{"gene":"NEK9","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2002,"finding":"Nercc1/NEK9 binds specifically to the Ran GTPase through both its catalytic and RCC1-like domains, preferring RanGDP in vivo. Nercc1 also binds Nek6 and exists as a homooligomer, capable of autoactivation in vitro by autophosphorylation. It is a cytoplasmic protein activated during mitosis and phosphorylated by active p34(Cdc2)/CDK1.","method":"Co-immunoprecipitation, in vitro autoactivation assay, subcellular fractionation, in vivo binding experiments","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, in vitro kinase assay, multiple orthogonal methods in foundational paper","pmids":["12101123"],"is_preprint":false},{"year":2003,"finding":"Nercc1/NEK9 directly phosphorylates and activates Nek6 at Ser206 on its activation loop (and Nek7 similarly) in vitro, resulting in 20–25-fold activation of Nek6 activity. Microinjection of anti-Nercc1 antibodies causes spindle abnormalities and prometaphase arrest or chromosome missegregation, establishing Nercc1/Nek9 as the upstream kinase in a mitotic NIMA-family kinase cascade.","method":"In vitro kinase assay with recombinant proteins, co-expression of activated Nercc1 mutant, antibody microinjection, mass spectrometry phosphosite identification","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with defined phosphosite, mutagenesis, replicated across Nek6 and Nek7","pmids":["12840024"],"is_preprint":false},{"year":2003,"finding":"NEK9 forms a stable ~600 kDa complex with the FACT chromatin-remodeling complex (Spt16-Pob3) in interphase nuclei. Within this complex, NEK9 exhibits elevated phosphorylation at Thr210 (activation loop). RNAi depletion of Nek9 impairs G1 and S phase progression, implicating Nek9-FACT complex in interphase cell cycle progression.","method":"Co-immunoprecipitation, dsRNAi knockdown, cell cycle analysis, gel mobility shift assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP and functional knockdown in single lab, two orthogonal methods","pmids":["14660563"],"is_preprint":false},{"year":2005,"finding":"Active Nercc1/NEK9 localizes to centrosomes and spindle poles during early mitosis. In Xenopus egg extracts, XNercc co-precipitates with gamma-tubulin ring complex components. Immunodepletion of XNercc causes delayed spindle assembly, fewer bipolar spindles, and smaller Ran-GTP-induced asters; these defects are rescued by adding purified recombinant XNercc. Autoactivation in vitro requires phosphorylation of the activation loop at Thr210.","method":"Immunofluorescence, co-immunoprecipitation, immunodepletion from Xenopus egg extracts, recombinant protein rescue, in vitro kinase assay","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — immunodepletion with rescue by purified protein, co-IP with gamma-TuRC, multiple orthogonal methods","pmids":["16079175"],"is_preprint":false},{"year":2007,"finding":"Adenovirus E1A protein interacts with nuclear NEK9 and causes redistribution of NEK9 from nucleus to cytoplasm. A NEK9 deletion mutant lacking the central RCC1-like domain interacts stably with E1A and accumulates in the nucleus, suggesting the RCC1-like domain is required for the transient nature of the interaction.","method":"Co-immunoprecipitation, subcellular fractionation, immunofluorescence, deletion mutagenesis","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus subcellular fractionation and deletion mutagenesis, single lab","pmids":["17443675"],"is_preprint":false},{"year":2009,"finding":"Crystal structure of Nek7 reveals an autoinhibited conformation where Tyr97 protrudes into the active site and blocks the alphaC helix. The non-catalytic C-terminal domain (CTD) of Nek9 binds Nek6/Nek7 and releases this autoinhibitory tyrosine, activating the kinases. Tyr-to-Phe mutation of Nek7 and Nek6 renders them constitutively active independently of Nek9.","method":"X-ray crystallography, site-directed mutagenesis, in vitro kinase activity assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus mutagenesis and activity assays in single rigorous study","pmids":["19941817"],"is_preprint":false},{"year":2011,"finding":"PLK1 directly activates NEK9 during prophase via sequential phosphorylation by CDK1 then Plk1. Activated NEK9 in turn phosphorylates Nek6/Nek7, which phosphorylate the mitotic kinesin Eg5 at Ser1033; this Nek6/7-dependent phosphorylation together with the CDK1 site Thr926 promotes Eg5 accumulation at centrosomes and drives prophase centrosome separation.","method":"In vitro kinase assay, co-immunoprecipitation, siRNA knockdown, phosphosite mapping, live-cell imaging","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro kinase reconstitution, phosphosite mapping, epistasis by siRNA, multiple orthogonal methods","pmids":["21642957"],"is_preprint":false},{"year":2011,"finding":"DYNLL/LC8 binds Nek9 via a (K/R)XTQT motif adjacent to the Nek9 C-terminal coiled-coil, promotes Nek9 multimerization and accelerates Nek9 autoactivation. LC8 binding is negatively regulated by Nek9 autophosphorylation at Ser944. Importantly, LC8 binding to Nek9 interferes with Nek9-Nek6 interaction and inhibits Nek6 activation, thereby controlling signal transduction through the Nek9/Nek6/7 module.","method":"Co-immunoprecipitation, in vitro kinase assay, motif mutagenesis, biophysical binding assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, mutagenesis, in vitro assays, functional consequence on Nek6 activation established","pmids":["21454704"],"is_preprint":false},{"year":2012,"finding":"NEK9 phosphorylates NEDD1/GCP-WD at Ser377, driving NEDD1 recruitment to the centrosome and thereby promoting gamma-tubulin accumulation at the mitotic centrosome. This function requires Plk1-dependent activation of Nek9 but is independent of downstream Nek6/Nek7.","method":"In vitro kinase assay, phosphosite mutagenesis, Xenopus egg extracts, siRNA knockdown, immunofluorescence","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro phosphorylation of defined site, validated in two model systems (Xenopus and mammalian cells), epistasis analysis","pmids":["22818914"],"is_preprint":false},{"year":2012,"finding":"Nek9 localizes to spindle poles and the midbody during mouse oocyte meiosis. Morpholino-mediated depletion of Nek9 causes defective spindles, misaligned chromosomes, MI arrest, and failure of polar body extrusion, with concomitant loss of gamma-tubulin at spindle poles and retention of Bub3 at kinetochores.","method":"Morpholino knockdown in mouse oocytes, confocal immunofluorescence, live-cell imaging","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — specific knockdown with clear phenotypic readouts and checkpoint marker analysis, single lab","pmids":["23159858"],"is_preprint":false},{"year":2013,"finding":"Crystal structures of LC8 bound to phosphorylated and unphosphorylated Nek9 peptides (around Ser944) reveal