{"gene":"DOK5","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2003,"finding":"DOK5 (IRS6/DOK5) is tyrosine-phosphorylated in response to insulin and IGF-1 in transfected cells, identifying it as a substrate of insulin and IGF-1 receptors. Unlike IRS5/DOK4, DOK5 does not associate with RasGAP, Crk, Src, Fyn, PI3K p85, Grb2, SHP-2, Nck, or PLCγ SH2 domains, and does not activate MAPK.","method":"Transfection, tyrosine phosphorylation assays, SH2 domain-binding assays, MAPK activation assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple binding assays and functional readouts in transfected cells, single lab but orthogonal methods","pmids":["12730241"],"is_preprint":false},{"year":2001,"finding":"DOK5 directly associates with Y1062 of the c-Ret receptor tyrosine kinase, acts as a substrate of c-Ret, does not associate with rasGAP or Nck (unlike DOK1/DOK2), and enhances c-Ret-dependent MAPK activation. A c-Ret/DOK5 fusion protein induces ligand-dependent axonal outgrowth of PC12 cells.","method":"Co-immunoprecipitation, direct binding assays, PC12 neurite outgrowth assay, MAPK activation assay, c-Ret fusion protein constructs","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding assays, functional rescue with fusion constructs, neurite outgrowth readout, replicated with multiple orthogonal methods","pmids":["11470823"],"is_preprint":false},{"year":2006,"finding":"DOK5 is a substrate of TrkB and TrkC receptors. The DOK5 PTB domain interacts with the NPQY motif of TrkB/C in a kinase-activity-dependent manner, competes with N-Shc for binding at the same site, and DOK5 is involved in MAPK pathway activation induced by neurotrophin stimulation. DOK5 does not interact with TrkA.","method":"Yeast two-hybrid, GST pulldown, Co-immunoprecipitation, colocalization in differentiated PC12 cells, mutational analysis, competition assay, MAPK activation assay","journal":"Cellular signalling","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — multiple orthogonal methods (Y2H, GST pulldown, Co-IP, mutagenesis, competition assay), single lab","pmids":["16647839"],"is_preprint":false},{"year":2008,"finding":"DOK5 constitutively targets to the plasma membrane and partitions into plasma membrane microdomains. The PH domain is essential for plasma membrane targeting.","method":"Single-molecule fluorescence microscopy of eYFP-tagged DOK5 and PH-domain variants in live CHO cells","journal":"Biophysical chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct live-cell imaging with domain-deletion variants, single lab, single method","pmids":["18455289"],"is_preprint":false},{"year":2009,"finding":"FOXO3a acts as a transcriptional repressor of Dok-5, binding to a forkhead binding element in the Dok-5 promoter. Dok-5 expression is regulated via the PI3K/PKB/FOXO3a signaling pathway, and Dok-5 is required for cardiomyocyte differentiation: Dok-5 siRNA attenuates cardiomyocyte differentiation of P19CL6 cells.","method":"Promoter truncation/mutation analysis, EMSA, chromatin immunoprecipitation, FOXO3a overexpression, siRNA knockdown, cardiomyocyte differentiation assay","journal":"Journal of molecular and cellular cardiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — EMSA, ChIP, and functional siRNA knockdown with differentiation readout, multiple orthogonal methods, single lab","pmids":["19800350"],"is_preprint":false},{"year":2013,"finding":"DOK5 interacts with TrkC in dorsal root ganglia neurons and is required for NT-3-mediated protection against TrkC-induced apoptosis. siRNA knockdown of DOK5 partially abrogates NT-3 protection and alters caspase-3 activity.","method":"Immunoprecipitation, immunofluorescence colocalization, siRNA knockdown, caspase-3 activity assay, HEK293T apoptosis assay","journal":"Neuroscience letters","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP, colocalization, and functional siRNA knockdown, single lab","pmids":["23954828"],"is_preprint":false},{"year":2014,"finding":"IGFBP-5 upregulates DOK5 mRNA and protein in primary human fibroblasts via activation of the MAPK signaling cascade, triggers nuclear translocation of