivity_sites": 108, "shared_primary_sensitivity_splits": 36 }, "near_identical_pairs": [ { "complete_retained_strings_identical": false, "domain_A": "UP:Q9UBC3:PWWP1", "domain_B": "UP:O88509:PWWP1", "identical_amino_acids": 75, "paired_identity": 0.961538462, "paired_nongap_positions": 78, "scope": "Descriptive identity among mutually observed retained sites. Not an evolutionary distance or a pharmacology prediction." }, { "complete_retained_strings_identical": true, "domain_A": "UP:P51858:PWWP1", "domain_B": "UP:Q8VHK7:PWWP1", "identical_amino_acids": 77, "paired_identity": 1.0, "paired_nongap_positions": 77, "scope": "Descriptive identity among mutually observed retained sites. Not an evolutionary distance or a pharmacology prediction." }, { "complete_retained_strings_identical": false, "domain_A": "UP:Q9Y3E1:PWWP1", "domain_B": "UP:Q9JMG7:PWWP1", "identical_amino_acids": 74, "paired_identity": 1.0, "paired_nongap_positions": 74, "scope": "Descriptive identity among mutually observed retained sites. Not an evolutionary distance or a pharmacology prediction." }, { "complete_retained_strings_identical": false, "domain_A": "UP:Q15326:PWWP1", "domain_B": "UP:Q8R5C8:PWWP1", "identical_amino_acids": 71, "paired_identity": 0.986111111, "paired_nongap_positions": 72, "scope": "Descriptive identity among mutually observed retained sites. Not an evolutionary distance or a pharmacology prediction." } ], "release_date": "2026-10-26", "sample": { "boundary_methods": { "CDD_homology_model": 3, "experimentally_deposited_domain_construct": 24, "homology_mapped_construct": 3, "published_structure_assisted_alignment": 8, "structure_supported_subdomain": 1 }, "domain_instances": 39, "human_domain_instances": 30, "nonhuman_domain_instances": 9, "species_count": 7, "species_counts": { "Drosophila melanogaster": 1, "Homo sapiens": 30, "Mus musculus": 3, "Rattus norvegicus": 1, "Saccharomyces cerevisiae (strain ATCC 204508 / S288c)": 1, "Schizosaccharomyces pombe (strain 972 / ATCC 24843)": 2, "Trypanosoma brucei brucei (strain 927/4 GUTat10.1)": 1 } }, "source_analysis_id": "PWWP-EVO-1.0.0", "source_sha256": { "analysis/discovery_v1/atlas_discovery.json": "bd55b3a156b57e1c1fb1b6a477fbf4c000f6ef9e35a5446409caf38a7579d8de", "analysis/evolution_v1/alignment_masked.fasta": "339896b0952c2b12aef91f28d56f844a385a1ca8277bf18d11237079b7ac8840", "analysis/evolution_v1/atlas_evolution.json": "43207bd7947d128636d2a2a439cb427fb08afbe2551dc701cdfa0aa9a5a3e9f2", "analysis/evolution_v1/logs/iqtree_primary.stdout.log": "bde170b594bc6b5cfb135c2da0b34f29552e5d944eb86151a4b5172cf621376c", "analysis/evolution_v1/trees/primary.iqtree": "4b0e1832ffead87c9b415de06a67e54f0365119d9123b273ebbbe0945eb5f5b4", "analysis/evolution_v1/trees/sensitivity50.iqtree": "11f273c0e20f7694d7e883f8be593f7cb84a13f9b06a2564b26b49da9d162c85" }, "visualization_reference": { "authors": "Storm CE; Sonnhammer ELL", "doi": "10.1093/bioinformatics/17.4.343", "pmid": "11301303", "retrieved_date": "2026-10-26", "title": "NIFAS: visual analysis of domain evolution in proteins", "url": "https://pubmed.ncbi.nlm.nih.gov/11301303/", "verification_scope": "Primary bibliographic record and abstract; linked tree/domain architecture concept only. No code, layout or figure copied.", "year": 2001 } }, "published_comparison": [ { "comparison_scope": "Exact split in