that phosphorylation at Ser944 directly reduces binding affinity to LC8, explaining how Nek9 autophosphorylation controls its interaction with the dynein light chain and thereby regulates downstream Nek6 signaling.","method":"X-ray crystallography, isothermal titration calorimetry, biophysical binding assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structures with two peptide states plus biophysical validation, single lab","pmids":["23482567"],"is_preprint":false},{"year":2014,"finding":"NEK9 complexes with CHK1, and NEK9 depletion impairs CHK1 autophosphorylation and kinase activity in response to replication stress. NEK9-depleted cells show hypersensitivity to gemcitabine, spontaneous DNA damage foci, RPA70 foci accumulation, and impaired recovery from replication arrest, defining NEK9 as a component of the replication stress response that promotes CHK1 activity.","method":"siRNA knockdown, co-immunoprecipitation, kinase activity assay, RNAi synthetic lethal screen, immunofluorescence","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP of NEK9-CHK1 complex, functional knockdown with multiple readouts, single lab","pmids":["25217585"],"is_preprint":false},{"year":2015,"finding":"Crystal structure of Nek7(Y97F) bound to a Nek9 peptide (residues 810–828) maps the minimal Nek9-binding region on the C-lobe of the Nek7 kinase domain. Nek7(Y97F) crystallizes as a back-to-back dimer through N-lobe contacts coupled to the conformation of residue 97. Self-association of the Nek9 CTD is required for Nek7 activation, leading to the model that Nek9-CTD promotes Nek7 back-to-back dimerization to release autoinhibition.","method":"X-ray crystallography, binding domain mapping, in vitro kinase assay, structure-function mutagenesis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with mutagenesis and activity assays, mechanistic model supported by multiple orthogonal approaches","pmids":["26522158"],"is_preprint":false},{"year":2015,"finding":"NEK9 functions as a transcriptional repressor during adenovirus infection, colocalizing with viral replication centers and viral E4 orf3 protein. NEK9 depletion reduces viral genome replication and associates with promoters of p53 target gene GADD45A, silencing its expression.","method":"siRNA knockdown, chromatin immunoprecipitation, immunofluorescence colocalization, viral replication assay","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and functional knockdown with viral assays, single lab","pmids":["26676776"],"is_preprint":false},{"year":2016,"finding":"Somatic gain-of-function mutations in the kinase and RCC1 domains of NEK9 cause nevus comedonicus; each mutation increases phosphorylation at Thr210 (the NEK9 activation-loop marker of kinase activation), leading to loss of follicular differentiation markers and ectopic keratin expression, establishing NEK9 kinase activity as a regulator of follicular differentiation.","method":"Whole-exome sequencing, Western blot for pThr210, immunofluorescence for differentiation markers","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — human somatic mutations validated biochemically by pThr210 as activation readout, single study","pmids":["27153399"],"is_preprint":false},{"year":2017,"finding":"NEK9 phosphorylates TPX2 on its nuclear localization signal (NLS), preventing importin binding and thereby retaining a pool of TPX2 at centrosomes before nuclear envelope breakdown (NEBD). This centrosomal TPX2 pool, dependent on RHAMM/HMMR and NEK9, is required for microtubule aster organization, Eg5 localization, and prophase centrosome separation.","method":"In vitro kinase assay, co-immunoprecipitation, siRNA knockdown, live-cell imaging, importin-binding assay","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro phosphorylation of defined NLS site, importin interaction assay, functional rescue by siRNA epistasis, multiple orthogonal methods","pmids":["29276125"],"is_preprint":false},{"year":2020,"finding":"EML4-ALK variant 3 recruits NEK9 and NEK7 to microtubules via the N-terminal EML4 microtubule-binding region. Constitutively active NEK9 perturbs cell morphology and accelerates migration in a microtubule-dependent manner requiring downstream NEK7 but not ALK activity, establishing NEK9/NEK7 as effectors of EML4-ALK V3-driven microtubule stabilization and cell migration.","method":"Co-immunoprecipitation, siRNA knockdown, constitutively-active mutant overexpression, live-cell imaging, pharmacological inhibition","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP, constitutively active mutants, and siRNA epistasis in single lab","pmids":["32184261"],"is_preprint":false},{"year":2021,"finding":"NEK9 acts as a selective autophagy adaptor for MYH9 (myosin IIA) via its LC3-interacting region (LIR) motif, interacting with GABARAP-family proteins. NEK9-mediated autophagic degradation of MYH9 is required for primary cilia formation; LIR mutation in NEK9 causes MYH9 accumulation and impaired ciliogenesis both in cells and in mouse kidneys. MYH9 depletion rescues ciliogenesis in NEK9-LIR mutant cells.","method":"Co-immunoprecipitation, LIR mutagenesis, mouse knock-in model, knockdown rescue experiments, immunofluorescence, autophagy flux assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — genetic rescue in mice, mutagenesis, co-IP, multiple orthogonal methods, in vivo validation","pmids":["34078910"],"is_preprint":false},{"year":2021,"finding":"NEK9 directly interacts with PRLR-SF (short isoform of prolactin receptor) and serves as intermediator between PRLR-SF and Hippo signaling pathway activation, suppressing pentose phosphate pathway gene expression (G6PD, TKT) via TEAD1 in pancreatic cancer cells.","method":"Co-immunoprecipitation, proximity ligation assay, chromatin immunoprecipitation, promoter luciferase assay","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP and PLA for interaction, ChIP and luciferase for downstream pathway, single lab","pmids":["33664869"],"is_preprint":false},{"year":2021,"finding":"NEK9 directly phosphorylates ARHGEF2 (a RhoA guanine nucleotide exchange factor), as demonstrated by in vitro kinase assay and phosphoproteomics. This phosphorylation activates RhoA and drives gastric cancer cell motility. NEK9 is transcriptionally upregulated via STAT3 activation (by IL-6) through suppression of miR-520f-3p.","method":"In vitro kinase assay, phosphoproteomics, GST pull-down, co-immunoprecipitation, luciferase reporter, ChIP","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro kinase assay of defined substrate, phosphoproteomics, and functional migration assay, single lab","pmids":["33500736"],"is_preprint":false},{"year":2023,"finding":"NEK9 kinase domain directly interacts with the intracellular domain (ICD) of ROBO1, and this interaction is enhanced by SLIT2. NEK9 directly phosphorylates TRIM28 and cortactin (CTTN), with TRIM28 