DOK5, and DOK5 expression in human skin ex vivo increases dermal thickness, indicating a pro-fibrotic role for DOK5 downstream of IGFBP-5.","method":"Gene expression profiling, Western blot, siRNA/overexpression, nuclear translocation assay, human skin organ culture ex vivo, in vivo mouse model","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (expression profiling, western blot, ex vivo organ culture, in vivo), single lab","pmids":["24551065"],"is_preprint":false},{"year":2022,"finding":"DOK5 knockdown suppresses osteoblast proliferation and differentiation (reduces OPN, OCN, Runx2, β-catenin; increases GSK3-β and Axin), while DOK5 overexpression promotes osteogenesis and activates canonical Wnt/β-catenin signaling, placing DOK5 upstream of β-catenin in osteoblast differentiation.","method":"Lentiviral knockdown, overexpression, CCK-8 proliferation assay, ALP and AR-S staining, Western blot, RT-PCR","journal":"Journal of musculoskeletal & neuronal interactions","confidence":"Low","confidence_rationale":"Tier 3 / Weak — knockdown and overexpression with pathway readouts, single lab, no direct binding or epistasis confirmation of Wnt pathway placement","pmids":["35234166"],"is_preprint":false},{"year":2002,"finding":"The PTB domain of human DOK5 was crystallized and diffraction data collected to 2.3 Å resolution from a selenomethionine derivative, enabling structural determination of the DOK5 PTB domain.","method":"Recombinant protein expression in E. coli, vapor diffusion crystallization, X-ray crystallography (MAD, 2.3 Å)","journal":"Acta crystallographica. Section D, Biological crystallography","confidence":"Low","confidence_rationale":"Tier 1 / Weak — crystal structure data collected but only preliminary X-ray report (no functional validation described in the abstract)","pmids":["12454490"],"is_preprint":false}],"current_model":"DOK5 is a membrane-targeted adapter/docking protein whose PH domain mediates constitutive plasma membrane and microdomain localization; its PTB domain binds the NPQY motifs of c-Ret, TrkB, and TrkC receptor tyrosine kinases in a kinase-activity-dependent manner, leading to tyrosine phosphorylation of DOK5 and downstream MAPK activation, while transcription of DOK5 is repressed by FOXO3a downstream of PI3K/PKB signaling, and DOK5 plays functional roles in neuronal differentiation, NT-3/TrkC survival signaling, cardiomyocyte differentiation, and IGFBP-5-driven fibrosis."},"narrative":{"mechanistic_narrative":"DOK5 is a membrane-targeted docking/adapter protein that couples activated receptor tyrosine kinases to MAPK signaling in neuronal and developmental contexts [PMID:11470823, PMID:16647839]. Its PH domain drives constitutive targeting to the plasma membrane and partitioning into membrane microdomains, while its PTB domain engages the NPQY/Y1062 motifs of c-Ret, TrkB, and TrkC in a kinase-activity-dependent manner, positioning DOK5 as a direct substrate of these receptors [PMID:11470823, PMID:16647839, PMID:18455289]. Receptor engagement leads to DOK5 tyrosine phosphorylation and enhanced MAPK pathway activation; at the TrkB/C site DOK5 competes with N-Shc for binding, and a c-Ret/DOK5 fusion is sufficient to drive ligand-dependent axonal outgrowth in PC12 cells [PMID:11470823, PMID:16647839]. DOK5 is also a substrate of the insulin and IGF-1 receptors but, unlike the related DOK4, does not associate with the canonical SH2-domain effectors RasGAP, Crk, Grb2, SHP-2, Nck, PI3K p85, or PLCγ [PMID:12730241]. Functionally, DOK5 supports NT-3/TrkC survival signaling in dorsal root ganglia neurons [PMID:23954828] and is required for cardiomyocyte differentiation, where its transcription is repressed by FOXO3a acting downstream of PI3K/PKB signaling [PMID:19800350]. DOK5 additionally acts downstream of IGFBP-5 to promote a pro-fibrotic, dermal-thickening program in fibroblasts [PMID:24551065].","teleology":[{"year":2001,"claim":"Established DOK5 as a c-Ret docking protein that positively couples receptor activation to MAPK signaling and neurite outgrowth, distinguishing it from the inhibitory DOK1/DOK2 