this differently sampled dataset, with the explicitly listed comparators. An additional comparator nested in a group can prevent exact bipartition matching without disproving broad affinity.", "interpretation": "Recovered with both primary support thresholds; compare sensitivity before interpretation.", "primary_recovered": true, "primary_support": { "sh_alrt": 99.7, "ufboot": 100.0 }, "published_description": "BRPF1, BRPF2/BRD1 and BRPF3 subgroup", "reference_doi": "10.1186/1471-2148-12-101", "relationship": "BRPF subgroup", "sensitivity_recovered": true, "sensitivity_support": { "sh_alrt": 99.9, "ufboot": 100.0 }, "tested_leaves": [ "O95696_PWWP1", "P55201_PWWP1", "Q9ULD4_PWWP1" ] }, { "comparison_scope": "Exact split in this differently sampled dataset, with the explicitly listed comparators. An additional comparator nested in a group can prevent exact bipartition matching without disproving broad affinity.", "interpretation": "Recovered with both primary support thresholds; compare sensitivity before interpretation.", "primary_recovered": true, "primary_support": { "sh_alrt": 99.8, "ufboot": 100.0 }, "published_description": "The b/C-terminal NSD domains form a subgroup distinct from a/N-terminal domains", "reference_doi": "10.1186/1471-2148-12-101", "relationship": "NSD second PWWP domains", "sensitivity_recovered": true, "sensitivity_support": { "sh_alrt": 100.0, "ufboot": 100.0 }, "tested_leaves": [ "O96028_PWWP2", "Q96L73_PWWP2", "Q9BZ95_PWWP2" ] }, { "comparison_scope": "Exact split in this differently sampled dataset, with the explicitly listed comparators. An additional comparator nested in a group can prevent exact bipartition matching without disproving broad affinity.", "interpretation": "Recovered with both primary support thresholds; compare sensitivity before interpretation.", "primary_recovered": true, "primary_support": { "sh_alrt": 97.1, "ufboot": 99.0 }, "published_description": "NSD a/N-terminal domains; published broader group includes MSH6", "reference_doi": "10.1186/1471-2148-12-101", "relationship": "NSD first PWWP domains", "sensitivity_recovered": true, "sensitivity_support": { "sh_alrt": 98.3, "ufboot": 99.0 }, "tested_leaves": [ "O96028_PWWP1", "Q96L73_PWWP1", "Q9BZ95_PWWP1" ] }, { "comparison_scope": "Exact split in this differently sampled dataset, with the explicitly listed comparators. An additional comparator nested in a group can prevent exact bipartition matching without disproving broad affinity.", "interpretation": "Present in best tree but below one or both support thresholds; unresolved.", "primary_recovered": true, "primary_support": { "sh_alrt": 77.7, "ufboot": 52.0 }, "published_description": "Published a-type grouping with MSH6", "reference_doi": "10.1186/1471-2148-12-101", "relationship": "NSD first domains plus MSH6", "sensitivity_recovered": true, "sensitivity_support": { "sh_alrt": 84.0, "ufboot": 47.0 }, "tested_leaves": [ "O96028_PWWP1", "P52701_PWWP1", "Q96L73_PWWP1", "Q9BZ95_PWWP1" ] }, { "comparison_scope": "Exact split in this differently sampled dataset, with the explicitly listed comparators. An additional comparator nested in a group can prevent exact bipartition matching without disproving broad affinity.", "interpretation": "Exact sampled split not recovered; this short differently sampled analysis does not establish a