functioning as a transcriptional elongation factor that facilitates CTTN transcription via STAT3 and NF-κB p100.","method":"Mass spectrometry, co-immunoprecipitation, in vitro kinase assay, domain deletion analysis","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS-identified interaction confirmed by co-IP and in vitro kinase assay for substrates, single lab","pmids":["37443302"],"is_preprint":false},{"year":2024,"finding":"USP19 deubiquitylase directly interacts with and stabilizes NEK9 by removing K48-linked polyubiquitin chains at Lys525, preventing its proteasomal degradation. NEK9, in turn, phosphorylates Raptor at Ser792, inhibiting mTORC1 signaling and promoting autophagic cell death in pancreatic cancer cells.","method":"Co-immunoprecipitation, in vitro deubiquitylation assay, in vitro kinase assay, siRNA/overexpression functional studies","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP, in vitro kinase and deubiquitylation assays, defined ubiquitylation site, single lab","pmids":["39627360"],"is_preprint":false},{"year":2025,"finding":"NEK7 (downstream of NEK9 in the EML4-ALK V3 pathway) phosphorylates cortactin within its F-actin-binding repeat region (ABR). Phospho-mimetic cortactin mutations promote filopodia-like extensions and increased migration, while phospho-null mutations dissociate cortactin from F-actin. Constitutively active NEK9 or NEK7 produces similar cortactin-dependent morphological changes.","method":"In vitro kinase assay, phospho-mimetic/null mutagenesis, siRNA depletion, live-cell imaging, co-localization","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro kinase assay with defined phosphosites and mutagenesis functional validation; preprint, not yet peer-reviewed","pmids":["bio_10.1101_2025.08.30.672807"],"is_preprint":true},{"year":2025,"finding":"FAM49B directly interacts with NEK9 and promotes Thr210 phosphorylation (NEK9 activation). In FAM49B-overexpressing colorectal cancer cells, NEK9 knockdown significantly reduces c-Myc expression and c-Myc-Ser62 phosphorylation, placing NEK9 between FAM49B and c-Myc stabilization.","method":"Co-immunoprecipitation, siRNA knockdown, Western blot for pThr210 and pSer62-c-Myc, ubiquitination assay","journal":"BioFactors (Oxford, England)","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single co-IP and functional knockdown, single lab, limited mechanistic detail in abstract","pmids":["39780509"],"is_preprint":false}],"current_model":"NEK9 (Nercc1) is a NIMA-family serine/threonine kinase that functions as the master upstream kinase of a mitotic cascade: it is sequentially activated by CDK1 and Plk1 phosphorylation at centrosomes in prophase, whereupon it phosphorylates and activates the downstream kinases Nek6 and Nek7 (after releasing their autoinhibitory tyrosine via CTD-induced back-to-back dimerization), drives centrosome maturation by phosphorylating NEDD1 to recruit gamma-tubulin, promotes Eg5 accumulation and centrosome separation by phosphorylating TPX2 (blocking its nuclear import) and via Nek6/7-mediated Eg5 phosphorylation, and outside mitosis acts as a selective autophagy adaptor for MYH9 to enable ciliogenesis, interacts with FACT for interphase progression, promotes CHK1 activity during replication stress, and phosphorylates substrates including ARHGEF2 and Raptor to influence RhoA signaling and mTORC1 activity respectively."},"narrative":{"mechanistic_narrative":"NEK9 (Nercc1) is a NIMA-family serine/threonine kinase that serves as the master upstream node of a mitotic kinase cascade controlling centrosome maturation and spindle assembly [PMID:12840024, PMID:16079175]. It is a cytoplasmic kinase activated during mitosis, binding the Ran GTPase through both its catalytic and RCC1-like domains and self-oligomerizing for autoactivation via activation-loop phosphorylation at Thr210 [PMID:12101123, PMID:16079175]. In prophase NEK9 is switched on by sequential CDK1 then Plk1 phosphorylation, after which it phosphorylates and activates the downstream kinases Nek6 and Nek7 by binding their kinase domains through its non-catalytic C-terminal domain and releasing an autoinhibitory tyrosine (Tyr97) via back-to-back dimerization [PMID:12840024, PMID:19941817, PMID:21642957, PMID:26522158]. Through this module NEK9 drives prophase centrosome separation: it promotes Nek6/7-dependent phosphorylation of the kinesin Eg5 at Ser1033 and phosphorylates TPX2 on its nuclear localization signal to retain a centrosomal TPX2 pool that organizes microtubule asters [PMID:21642957, PMID:29276125]. Independently of Nek6/7, NEK9 phosphorylates NEDD1/GCP-WD at Ser377 to recruit gamma-tubulin and mature the centrosome [PMID:22818914]. Signal flux through the cascade is gated by the dynein light chain DYNLL/LC8, which binds a motif near the NEK9 coiled-coil to promote multimerization while competing with Nek6 binding, a interaction abolished by NEK9 autophosphorylation at Ser944 [PMID:21454704, PMID:23482567]. Beyond mitosis, NEK9 acts as a selective autophagy adaptor that targets MYH9 (myosin IIA) for degradation via its LIR motif to enable primary ciliogenesis [PMID:34078910], promotes CHK1 activity during replication stress [PMID:25217585], and phosphorylates substrates including ARHGEF2 to activate RhoA and Raptor at Ser792 to inhibit mTORC1 [PMID:33500736, PMID:39627360]. Activating mutations in the kinase and RCC1 domains, which elevate Thr210 phosphorylation, cause the cutaneous disorder nevus comedonicus by disrupting follicular differentiation [PMID:27153399].","teleology":[{"year":2002,"claim":"Establishing NEK9 as a Ran-binding, mitotically activated kinase defined its identity as a cytoplasmic cell-cycle kinase and first linked it to the Ran GTPase and Nek6.","evidence":"Co-IP, subcellular fractionation, and in vitro autoactivation assays in the founding paper","pmids":["12101123"],"confidence":"High","gaps":["Functional consequence of RanGDP binding not resolved","No downstream substrates yet identified"]},{"year":2003,"claim":"Identifying Nek6/Nek7 as direct activation-loop substrates established NEK9 as the apex of a mitotic NIMA-family kinase cascade required for spindle integrity.","evidence":"In vitro kinase assays with recombinant proteins, phosphosite mapping (Ser206), and antibody microinjection","pmids":["12840024"],"confidence":"High","gaps":["Structural basis of substrate recognition unknown at this stage","Upstream activator of NEK9 itself not yet defined"]},{"year":2003,"claim":"Discovery of a stable NEK9-FACT complex extended NEK9 function beyond mitosis into interphase G1/S progression.","evidence":"Co-IP of ~600 kDa complex with Spt16-Pob3 and RNAi cell-cycle analysis","pmids":["14660563"],"confidence":"Medium","gaps":["FACT substrate/phosphorylation target within complex not defined","Single lab, no reciprocal validation"]},{"year":2005,"claim":"Localizing active