adapters.","evidence":"Co-immunoprecipitation, direct binding assays, c-Ret/DOK5 fusion constructs, and PC12 neurite outgrowth and MAPK activation assays","pmids":["11470823"],"confidence":"High","gaps":["Did not resolve which downstream effectors transmit the MAPK signal, since DOK5 lacks canonical SH2 effector binding","Structural basis of the Y1062 interaction not defined"]},{"year":2002,"claim":"Crystallization of the DOK5 PTB domain provided the structural reagent needed to understand receptor-motif recognition.","evidence":"Recombinant expression, vapor diffusion crystallization, and X-ray diffraction to 2.3 Å from a selenomethionine derivative","pmids":["12454490"],"confidence":"Low","gaps":["Preliminary diffraction report only; no functional or complex structure described","No co-crystal with a receptor phosphopeptide"]},{"year":2003,"claim":"Identified DOK5 as a substrate of the insulin and IGF-1 receptors and defined its negative interaction profile, showing it does not engage the SH2 effectors used by other DOK family members.","evidence":"Transfection, tyrosine phosphorylation assays, SH2-domain binding panels, and MAPK activation assays","pmids":["12730241"],"confidence":"Medium","gaps":["Effectors that DOK5 does recruit remain unidentified","Physiological relevance in insulin/IGF-1 signaling not tested beyond transfected cells"]},{"year":2006,"claim":"Extended DOK5's receptor repertoire to neurotrophin receptors, showing PTB-domain binding to the TrkB/TrkC NPQY motif in a kinase-dependent manner and competition with N-Shc.","evidence":"Yeast two-hybrid, GST pulldown, Co-IP, mutagenesis, competition assays, and MAPK activation in differentiated PC12 cells","pmids":["16647839"],"confidence":"High","gaps":["Selectivity against TrkA explained only descriptively","Quantitative balance between DOK5 and N-Shc occupancy in cells not determined"]},{"year":2008,"claim":"Defined the membrane-targeting logic of DOK5, showing the PH domain is necessary for constitutive plasma membrane localization and microdomain partitioning.","evidence":"Single-molecule fluorescence microscopy of eYFP-tagged DOK5 and PH-domain variants in live CHO cells","pmids":["18455289"],"confidence":"Medium","gaps":["Lipid ligand of the PH domain not identified","Single method and cell type"]},{"year":2009,"claim":"Placed DOK5 transcription under negative control by FOXO3a downstream of PI3K/PKB and showed DOK5 is required for cardiomyocyte differentiation.","evidence":"Promoter truncation/mutation, EMSA, ChIP, FOXO3a overexpression, and siRNA knockdown with cardiomyocyte differentiation readout in P19CL6 cells","pmids":["19800350"],"confidence":"Medium","gaps":["Receptor input driving DOK5's role in differentiation not identified","Mechanism linking DOK5 to the differentiation program not defined"]},{"year":2013,"claim":"Demonstrated a survival function for DOK5 in NT-3/TrkC signaling in primary neurons, linking its receptor docking role to anti-apoptotic output.","evidence":"Co-IP, immunofluorescence colocalization, siRNA knockdown, and caspase-3 activity assays in DRG neurons and HEK293T apoptosis assays","pmids":["23954828"],"confidence":"Medium","gaps":["Knockdown only partially abrogated protection, leaving parallel pathways unaccounted","Direct anti-apoptotic effectors downstream of DOK5 not identified"]},{"year":2014,"claim":"Identified a pro-fibrotic role for DOK5 downstream of IGFBP-5, including transcriptional upregulation, nuclear translocation, and increased dermal thickness.","evidence":"Expression profiling, Western blot, siRNA/overexpression, nuclear translocation assay, human skin organ culture ex vivo, and in vivo mouse model","pmids":["24551065"],"confidence":"Medium","gaps":["Function of nuclear DOK5 not mechanistically explained","Direct fibrotic targets downstream of DOK5 unidentified"]},{"year":2022,"claim":"Proposed DOK5 as a positive regulator of osteoblast proliferation and differentiation acting upstream of canonical Wnt/β-catenin signaling.","evidence":"Lentiviral knockdown, overexpression, CCK-8 proliferation, ALP/AR-S staining, Western blot, and RT-PCR","pmids":["35234166"],"confidence":"Low","gaps":["No