contradiction of the published history.", "primary_recovered": false, "primary_support": null, "published_description": "Published b-type grouping with GLYR1", "reference_doi": "10.1186/1471-2148-12-101", "relationship": "NSD second domains plus GLYR1", "sensitivity_recovered": false, "sensitivity_support": null, "tested_leaves": [ "O96028_PWWP2", "Q49A26_PWWP1", "Q96L73_PWWP2", "Q9BZ95_PWWP2" ] }, { "comparison_scope": "Exact split in this differently sampled dataset, with the explicitly listed comparators. An additional comparator nested in a group can prevent exact bipartition matching without disproving broad affinity.", "interpretation": "Recovered with both primary support thresholds; compare sensitivity before interpretation.", "primary_recovered": true, "primary_support": { "sh_alrt": 99.5, "ufboot": 100.0 }, "published_description": "ZMYND/BS69 subgroup", "reference_doi": "10.1186/1471-2148-12-101", "relationship": "ZMYND subgroup including mouse comparator", "sensitivity_recovered": true, "sensitivity_support": { "sh_alrt": 98.8, "ufboot": 99.0 }, "tested_leaves": [ "Q15326_PWWP1", "Q8R5C8_PWWP1", "Q9ULU4_PWWP1" ] }, { "comparison_scope": "Exact split in this differently sampled dataset, with the explicitly listed comparators. An additional comparator nested in a group can prevent exact bipartition matching without disproving broad affinity.", "interpretation": "Recovered with both primary support thresholds; compare sensitivity before interpretation.", "primary_recovered": true, "primary_support": { "sh_alrt": 99.3, "ufboot": 97.0 }, "published_description": "HDGF-like family including PSIP1; sampled taxa differ from2012", "reference_doi": "10.1186/1471-2148-12-101", "relationship": "HDGF subgroup with sampled rodent comparators", "sensitivity_recovered": true, "sensitivity_support": { "sh_alrt": 99.1, "ufboot": 100.0 }, "tested_leaves": [ "O75475_PWWP1", "P51858_PWWP1", "Q5TGJ6_PWWP1", "Q7Z4V5_PWWP1", "Q8VHK7_PWWP1", "Q9JMG7_PWWP1", "Q9Y3E1_PWWP1" ] } ], "qualification": { "cautions": [ "No outgroup/root specified.", "Structural superposition is not a proof of evolutionary homology.", "Mask thresholds are predeclared data-quality rules, not chosen to optimize bootstrap support." ], "excluded_columns": 179, 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{ "aligned_length": 50, "domain_A": "UP:O75475:PWWP1", "domain_B": "UP:Q2TAK8:PWWP1", "gene_A": "PSIP1", "gene_B": "PWWP3A", "url": "/compare?a=UP%3AO75475%3APWWP1&b=UP%3AQ2TAK8%3APWWP1" }, { "aligned_length": 50, "domain_A": "UP:O75475:PWWP1", "domain_B": "UP:Q15326:PWWP1", "gene_A": "PSIP1", "gene_B": "ZMYND11", "url": "/compare?a=UP%3AO75475%3APWWP1&b=UP%3AQ15326%3APWWP1" }, { "aligned_length": 51, "domain_A": "UP:O75475:PWWP1", "domain_B": "UP:Q9ULU4:PWWP1", "gene_A": "PSIP1", "gene_B": "ZMYND8", "url": "/compare?a=UP%3AO75475%3APWWP1&b=UP%3AQ9ULU4%3APWWP1" } ], "domain_id": "UP:O75475:PWWP1", "domain_name": "PWWP1", "domain_url": "/domain/UP:O75475:PWWP1", "end": 64, "evidence": "[{\"evidenceCode\":\"ECO:0000255\",\"source\":\"PROSITE-ProRule\",\"id\":\"PRU00162\"}]", "gene": "PSIP1", "identifiers": "[\"IPR000313\",\"PF00855\",\"PS50812\",\"SM00293\",\"cd20151\"]", "length": 64, "membership_tier": "annotation_supported", "name": "PC4 and SFRS1-interacting protein", 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