{"gene":"TG_290630","gene_symbol":"AP2IX7","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2019,"finding":"AP2IX-7 (AP2IX7) was identified as a component of a GCN5b lysine acetyltransferase complex in Toxoplasma gondii. Reciprocal co-immunoprecipitation of AP2IX-7 delineated its interactome, showing it associates with GCN5b and other AP2 factors as part of at least two distinct GCN5b-containing complexes involved in epigenetic gene regulation.","method":"Co-immunoprecipitation (reciprocal Co-IP) followed by mass spectrometry proteomics","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP with MS, single lab, two orthogonal methods (Co-IP + proteomics)","pmids":["31381949"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2010,"finding":"AP2IX-7 mRNA and protein show a cyclical expression pattern during the tachyzoite cell cycle, with a sharp peak of protein expression in a defined timeframe, suggesting its activity is timed by AP2 domain promoter recognition specificities during cell cycle progression.","method":"Genome-wide transcriptional profiling and protein expression analysis across the tachyzoite cell cycle","journal":"PloS one","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, transcriptome-level observation with some protein data, no direct functional manipulation of AP2IX-7 specifically","pmids":["20865045"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"AP2IX-7 is a cell cycle-regulated nuclear ApiAP2 transcription factor in Toxoplasma gondii that physically associates with the essential lysine acetyltransferase GCN5b as part of at least one distinct multisubunit complex, implicating it in GCN5b-mediated epigenetic gene regulation, though its specific target genes and direct functional role remain to be experimentally defined."},"narrative":{"mechanistic_narrative":"AP2IX-7 is an ApiAP2 transcription factor in Toxoplasma gondii implicated in GCN5b-mediated epigenetic gene regulation [PMID:31381949]. Reciprocal co-immunoprecipitation coupled to mass spectrometry places AP2IX-7 in a physical association with the lysine acetyltransferase GCN5b and additional AP2 factors, defining it as a component of at least two distinct GCN5b-containing complexes [PMID:31381949]. Beyond this complex membership [PMID:31381949] and a cell cycle-timed expression pattern [PMID:20865045], the specific target genes and direct functional role of AP2IX-7 have not been characterized in the available corpus.","teleology":[{"year":2010,"claim":"It was unknown whether AP2IX-7 expression was constitutive or dynamically regulated; profiling across the tachyzoite cell cycle established that its mRNA and protein peak sharply within a defined cell cycle window, framing its activity as temporally gated.","evidence":"Genome-wide transcriptional profiling with protein expression analysis across the tachyzoite cell cycle","pmids":["20865045"],"confidence":"Low","gaps":["No direct functional manipulation of AP2IX-7 to test the significance of its cyclical expression","The promoter targets and DNA-binding specificity of the AP2 domain were not defined","Cell cycle stage of the expression peak inferred from population profiling, not single-cell resolution"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"claim":"The molecular context of AP2IX-7 was unresolved until reciprocal Co-IP mass spectrometry showed it physically associates with the essential acetyltransferase GCN5b and other AP2 factors in at least two distinct multisubunit complexes, placing it within an epigenetic gene-regulatory machinery.","evidence":"Reciprocal co-immunoprecipitation followed by mass spectrometry proteomics in T. gondii","pmids":["31381949"],"confidence":"Medium","gaps":["Direct target genes of AP2IX-7 within the GCN5b complexes are not identified","Whether AP2IX-7 recruits GCN5b to chromatin or is recruited by it is undetermined","Functional consequence of complex membership was not tested by genetic ablation"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"The direct functional role of AP2IX-7 — its genomic binding sites, target genes, and the phenotypic consequence of its loss — remains undefined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No knockout or conditional-depletion phenotype reported","No ChIP or genome-wide DNA-binding map for AP2IX-7","The distinct roles of the two GCN5b complexes containing AP2IX-7 are not resolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["GCN5b lysine acetyltransferase complex (at least two distinct GCN5b-containing complexes)"],"partners":["GCN5B","OTHER APIAP2 