direct binding or epistasis data confirming Wnt pathway placement","Single lab, no in vivo validation"]},{"year":null,"claim":"The downstream effectors that DOK5 recruits to transmit receptor signals to MAPK remain unidentified, given its lack of canonical SH2-effector binding.","evidence":"","pmids":[],"confidence":"Low","gaps":["No DOK5-binding effector defined","Phospho-tyrosine sites on DOK5 and their readers not mapped","Function of nuclear-translocated DOK5 unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,2]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[3]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[4]}],"complexes":[],"partners":["RET","NTRK2","NTRK3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9P104","full_name":"Docking protein 5","aliases":["Downstream of tyrosine kinase 5","Insulin receptor substrate 6","IRS-6","IRS6"],"length_aa":306,"mass_kda":35.5,"function":"DOK proteins are enzymatically inert adaptor or scaffolding proteins. They provide a docking platform for the assembly of multimolecular signaling complexes. DOK5 functions in RET-mediated neurite outgrowth and plays a positive role in activation of the MAP kinase pathway. Putative link with downstream effectors of RET in neuronal differentiation","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q9P104/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DOK5","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/DOK5","total_profiled":1310},"omim":[{"mim_id":"611402","title":"DOCKING PROTEIN 6; DOK6","url":"https://www.omim.org/entry/611402"},{"mim_id":"608334","title":"DOCKING PROTEIN 5; DOK5","url":"https://www.omim.org/entry/608334"},{"mim_id":"608333","title":"DOCKING PROTEIN 4; DOK4","url":"https://www.omim.org/entry/608333"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Focal adhesion sites","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"skeletal muscle","ntpm":43.1},{"tissue":"tongue","ntpm":22.7}],"url":"https://www.proteinatlas.org/search/DOK5"},"hgnc":{"alias_symbol":["dJ805C22.1"],"prev_symbol":["C20orf180"]},"alphafold":{"accession":"Q9P104","domains":[{"cath_id":"2.30.29.30","chopping":"7-111","consensus_level":"high","plddt":89.861,"start":7,"end":111},{"cath_id":"2.30.29.30","chopping":"136-252","consensus_level":"medium","plddt":90.8274,"start":136,"end":252}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9P104","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9P104-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9P104-F1-predicted_aligned_error_v6.png","plddt_mean":78.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DOK5","jax_strain_url":"https://www.jax.org/strain/search?query=DOK5"},"sequence":{"accession":"Q9P104","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9P104.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9P104/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9P104"}},"corpus_meta":[{"pmid":"12730241","id":"PMC_12730241","title":"Two new substrates in insulin signaling, IRS5/DOK4 and IRS6/DOK5.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12730241","citation_count":152,"is_preprint":false},{"pmid":"11470823","id":"PMC_11470823","title":"Novel p62dok family members, dok-4 and dok-5, are substrates of the c-Ret receptor tyrosine kinase and mediate neuronal differentiation.","date":"2001","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/11470823","citation_count":142,"is_preprint":false},{"pmid":"12595900","id":"PMC_12595900","title":"DOK4 and DOK5: new Dok-related genes expressed in human T cells.","date":"2003","source":"Genes and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/12595900","citation_count":36,"is_preprint":false},{"pmid":"20187968","id":"PMC_20187968","title":"Evaluation of DOK5 as a susceptibility gene for type 2 diabetes and obesity in North Indian population.","date":"2010","source":"BMC medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/20187968","citation_count":25,"is_preprint":false},{"pmid":"16647839","id":"PMC_16647839","title":"Dok5 is substrate of TrkB and TrkC receptors and involved in neurotrophin induced MAPK activation.","date":"2006","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/16647839","citation_count":23,"is_preprint":false},{"pmid":"24551065","id":"PMC_24551065","title":"The membrane-associated adaptor protein DOK5 is upregulated in systemic sclerosis and associated with IGFBP-5-induced fibrosis.