NEK9 to centrosomes and showing rescue of spindle defects established a direct role in spindle assembly and gamma-TuRC association.","evidence":"Immunodepletion from Xenopus egg extracts with recombinant rescue and gamma-tubulin co-IP","pmids":["16079175"],"confidence":"High","gaps":["Direct gamma-TuRC substrate not yet identified","Mechanism of centrosomal targeting unresolved"]},{"year":2009,"claim":"The Nek7 autoinhibited structure and the role of the NEK9 CTD in releasing Tyr97 revealed the molecular mechanism of downstream kinase activation.","evidence":"X-ray crystallography of Nek7 plus Tyr-to-Phe mutagenesis and activity assays","pmids":["19941817"],"confidence":"High","gaps":["Exact stoichiometry and dimerization geometry not resolved here","How CTD engagement is regulated in cells unclear"]},{"year":2011,"claim":"Defining sequential CDK1-then-Plk1 activation of NEK9 and the NEK9-Nek6/7-Eg5 axis placed the cascade in the prophase centrosome-separation program.","evidence":"In vitro kinase reconstitution, phosphosite mapping (Eg5 Ser1033), siRNA epistasis, and live imaging","pmids":["21642957"],"confidence":"High","gaps":["Spatiotemporal coordination of the two upstream kinases not fully mapped","Other Nek6/7 mitotic substrates unaccounted for"]},{"year":2011,"claim":"Showing LC8/DYNLL binding promotes multimerization yet competes with Nek6 revealed an autophosphorylation-gated switch controlling cascade output.","evidence":"Reciprocal co-IP, motif mutagenesis, and in vitro kinase assays defining Ser944 regulation","pmids":["21454704"],"confidence":"High","gaps":["Cellular trigger for Ser944 autophosphorylation timing unknown","Whether LC8 links NEK9 to dynein-based transport untested"]},{"year":2012,"claim":"Identifying NEDD1 Ser377 as a direct NEK9 substrate explained how NEK9 drives gamma-tubulin recruitment independently of Nek6/7.","evidence":"In vitro kinase assay, phosphosite mutagenesis, and validation in Xenopus and mammalian cells","pmids":["22818914"],"confidence":"High","gaps":["Branch-point logic separating NEDD1 from Nek6/7 arms not fully defined"]},{"year":2012,"claim":"Oocyte meiosis phenotypes confirmed NEK9 requirement for spindle organization, chromosome alignment, and checkpoint silencing in a physiological division.","evidence":"Morpholino knockdown in mouse oocytes with confocal imaging and checkpoint marker analysis","pmids":["23159858"],"confidence":"Medium","gaps":["Direct meiotic substrates not identified","Single knockdown approach"]},{"year":2013,"claim":"Structures of LC8 bound to phospho- and unphospho-Nek9 peptides established the atomic basis for Ser944-dependent affinity regulation of the cascade switch.","evidence":"X-ray crystallography of two peptide states plus ITC","pmids":["23482567"],"confidence":"High","gaps":["In-cell kinetics of the switch not measured"]},{"year":2014,"claim":"Linking NEK9 to CHK1 activity defined a role in the replication stress response distinct from its mitotic functions.","evidence":"Co-IP, kinase activity assays, RNAi synthetic-lethal screen, and gemcitabine sensitivity","pmids":["25217585"],"confidence":"Medium","gaps":["Whether NEK9 directly phosphorylates CHK1 not established","Single lab"]},{"year":2015,"claim":"The Nek7(Y97F)-Nek9 peptide structure showing back-to-back dimerization completed the mechanistic model for how the NEK9 CTD activates downstream kinases.","evidence":"X-ray crystallography, binding-domain mapping (Nek9 810-828), and structure-function mutagenesis","pmids":["26522158"],"confidence":"High","gaps":["Dynamics of dimer assembly in vivo not visualized"]},{"year":2015,"claim":"Identifying NEK9 as a viral-recruited transcriptional repressor at GADD45A revealed an unexpected chromatin-associated, infection-dependent activity.","evidence":"siRNA knockdown, ChIP, colocalization with viral E4 orf3, and replication assays","pmids":["26676776"],"confidence":"Medium","gaps":["Mechanism of promoter recruitment unknown","Relevance outside viral infection unclear"]},{"year":2016,"claim":"Discovering activating somatic NEK9 mutations in nevus comedonicus established a direct disease link and showed NEK9 kinase activity regulates follicular differentiation.","evidence":"Whole-exome sequencing with pThr210 Western blot and differentiation-marker immunofluorescence","pmids":["27153399"],"confidence":"Medium","gaps":["Downstream effectors in keratinocyte differentiation not identified","Single study"]},{"year":2017,"claim":"Showing NEK9 phosphorylates the TPX2 NLS to block importin binding explained how a centrosomal TPX2 pool is maintained for prophase aster organization.","evidence":"In vitro kinase assay, importin-binding assay, siRNA epistasis with RHAMM/HMMR, and live imaging","pmids":["29276125"],"confidence":"High","gaps":["Coordination with the Eg5 and NEDD1 arms not unified mechanistically"]},{"year":2020,"claim":"Demonstrating EML4-ALK V3 recruitment of NEK9/NEK7 to microtubules implicated the cascade in oncogenic cell migration independent of ALK catalytic activity.","evidence":"Co-IP, constitutively-active mutants, siRNA epistasis, and live imaging","pmids":["32184261"],"confidence":"Medium","gaps":["Microtubule substrate of NEK9/NEK7 in this context not defined here","Single lab"]},{"year":2021,"claim":"Identifying NEK9 as a LIR-motif selective autophagy adaptor for MYH9 required for ciliogenesis revealed a non-mitotic degradative function validated in vivo.","evidence":"Co-IP, LIR mutagenesis, mouse knock-in, and MYH9-depletion rescue of ciliogenesis","pmids":["34078910"],"confidence":"High","gaps":["How NEK9 selects MYH9 cargo signal is unresolved","Relationship between kinase activity and adaptor function unclear"]},{"year":2021,"claim":"Defining ARHGEF2 as a direct NEK9 substrate connected the kinase to RhoA activation and cancer cell motility.","evidence":"In vitro kinase assay, phosphoproteomics, GST pull-down, and migration assays","pmids":["33500736"],"confidence":"Medium","gaps":["ARHGEF2 phosphosite not specified","Single lab cancer model"]},{"year":2021,"claim":"Linking NEK9 to PRLR-SF and Hippo/TEAD signaling extended its reach to metabolic gene regulation in pancreatic cancer.","evidence":"Co-IP, PLA, ChIP, and promoter luciferase assays","pmids":["33664869"],"confidence":"Medium","gaps":["Whether the effect requires NEK9 kinase activity not established","Single lab"]},{"year":2023,"claim":"Mapping a NEK9-ROBO1 interaction and TRIM28/cortactin substrates placed NEK9 in SLIT2-ROBO1 signaling and transcriptional regulation of CTTN.","evidence":"Mass spectrometry, co-IP, in vitro kinase assay, and domain-deletion analysis","pmids":["37443302"],"confidence":"Medium","gaps":["Phosphosites on TRIM28/cortactin not defined here","Single lab"]},{"year":2024,"claim":"Identifying USP19-mediated stabilization and NEK9 phosphorylation of Raptor Ser792 connected NEK9 abundance to