FACTORS"],"other_free_text":["AP2IX-7 protein and mRNA show cyclical expression with a sharp peak during the tachyzoite cell cycle [#1]","Target genes and direct functional role remain uncharacterized in the available corpus"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"20865045","id":"PMC_20865045","title":"Coordinated progression through two subtranscriptomes underlies the tachyzoite cycle of Toxoplasma gondii.","date":"2010","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/20865045","citation_count":234,"is_preprint":false},{"pmid":"29932347","id":"PMC_29932347","title":"The Epigenome, Cell Cycle, and Development in Toxoplasma.","date":"2018","source":"Annual review of microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/29932347","citation_count":51,"is_preprint":false},{"pmid":"20657661","id":"PMC_20657661","title":"The construction and use of log-odds substitution scores for multiple sequence alignment.","date":"2010","source":"PLoS computational biology","url":"https://pubmed.ncbi.nlm.nih.gov/20657661","citation_count":48,"is_preprint":false},{"pmid":"22486860","id":"PMC_22486860","title":"Cactin is essential for G1 progression in Toxoplasma gondii.","date":"2012","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/22486860","citation_count":23,"is_preprint":false},{"pmid":"25393307","id":"PMC_25393307","title":"Distinct strains of Toxoplasma gondii feature divergent transcriptomes regardless of developmental stage.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/25393307","citation_count":22,"is_preprint":false},{"pmid":"31381949","id":"PMC_31381949","title":"A novel GCN5b lysine acetyltransferase complex associates with distinct transcription factors in the protozoan parasite Toxoplasma gondii.","date":"2019","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/31381949","citation_count":20,"is_preprint":false},{"pmid":"18983845","id":"PMC_18983845","title":"New eukaryotic systematics: a phylogenetic perspective of developmental gene expression in the Apicomplexa.","date":"2008","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/18983845","citation_count":12,"is_preprint":false},{"pmid":"39690155","id":"PMC_39690155","title":"Apicomplexan mitoribosome from highly fragmented rRNAs to a functional machine.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/39690155","citation_count":9,"is_preprint":false},{"pmid":"36178892","id":"PMC_36178892","title":"Genomic insights into host and parasite interactions during intracellular infection by Toxoplasma gondii.","date":"2022","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/36178892","citation_count":2,"is_preprint":false},{"pmid":"42087241","id":"PMC_42087241","title":"Host-cell dependent epigenetic profiles associated with survival outcomes in T. gondii infection.","date":"2026","source":"Epigenetics & chromatin","url":"https://pubmed.ncbi.nlm.nih.gov/42087241","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":19320,"output_tokens":613,"usd":0.033578,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5335,"output_tokens":1586,"usd":0.033162,"stage2_stop_reason":"end_turn"},"total_usd":0.06674,"stage1_batch_id":"msgbatch_015xmQKDRqnTh9anE4m7LiD6","stage2_batch_id":"msgbatch_01JLpkFTVhoQBNgqHCKFrVVU","note":"batch pricing = 50% of standard","corrective_rerun":"2026-09-10 wrong-gene rerun (round-4 rules)","corrective_reason":"paper list: removed papers about other genes"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"AP2IX-7 (AP2IX7) was identified as a component of a GCN5b lysine acetyltransferase complex in Toxoplasma gondii. Reciprocal co-immunoprecipitation of AP2IX-7 delineated its interactome, showing it associates with GCN5b and other AP2 factors as part of at least two distinct GCN5b-containing complexes involved in epigenetic gene regulation.\",\n      \"method\": \"Co-immunoprecipitation (reciprocal Co-IP) followed by mass spectrometry proteomics\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP with MS, single lab, two orthogonal methods (Co-IP + proteomics)\",\n      \"pmids\": [\"31381949\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"AP2IX-7 mRNA and protein show a cyclical expression pattern during the tachyzoite cell cycle, with a sharp peak of protein expression in a defined timeframe, suggesting its activity is timed by AP2 domain promoter recognition specificities during cell cycle progression.