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24551065","citation_count":16,"is_preprint":false},{"pmid":"19800350","id":"PMC_19800350","title":"Dok-5 is involved in cardiomyocyte differentiation through PKB/FOXO3a pathway.","date":"2009","source":"Journal of molecular and cellular cardiology","url":"https://pubmed.ncbi.nlm.nih.gov/19800350","citation_count":10,"is_preprint":false},{"pmid":"35234166","id":"PMC_35234166","title":"Dok5 regulates proliferation and differentiation of osteoblast via canonical Wnt/β-catenin signaling.","date":"2022","source":"Journal of musculoskeletal & neuronal interactions","url":"https://pubmed.ncbi.nlm.nih.gov/35234166","citation_count":9,"is_preprint":false},{"pmid":"18455289","id":"PMC_18455289","title":"Constitutive plasma membrane targeting and microdomain localization of Dok5 studied by single-molecule microscopy.","date":"2008","source":"Biophysical chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/18455289","citation_count":7,"is_preprint":false},{"pmid":"23954828","id":"PMC_23954828","title":"Dok5 is involved in the signaling pathway of neurotrophin-3 against TrkC-induced apoptosis.","date":"2013","source":"Neuroscience letters","url":"https://pubmed.ncbi.nlm.nih.gov/23954828","citation_count":5,"is_preprint":false},{"pmid":"12454490","id":"PMC_12454490","title":"Expression, crystallization and preliminary X-ray studies of the recombinant PTB domain of human dok-5 protein.","date":"2002","source":"Acta crystallographica. Section D, Biological crystallography","url":"https://pubmed.ncbi.nlm.nih.gov/12454490","citation_count":4,"is_preprint":false},{"pmid":"41824480","id":"PMC_41824480","title":"From genes to diagnosis: The impact of UNC5B and DOK5 in intracranial aneurysm detection and pathogenesis.","date":"2026","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/41824480","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8005,"output_tokens":2319,"usd":0.0294,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9392,"output_tokens":3145,"usd":0.062793,"stage2_stop_reason":"end_turn"},"total_usd":0.092193,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2003,\n      \"finding\": \"DOK5 (IRS6/DOK5) is tyrosine-phosphorylated in response to insulin and IGF-1 in transfected cells, identifying it as a substrate of insulin and IGF-1 receptors. Unlike IRS5/DOK4, DOK5 does not associate with RasGAP, Crk, Src, Fyn, PI3K p85, Grb2, SHP-2, Nck, or PLCγ SH2 domains, and does not activate MAPK.\",\n      \"method\": \"Transfection, tyrosine phosphorylation assays, SH2 domain-binding assays, MAPK activation assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple binding assays and functional readouts in transfected cells, single lab but orthogonal methods\",\n      \"pmids\": [\"12730241\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"DOK5 directly associates with Y1062 of the c-Ret receptor tyrosine kinase, acts as a substrate of c-Ret, does not associate with rasGAP or Nck (unlike DOK1/DOK2), and enhances c-Ret-dependent MAPK activation. A c-Ret/DOK5 fusion protein induces ligand-dependent axonal outgrowth of PC12 cells.\",\n      \"method\": \"Co-immunoprecipitation, direct binding assays, PC12 neurite outgrowth assay, MAPK activation assay, c-Ret fusion protein constructs\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding assays, functional rescue with fusion constructs, neurite outgrowth readout, replicated with multiple orthogonal methods\",\n      \"pmids\": [\"11470823\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"DOK5 is a substrate of TrkB and TrkC receptors. The DOK5 PTB domain interacts with the NPQY motif of TrkB/C in a kinase-activity-dependent manner, competes with N-Shc for binding at the same site, and DOK5 is involved in MAPK pathway activation induced by neurotrophin stimulation. DOK5 does not interact with TrkA.