mTORC1 inhibition and autophagic cell death.","evidence":"Co-IP, in vitro deubiquitylation and kinase assays defining Lys525 ubiquitination and Ser792 phosphorylation","pmids":["39627360"],"confidence":"Medium","gaps":["Physiological signals controlling the USP19-NEK9 axis unclear","Single lab"]},{"year":2025,"claim":"Showing NEK7 phosphorylates cortactin in its actin-binding region links the NEK9/NEK7 cascade to actin-driven filopodia and migration.","evidence":"In vitro kinase assay with phospho-mimetic/null mutagenesis and live imaging (preprint)","pmids":["bio_10.1101_2025.08.30.672807"],"confidence":"Medium","gaps":["Preprint, not yet peer-reviewed","In vivo relevance of cortactin phosphorylation untested"]},{"year":null,"claim":"How NEK9 selects between its many distinct functional outputs—mitotic cascade, autophagy adaptor, replication stress, mTORC1, and cancer signaling—within a single cell remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unifying model for context-dependent substrate selection","Relationship between kinase-dependent and adaptor functions not integrated","Whether non-mitotic substrates require the same activation hierarchy unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,6,8,15,19,21]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[1,8,15]},{"term_id":"GO:0003924","term_label":"GTPase activity","supporting_discovery_ids":[0]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[17]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[13]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[3,9,15]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2,4]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[16]}],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[1,3,6,8,15]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[17,21]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[19,20,21]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[11]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[17]}],"complexes":["FACT (Spt16-Pob3)","gamma-tubulin ring complex (associated)"],"partners":["NEK6","NEK7","DYNLL1","PLK1","RAN","TPX2","MYH9","USP19"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8TD19","full_name":"Serine/threonine-protein kinase Nek9","aliases":["Nercc1 kinase","Never in mitosis A-related kinase 9","NimA-related protein kinase 9","NimA-related kinase 8","Nek8"],"length_aa":979,"mass_kda":107.2,"function":"Pleiotropic regulator of mitotic progression, participating in the control of spindle dynamics and chromosome separation (PubMed:12101123, PubMed:12840024, PubMed:14660563, PubMed:19941817). Phosphorylates different histones, myelin basic protein, beta-casein, and BICD2 (PubMed:11864968). Phosphorylates histone H3 on serine and threonine residues and beta-casein on serine residues (PubMed:11864968). Important for G1/S transition and S phase progression (PubMed:12840024, PubMed:14660563, PubMed:19941817). Phosphorylates NEK6 and NEK7 and stimulates their activity by releasing the autoinhibitory functions of Tyr-108 and Tyr-97 respectively (PubMed:12840024, PubMed:14660563, PubMed:19941817, PubMed:26522158)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q8TD19/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NEK9","classification":"Not Classified","n_dependent_lines":11,"n_total_lines":1208,"dependency_fraction":0.009105960264900662},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000119638","cell_line_id":"CID001227","localizations":[{"compartment":"cytoplasmic","grade":3}],"interactors":[{"gene":"DYNLL1","stoichiometry":10.0},{"gene":"DYNLL2","stoichiometry":10.0},{"gene":"DYNLL1;DYNLL2","stoichiometry":4.0},{"gene":"SMC1A","stoichiometry":0.2},{"gene":"EML4","stoichiometry":0.2},{"gene":"TOP2A","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001227","total_profiled":1310},"omim":[{"mim_id":"617025","title":"NEVUS COMEDONICUS; NC","url":"https://www.omim.org/entry/617025"},{"mim_id":"617022","title":"LETHAL CONGENITAL CONTRACTURE SYNDROME 10; LCCS10","url":"https://www.omim.org/entry/617022"},{"mim_id":"614262","title":"ARTHROGRYPOSIS, PERTHES DISEASE, AND UPWARD GAZE PALSY; APUG","url":"https://www.omim.org/entry/614262"},{"mim_id":"609799","title":"NIMA-RELATED KINASE 8; NEK8","url":"https://www.omim.org/entry/609799"},{"mim_id":"609798","title":"NIMA-RELATED KINASE 9; NEK9","url":"https://www.omim.org/entry/609798"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NEK9"},"hgnc":{"alias_symbol":["Nek8","NERCC","DKFZp434D0935","MGC16714","NERCC1"],"prev_symbol":[]},"alphafold":{"accession":"Q8TD19","domains":[{"cath_id":"3.30.200.20","chopping":"50-130","consensus_level":"medium","plddt":84.004,"start":50,"end":130},{"cath_id":"1.10.510.10","chopping":"135-324","consensus_level":"medium","plddt":88.5371,"start":135,"end":324},{"cath_id":"2.130.10.30","chopping":"349-377_616-740","consensus_level":"medium","plddt":84.9386,"start":349,"end":740}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TD19","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8TD19-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8TD19-F1-predicted_aligned_error_v6.png","plddt_mean":73.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NEK9","jax_strain_url":"https://www.jax.org/strain/search?query=NEK9"},"sequence":{"accession":"Q8TD19","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8TD19.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8TD19/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TD19"}},"corpus_meta":[{"pmid":"12840024","id":"PMC_12840024","title":"A mitotic cascade of NIMA family kinases. 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Nercc1 also binds Nek6 and exists as a homooligomer, capable of autoactivation in vitro by autophosphorylation. It is a cytoplasmic protein activated during mitosis and phosphorylated by active p34(Cdc2)/CDK1.\",\n      \"method\": \"Co-immunoprecipitation, in vitro autoactivation assay, subcellular fractionation, in vivo binding experiments\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, in vitro kinase assay, multiple orthogonal methods in foundational paper\",\n      \"pmids\": [\"12101123\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Nercc1/NEK9 directly phosphorylates and activates Nek6 at Ser206 on its activation loop (and Nek7 similarly) in vitro, resulting in 20–25-fold activation of Nek6 activity. Microinjection of anti-Nercc1 antibodies causes spindle abnormalities and prometaphase arrest or chromosome missegregation, establishing Nercc1/Nek9 as the upstream kinase in a mitotic NIMA-family kinase cascade.