\",\n      \"method\": \"Genome-wide transcriptional profiling and protein expression analysis across the tachyzoite cell cycle\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, transcriptome-level observation with some protein data, no direct functional manipulation of AP2IX-7 specifically\",\n      \"pmids\": [\"20865045\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"AP2IX-7 is a cell cycle-regulated nuclear ApiAP2 transcription factor in Toxoplasma gondii that physically associates with the essential lysine acetyltransferase GCN5b as part of at least one distinct multisubunit complex, implicating it in GCN5b-mediated epigenetic gene regulation, though its specific target genes and direct functional role remain to be experimentally defined.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"AP2IX-7 is an ApiAP2 transcription factor in Toxoplasma gondii implicated in GCN5b-mediated epigenetic gene regulation [#0]. Reciprocal co-immunoprecipitation coupled to mass spectrometry places AP2IX-7 in a physical association with the lysine acetyltransferase GCN5b and additional AP2 factors, defining it as a component of at least two distinct GCN5b-containing complexes [#0]. Beyond this complex membership [#0] and a cell cycle-timed expression pattern [#1], the specific target genes and direct functional role of AP2IX-7 have not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"It was unknown whether AP2IX-7 expression was constitutive or dynamically regulated; profiling across the tachyzoite cell cycle established that its mRNA and protein peak sharply within a defined cell cycle window, framing its activity as temporally gated.\",\n      \"evidence\": \"Genome-wide transcriptional profiling with protein expression analysis across the tachyzoite cell cycle\",\n      \"pmids\": [\"20865045\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No direct functional manipulation of AP2IX-7 to test the significance of its cyclical expression\",\n        \"The promoter targets and DNA-binding specificity of the AP2 domain were not defined\",\n        \"Cell cycle stage of the expression peak inferred from population profiling, not single-cell resolution\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"The molecular context of AP2IX-7 was unresolved until reciprocal Co-IP mass spectrometry showed it physically associates with the essential acetyltransferase GCN5b and other AP2 factors in at least two distinct multisubunit complexes, placing it within an epigenetic gene-regulatory machinery.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation followed by mass spectrometry proteomics in T. gondii\",\n      \"pmids\": [\"31381949\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct target genes of AP2IX-7 within the GCN5b complexes are not identified\",\n        \"Whether AP2IX-7 recruits GCN5b to chromatin or is recruited by it is undetermined\",\n        \"Functional consequence of complex membership was not tested by genetic ablation\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct functional role of AP2IX-7 — its genomic binding sites, target genes, and the phenotypic consequence of its loss — remains undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No knockout or conditional-depletion phenotype reported\",\n        \"No ChIP or genome-wide DNA-binding map for AP2IX-7\",\n        \"The distinct roles of the two GCN5b complexes containing AP2IX-7 are not resolved\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003700\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006325\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\n      \"GCN5b lysine acetyltransferase complex (at least two distinct GCN5b-containing complexes)\"\n    ],\n    \"partners\": [\n      \"GCN5b\",\n      \"other ApiAP2 factors\"\n    ],\n    \"other_free_text\": [\n      \"AP2IX-7 protein and mRNA show cyclical expression with a sharp peak during the tachyzoite cell cycle [#1]\",\n      \"Target genes and direct functional role remain uncharacterized in the available corpus\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_290630","name":"AP2IX7","product":"AP2 domain transcription factor AP2IX-7","uniprot_acc":"S8GHU6","chromosome":"TGME49_chrIX","start_pos":3784225},{"strain":"GT1","gene_id":"TGGT1_290630","name":null,"product":"AP2 domain transcription factor AP2IX-7","uniprot_acc":null,"chromosome":"TGGT1_chrIX","start_pos":3593432},{"strain":"RH88","gene_id":"TGRH88_015080","name":null,"product":"AP2 domain transcription factor AP2IX-7","uniprot_acc":null,"chromosome":"CM023090","start_pos":3849396},{"strain":"VEG","gene_id":"TGVEG_290630","name":null,"product":"AP2 domain transcription factor AP2IX-7","uniprot_acc":"V4ZFD5","chromosome":"TGVEG_chrIX","start_pos":3820260}]}