\",\n      \"method\": \"Yeast two-hybrid, GST pulldown, Co-immunoprecipitation, colocalization in differentiated PC12 cells, mutational analysis, competition assay, MAPK activation assay\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — multiple orthogonal methods (Y2H, GST pulldown, Co-IP, mutagenesis, competition assay), single lab\",\n      \"pmids\": [\"16647839\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"DOK5 constitutively targets to the plasma membrane and partitions into plasma membrane microdomains. The PH domain is essential for plasma membrane targeting.\",\n      \"method\": \"Single-molecule fluorescence microscopy of eYFP-tagged DOK5 and PH-domain variants in live CHO cells\",\n      \"journal\": \"Biophysical chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct live-cell imaging with domain-deletion variants, single lab, single method\",\n      \"pmids\": [\"18455289\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"FOXO3a acts as a transcriptional repressor of Dok-5, binding to a forkhead binding element in the Dok-5 promoter. Dok-5 expression is regulated via the PI3K/PKB/FOXO3a signaling pathway, and Dok-5 is required for cardiomyocyte differentiation: Dok-5 siRNA attenuates cardiomyocyte differentiation of P19CL6 cells.\",\n      \"method\": \"Promoter truncation/mutation analysis, EMSA, chromatin immunoprecipitation, FOXO3a overexpression, siRNA knockdown, cardiomyocyte differentiation assay\",\n      \"journal\": \"Journal of molecular and cellular cardiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — EMSA, ChIP, and functional siRNA knockdown with differentiation readout, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"19800350\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"DOK5 interacts with TrkC in dorsal root ganglia neurons and is required for NT-3-mediated protection against TrkC-induced apoptosis. siRNA knockdown of DOK5 partially abrogates NT-3 protection and alters caspase-3 activity.\",\n      \"method\": \"Immunoprecipitation, immunofluorescence colocalization, siRNA knockdown, caspase-3 activity assay, HEK293T apoptosis assay\",\n      \"journal\": \"Neuroscience letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP, colocalization, and functional siRNA knockdown, single lab\",\n      \"pmids\": [\"23954828\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"IGFBP-5 upregulates DOK5 mRNA and protein in primary human fibroblasts via activation of the MAPK signaling cascade, triggers nuclear translocation of DOK5, and DOK5 expression in human skin ex vivo increases dermal thickness, indicating a pro-fibrotic role for DOK5 downstream of IGFBP-5.\",\n      \"method\": \"Gene expression profiling, Western blot, siRNA/overexpression, nuclear translocation assay, human skin organ culture ex vivo, in vivo mouse model\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (expression profiling, western blot, ex vivo organ culture, in vivo), single lab\",\n      \"pmids\": [\"24551065\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DOK5 knockdown suppresses osteoblast proliferation and differentiation (reduces OPN, OCN, Runx2, β-catenin; increases GSK3-β and Axin), while DOK5 overexpression promotes osteogenesis and activates canonical Wnt/β-catenin signaling, placing DOK5 upstream of β-catenin in osteoblast differentiation.\",\n      \"method\": \"Lentiviral knockdown, overexpression, CCK-8 proliferation assay, ALP and AR-S staining, Western blot, RT-PCR\",\n      \"journal\": \"Journal of musculoskeletal & neuronal interactions\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — knockdown and overexpression with pathway readouts, single lab, no direct binding or epistasis confirmation of Wnt pathway placement\",\n      \"pmids\": [\"35234166\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"The PTB domain of human DOK5 was crystallized and diffraction data collected to 2.3 Å resolution from a selenomethionine derivative, enabling structural determination of the DOK5 PTB domain.