\",\n      \"method\": \"In vitro kinase assay with recombinant proteins, co-expression of activated Nercc1 mutant, antibody microinjection, mass spectrometry phosphosite identification\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with defined phosphosite, mutagenesis, replicated across Nek6 and Nek7\",\n      \"pmids\": [\"12840024\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"NEK9 forms a stable ~600 kDa complex with the FACT chromatin-remodeling complex (Spt16-Pob3) in interphase nuclei. Within this complex, NEK9 exhibits elevated phosphorylation at Thr210 (activation loop). RNAi depletion of Nek9 impairs G1 and S phase progression, implicating Nek9-FACT complex in interphase cell cycle progression.\",\n      \"method\": \"Co-immunoprecipitation, dsRNAi knockdown, cell cycle analysis, gel mobility shift assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP and functional knockdown in single lab, two orthogonal methods\",\n      \"pmids\": [\"14660563\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Active Nercc1/NEK9 localizes to centrosomes and spindle poles during early mitosis. In Xenopus egg extracts, XNercc co-precipitates with gamma-tubulin ring complex components. Immunodepletion of XNercc causes delayed spindle assembly, fewer bipolar spindles, and smaller Ran-GTP-induced asters; these defects are rescued by adding purified recombinant XNercc. Autoactivation in vitro requires phosphorylation of the activation loop at Thr210.\",\n      \"method\": \"Immunofluorescence, co-immunoprecipitation, immunodepletion from Xenopus egg extracts, recombinant protein rescue, in vitro kinase assay\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — immunodepletion with rescue by purified protein, co-IP with gamma-TuRC, multiple orthogonal methods\",\n      \"pmids\": [\"16079175\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Adenovirus E1A protein interacts with nuclear NEK9 and causes redistribution of NEK9 from nucleus to cytoplasm. A NEK9 deletion mutant lacking the central RCC1-like domain interacts stably with E1A and accumulates in the nucleus, suggesting the RCC1-like domain is required for the transient nature of the interaction.\",\n      \"method\": \"Co-immunoprecipitation, subcellular fractionation, immunofluorescence, deletion mutagenesis\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus subcellular fractionation and deletion mutagenesis, single lab\",\n      \"pmids\": [\"17443675\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Crystal structure of Nek7 reveals an autoinhibited conformation where Tyr97 protrudes into the active site and blocks the alphaC helix. The non-catalytic C-terminal domain (CTD) of Nek9 binds Nek6/Nek7 and releases this autoinhibitory tyrosine, activating the kinases. Tyr-to-Phe mutation of Nek7 and Nek6 renders them constitutively active independently of Nek9.\",\n      \"method\": \"X-ray crystallography, site-directed mutagenesis, in vitro kinase activity assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus mutagenesis and activity assays in single rigorous study\",\n      \"pmids\": [\"19941817\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"PLK1 directly activates NEK9 during prophase via sequential phosphorylation by CDK1 then Plk1. Activated NEK9 in turn phosphorylates Nek6/Nek7, which phosphorylate the mitotic kinesin Eg5 at Ser1033; this Nek6/7-dependent phosphorylation together with the CDK1 site Thr926 promotes Eg5 accumulation at centrosomes and drives prophase centrosome separation.\",\n      \"method\": \"In vitro kinase assay, co-immunoprecipitation, siRNA knockdown, phosphosite mapping, live-cell imaging\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro kinase reconstitution, phosphosite mapping, epistasis by siRNA, multiple orthogonal methods\",\n      \"pmids\": [\"21642957\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"DYNLL/LC8 binds Nek9 via a (K/R)XTQT motif adjacent to the Nek9 C-terminal coiled-coil, promotes Nek9 multimerization and accelerates Nek9 autoactivation. LC8 binding is negatively regulated by Nek9 autophosphorylation at Ser944. Importantly, LC8 binding to Nek9 interferes with Nek9-Nek6 interaction and inhibits Nek6 activation, thereby controlling signal transduction through the Nek9/Nek6/7 module.\",\n      \"method\": \"Co-immunoprecipitation, in vitro kinase assay, motif mutagenesis, biophysical binding assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, mutagenesis, in vitro assays, functional consequence on Nek6 activation established\",\n      \"pmids\": [\"21454704\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"NEK9 phosphorylates NEDD1/GCP-WD at Ser377, driving NEDD1 recruitment to the centrosome and thereby promoting gamma-tubulin accumulation at the mitotic centrosome. This function requires Plk1-dependent activation of Nek9 but is independent of downstream Nek6/Nek7.\",\n      \"method\": \"In vitro kinase assay, phosphosite mutagenesis, Xenopus egg extracts, siRNA knockdown, immunofluorescence\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro phosphorylation of defined site, validated in two model systems (Xenopus and mammalian cells), epistasis analysis\",\n      \"pmids\": [\"22818914\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Nek9 localizes to spindle poles and the midbody during mouse oocyte meiosis. Morpholino-mediated depletion of Nek9 causes defective spindles, misaligned chromosomes, MI arrest, and failure of polar body extrusion, with concomitant loss of gamma-tubulin at spindle poles and retention of Bub3 at kinetochores.\",\n      \"method\": \"Morpholino knockdown in mouse oocytes, confocal immunofluorescence, live-cell imaging\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — specific knockdown with clear phenotypic readouts and checkpoint marker analysis, single lab\",\n      \"pmids\": [\"23159858\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Crystal structures of LC8 bound to phosphorylated and unphosphorylated Nek9 peptides (around Ser944) reveal that phosphorylation at Ser944 directly reduces binding affinity to LC8, explaining how Nek9 autophosphorylation controls its interaction with the dynein light chain and thereby regulates downstream Nek6 signaling.\",\n      \"method\": \"X-ray crystallography, isothermal titration calorimetry, biophysical binding assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structures with two peptide states plus biophysical validation, single lab\",\n      \"pmids\": [\"23482567\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NEK9 complexes with CHK1, and NEK9 depletion impairs CHK1 autophosphorylation and kinase activity in response to replication stress. NEK9-depleted cells show hypersensitivity to gemcitabine, spontaneous DNA damage foci, RPA70 foci accumulation, and impaired recovery from replication arrest, defining NEK9 as a component of the replication stress response that promotes CHK1 activity.