\",\n      \"method\": \"Recombinant protein expression in E. coli, vapor diffusion crystallization, X-ray crystallography (MAD, 2.3 Å)\",\n      \"journal\": \"Acta crystallographica. Section D, Biological crystallography\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 1 / Weak — crystal structure data collected but only preliminary X-ray report (no functional validation described in the abstract)\",\n      \"pmids\": [\"12454490\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DOK5 is a membrane-targeted adapter/docking protein whose PH domain mediates constitutive plasma membrane and microdomain localization; its PTB domain binds the NPQY motifs of c-Ret, TrkB, and TrkC receptor tyrosine kinases in a kinase-activity-dependent manner, leading to tyrosine phosphorylation of DOK5 and downstream MAPK activation, while transcription of DOK5 is repressed by FOXO3a downstream of PI3K/PKB signaling, and DOK5 plays functional roles in neuronal differentiation, NT-3/TrkC survival signaling, cardiomyocyte differentiation, and IGFBP-5-driven fibrosis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DOK5 is a membrane-targeted docking/adapter protein that couples activated receptor tyrosine kinases to MAPK signaling in neuronal and developmental contexts [#1, #2]. Its PH domain drives constitutive targeting to the plasma membrane and partitioning into membrane microdomains, while its PTB domain engages the NPQY/Y1062 motifs of c-Ret, TrkB, and TrkC in a kinase-activity-dependent manner, positioning DOK5 as a direct substrate of these receptors [#1, #2, #3]. Receptor engagement leads to DOK5 tyrosine phosphorylation and enhanced MAPK pathway activation; at the TrkB/C site DOK5 competes with N-Shc for binding, and a c-Ret/DOK5 fusion is sufficient to drive ligand-dependent axonal outgrowth in PC12 cells [#1, #2]. DOK5 is also a substrate of the insulin and IGF-1 receptors but, unlike the related DOK4, does not associate with the canonical SH2-domain effectors RasGAP, Crk, Grb2, SHP-2, Nck, PI3K p85, or PLCγ [#0]. Functionally, DOK5 supports NT-3/TrkC survival signaling in dorsal root ganglia neurons [#5] and is required for cardiomyocyte differentiation, where its transcription is repressed by FOXO3a acting downstream of PI3K/PKB signaling [#4]. DOK5 additionally acts downstream of IGFBP-5 to promote a pro-fibrotic, dermal-thickening program in fibroblasts [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Established DOK5 as a c-Ret docking protein that positively couples receptor activation to MAPK signaling and neurite outgrowth, distinguishing it from the inhibitory DOK1/DOK2 adapters.\",\n      \"evidence\": \"Co-immunoprecipitation, direct binding assays, c-Ret/DOK5 fusion constructs, and PC12 neurite outgrowth and MAPK activation assays\",\n      \"pmids\": [\"11470823\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Did not resolve which downstream effectors transmit the MAPK signal, since DOK5 lacks canonical SH2 effector binding\",\n        \"Structural basis of the Y1062 interaction not defined\"\n      ]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Crystallization of the DOK5 PTB domain provided the structural reagent needed to understand receptor-motif recognition.\",\n      \"evidence\": \"Recombinant expression, vapor diffusion crystallization, and X-ray diffraction to 2.3 Å from a selenomethionine derivative\",\n      \"pmids\": [\"12454490\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Preliminary diffraction report only; no functional or complex structure described\",\n        \"No co-crystal with a receptor phosphopeptide\"\n      ]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Identified DOK5 as a substrate of the insulin and IGF-1 receptors and defined its negative interaction profile, showing it does not engage the SH2 effectors used by other DOK family members.\",\n      \"evidence\": \"Transfection, tyrosine phosphorylation assays, SH2-domain binding panels, and MAPK activation assays\",\n      \"pmids\": [\"12730241\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Effectors that DOK5 does recruit remain unidentified\",\n        \"Physiological relevance in insulin/IGF-1 signaling not tested beyond transfected cells\"\n      ]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Extended DOK5's receptor repertoire to neurotrophin receptors, showing PTB-domain binding to the TrkB/TrkC NPQY motif in a kinase-dependent manner and competition with N-Shc.\",\n      \"evidence\": \"Yeast two-hybrid, GST pulldown, Co-IP, mutagenesis, competition assays, and MAPK activation in differentiated PC12 cells\",\n      \"pmids\": [\"16647839\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Selectivity against TrkA explained only descriptively\",\n        \"Quantitative balance between DOK5 and N-Shc occupancy in cells not determined\"\n      ]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Defined the membrane-targeting logic of DOK5, showing the PH domain is necessary for constitutive plasma membrane localization and microdomain partitioning.\",\n      \"evidence\": \"Single-molecule fluorescence microscopy of eYFP-tagged DOK5 and PH-domain variants in live CHO cells\",\n      \"pmids\": [\"18455289\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Lipid ligand of the PH domain not identified\",\n        \"Single method and cell type\"\n      ]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Placed DOK5 transcription under negative control by FOXO3a downstream of PI3K/PKB and showed DOK5 is required for cardiomyocyte differentiation.\",\n      \"evidence\": \"Promoter truncation/mutation, EMSA, ChIP, FOXO3a overexpression, and siRNA knockdown with cardiomyocyte differentiation readout in P19CL6 cells\",\n      \"pmids\": [\"19800350\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Receptor input driving DOK5's role in differentiation not identified\",\n        \"Mechanism linking DOK5 to the differentiation program not defined\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Demonstrated a survival function for DOK5 in NT-3/TrkC signaling in primary neurons, linking its receptor docking role to anti-apoptotic output.\",\n      \"evidence\": \"Co-IP, immunofluorescence colocalization, siRNA knockdown, and caspase-3 activity assays in DRG neurons and HEK293T apoptosis assays\",\n      \"pmids\": [\"23954828\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Knockdown only partially abrogated protection, leaving parallel pathways unaccounted\",\n        \"Direct anti-apoptotic effectors downstream of DOK5 not identified\"\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identified a pro-fibrotic role for DOK5 downstream of IGFBP-5, including transcriptional upregulation, nuclear translocation, and increased dermal thickness.\",\n      \"evidence\": \"Expression profiling, Western blot, siRNA/overexpression, nuclear translocation assay, human skin organ culture ex vivo, and in vivo mouse model\",\n      \"pmids\": [\"24551065\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Function of nuclear DOK5 not mechanistically explained\",\n        \"Direct fibrotic targets downstream of DOK5 unidentified\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Proposed DOK5 as a positive regulator of osteoblast proliferation and differentiation acting upstream of canonical Wnt/β-catenin signaling.\",\n      \"evidence\": \"Lentiviral knockdown, overexpression, CCK-8 proliferation, ALP/AR-S staining, Western blot, and RT-PCR\",\n      \"pmids\": [\"35234166\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No direct binding or epistasis data confirming Wnt pathway placement\",\n        \"Single lab, no in vivo validation\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The downstream effectors that DOK5 recruits to transmit receptor signals to MAPK remain unidentified, given its lack of canonical SH2-effector binding.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No DOK5-binding effector defined\",\n        \"Phospho-tyrosine sites on DOK5 and their readers not mapped\",\n        \"Function of nuclear-translocated DOK5 unknown\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RET\", \"NTRK2\", \"NTRK3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}