\",\n      \"method\": \"siRNA knockdown, co-immunoprecipitation, kinase activity assay, RNAi synthetic lethal screen, immunofluorescence\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP of NEK9-CHK1 complex, functional knockdown with multiple readouts, single lab\",\n      \"pmids\": [\"25217585\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Crystal structure of Nek7(Y97F) bound to a Nek9 peptide (residues 810–828) maps the minimal Nek9-binding region on the C-lobe of the Nek7 kinase domain. Nek7(Y97F) crystallizes as a back-to-back dimer through N-lobe contacts coupled to the conformation of residue 97. Self-association of the Nek9 CTD is required for Nek7 activation, leading to the model that Nek9-CTD promotes Nek7 back-to-back dimerization to release autoinhibition.\",\n      \"method\": \"X-ray crystallography, binding domain mapping, in vitro kinase assay, structure-function mutagenesis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with mutagenesis and activity assays, mechanistic model supported by multiple orthogonal approaches\",\n      \"pmids\": [\"26522158\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"NEK9 functions as a transcriptional repressor during adenovirus infection, colocalizing with viral replication centers and viral E4 orf3 protein. NEK9 depletion reduces viral genome replication and associates with promoters of p53 target gene GADD45A, silencing its expression.\",\n      \"method\": \"siRNA knockdown, chromatin immunoprecipitation, immunofluorescence colocalization, viral replication assay\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and functional knockdown with viral assays, single lab\",\n      \"pmids\": [\"26676776\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Somatic gain-of-function mutations in the kinase and RCC1 domains of NEK9 cause nevus comedonicus; each mutation increases phosphorylation at Thr210 (the NEK9 activation-loop marker of kinase activation), leading to loss of follicular differentiation markers and ectopic keratin expression, establishing NEK9 kinase activity as a regulator of follicular differentiation.\",\n      \"method\": \"Whole-exome sequencing, Western blot for pThr210, immunofluorescence for differentiation markers\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — human somatic mutations validated biochemically by pThr210 as activation readout, single study\",\n      \"pmids\": [\"27153399\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"NEK9 phosphorylates TPX2 on its nuclear localization signal (NLS), preventing importin binding and thereby retaining a pool of TPX2 at centrosomes before nuclear envelope breakdown (NEBD). This centrosomal TPX2 pool, dependent on RHAMM/HMMR and NEK9, is required for microtubule aster organization, Eg5 localization, and prophase centrosome separation.\",\n      \"method\": \"In vitro kinase assay, co-immunoprecipitation, siRNA knockdown, live-cell imaging, importin-binding assay\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro phosphorylation of defined NLS site, importin interaction assay, functional rescue by siRNA epistasis, multiple orthogonal methods\",\n      \"pmids\": [\"29276125\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"EML4-ALK variant 3 recruits NEK9 and NEK7 to microtubules via the N-terminal EML4 microtubule-binding region. Constitutively active NEK9 perturbs cell morphology and accelerates migration in a microtubule-dependent manner requiring downstream NEK7 but not ALK activity, establishing NEK9/NEK7 as effectors of EML4-ALK V3-driven microtubule stabilization and cell migration.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, constitutively-active mutant overexpression, live-cell imaging, pharmacological inhibition\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP, constitutively active mutants, and siRNA epistasis in single lab\",\n      \"pmids\": [\"32184261\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NEK9 acts as a selective autophagy adaptor for MYH9 (myosin IIA) via its LC3-interacting region (LIR) motif, interacting with GABARAP-family proteins. NEK9-mediated autophagic degradation of MYH9 is required for primary cilia formation; LIR mutation in NEK9 causes MYH9 accumulation and impaired ciliogenesis both in cells and in mouse kidneys. MYH9 depletion rescues ciliogenesis in NEK9-LIR mutant cells.\",\n      \"method\": \"Co-immunoprecipitation, LIR mutagenesis, mouse knock-in model, knockdown rescue experiments, immunofluorescence, autophagy flux assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — genetic rescue in mice, mutagenesis, co-IP, multiple orthogonal methods, in vivo validation\",\n      \"pmids\": [\"34078910\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NEK9 directly interacts with PRLR-SF (short isoform of prolactin receptor) and serves as intermediator between PRLR-SF and Hippo signaling pathway activation, suppressing pentose phosphate pathway gene expression (G6PD, TKT) via TEAD1 in pancreatic cancer cells.\",\n      \"method\": \"Co-immunoprecipitation, proximity ligation assay, chromatin immunoprecipitation, promoter luciferase assay\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP and PLA for interaction, ChIP and luciferase for downstream pathway, single lab\",\n      \"pmids\": [\"33664869\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NEK9 directly phosphorylates ARHGEF2 (a RhoA guanine nucleotide exchange factor), as demonstrated by in vitro kinase assay and phosphoproteomics. This phosphorylation activates RhoA and drives gastric cancer cell motility. NEK9 is transcriptionally upregulated via STAT3 activation (by IL-6) through suppression of miR-520f-3p.\",\n      \"method\": \"In vitro kinase assay, phosphoproteomics, GST pull-down, co-immunoprecipitation, luciferase reporter, ChIP\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro kinase assay of defined substrate, phosphoproteomics, and functional migration assay, single lab\",\n      \"pmids\": [\"33500736\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NEK9 kinase domain directly interacts with the intracellular domain (ICD) of ROBO1, and this interaction is enhanced by SLIT2. NEK9 directly phosphorylates TRIM28 and cortactin (CTTN), with TRIM28 functioning as a transcriptional elongation factor that facilitates CTTN transcription via STAT3 and NF-κB p100.\",\n      \"method\": \"Mass spectrometry, co-immunoprecipitation, in vitro kinase assay, domain deletion analysis\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS-identified interaction confirmed by co-IP and in vitro kinase assay for substrates, single lab\",\n      \"pmids\": [\"37443302\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"USP19 deubiquitylase directly interacts with and stabilizes NEK9 by removing K48-linked polyubiquitin chains at Lys525, preventing its proteasomal degradation. NEK9, in turn, phosphorylates Raptor at Ser792, inhibiting mTORC1 signaling and promoting autophagic cell death in pancreatic cancer cells.\",\n      \"method\": \"Co-immunoprecipitation, in vitro deubiquitylation assay, in vitro kinase assay, siRNA/overexpression functional studies\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP, in vitro kinase and deubiquitylation assays, defined ubiquitylation site, single lab\",\n      \"pmids\": [\"39627360\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NEK7 (downstream of NEK9 in the EML4-ALK V3 pathway) phosphorylates cortactin within its F-actin-binding repeat region (ABR). Phospho-mimetic cortactin mutations promote filopodia-like extensions and increased migration, while phospho-null mutations dissociate cortactin from F-actin. Constitutively active NEK9 or NEK7 produces similar cortactin-dependent morphological changes.\",\n      \"method\": \"In vitro kinase assay, phospho-mimetic/null mutagenesis, siRNA depletion, live-cell imaging, co-localization\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro kinase assay with defined phosphosites and mutagenesis functional validation; preprint, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.08.30.672807\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FAM49B directly interacts with NEK9 and promotes Thr210 phosphorylation (NEK9 activation). In FAM49B-overexpressing colorectal cancer cells, NEK9 knockdown significantly reduces c-Myc expression and c-Myc-Ser62 phosphorylation, placing NEK9 between FAM49B and c-Myc stabilization.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, Western blot for pThr210 and pSer62-c-Myc, ubiquitination assay\",\n      \"journal\": \"BioFactors (Oxford, England)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single co-IP and functional knockdown, single lab, limited mechanistic detail in abstract\",\n      \"pmids\": [\"39780509\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NEK9 (Nercc1) is a NIMA-family serine/threonine kinase that functions as the master upstream kinase of a mitotic cascade: it is sequentially activated by CDK1 and Plk1 phosphorylation at centrosomes in prophase, whereupon it phosphorylates and activates the downstream kinases Nek6 and Nek7 (after releasing their autoinhibitory tyrosine via CTD-induced back-to-back dimerization), drives centrosome maturation by phosphorylating NEDD1 to recruit gamma-tubulin, promotes Eg5 accumulation and centrosome separation by phosphorylating TPX2 (blocking its nuclear import) and via Nek6/7-mediated Eg5 phosphorylation, and outside mitosis acts as a selective autophagy adaptor for MYH9 to enable ciliogenesis, interacts with FACT for interphase progression, promotes CHK1 activity during replication stress, and phosphorylates substrates including ARHGEF2 and Raptor to influence RhoA signaling and mTORC1 activity respectively.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NEK9 (Nercc1) is a NIMA-family serine/threonine kinase that serves as the master upstream node of a mitotic kinase cascade controlling centrosome maturation and spindle assembly [#1, #3]. It is a cytoplasmic kinase activated during mitosis, binding the Ran GTPase through both its catalytic and RCC1-like domains and self-oligomerizing for autoactivation via activation-loop phosphorylation at Thr210 [#0, #3]. In prophase NEK9 is switched on by sequential CDK1 then Plk1 phosphorylation, after which it phosphorylates and activates the downstream kinases Nek6 and Nek7 by binding their kinase domains through its non-catalytic C-terminal domain and releasing an autoinhibitory tyrosine (Tyr97) via back-to-back dimerization [#1, #5, #6, #12]. Through this module NEK9 drives prophase centrosome separation: it promotes Nek6/7-dependent phosphorylation of the kinesin Eg5 at Ser1033 and phosphorylates TPX2 on its nuclear localization signal to retain a centrosomal TPX2 pool that organizes microtubule asters [#6, #15]. Independently of Nek6/7, NEK9 phosphorylates NEDD1/GCP-WD at Ser377 to recruit gamma-tubulin and mature the centrosome [#8]. Signal flux through the cascade is gated by the dynein light chain DYNLL/LC8, which binds a motif near the NEK9 coiled-coil to promote multimerization while competing with Nek6 binding, a interaction abolished by NEK9 autophosphorylation at Ser944 [#7, #10]. Beyond mitosis, NEK9 acts as a selective autophagy adaptor that targets MYH9 (myosin IIA) for degradation via its LIR motif to enable primary ciliogenesis [#17], promotes CHK1 activity during replication stress [#11], and phosphorylates substrates including ARHGEF2 to activate RhoA and Raptor at Ser792 to inhibit mTORC1 [#19, #21]. Activating mutations in the kinase and RCC1 domains, which elevate Thr210 phosphorylation, cause the cutaneous disorder nevus comedonicus by disrupting follicular differentiation [#14].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Establishing NEK9 as a Ran-binding, mitotically activated kinase defined its identity as a cytoplasmic cell-cycle kinase and first linked it to the Ran GTPase and Nek6.\",\n      \"evidence\": \"Co-IP, subcellular fractionation, and in vitro autoactivation assays in the founding paper\",\n      \"pmids\": [\"12101123\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of RanGDP binding not resolved\", \"No downstream substrates yet identified\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Identifying Nek6/Nek7 as direct activation-loop substrates established NEK9 as the apex of a mitotic NIMA-family kinase cascade required for spindle integrity.\",\n      \"evidence\": \"In vitro kinase assays with recombinant proteins, phosphosite mapping (Ser206), and antibody microinjection\",\n      \"pmids\": [\"12840024\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of substrate recognition unknown at this stage\", \"Upstream activator of NEK9 itself not yet defined\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Discovery of a stable NEK9-FACT complex extended NEK9 function beyond mitosis into interphase G1/S progression.\",\n      \"evidence\": \"Co-IP of ~600 kDa complex with Spt16-Pob3 and RNAi cell-cycle analysis\",\n      \"pmids\": [\"14660563\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"FACT substrate/phosphorylation target within complex not defined\", \"Single lab, no reciprocal validation\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Localizing active NEK9 to centrosomes and showing rescue of spindle defects established a direct role in spindle assembly and gamma-TuRC association.\",\n      \"evidence\": \"Immunodepletion from Xenopus egg extracts with recombinant rescue and gamma-tubulin co-IP\",\n      \"pmids\": [\"16079175\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct gamma-TuRC substrate not yet identified\", \"Mechanism of centrosomal targeting unresolved\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"The Nek7 autoinhibited structure and the role of the NEK9 CTD in releasing Tyr97 revealed the molecular mechanism of downstream kinase activation.\",\n      \"evidence\": \"X-ray crystallography of Nek7 plus Tyr-to-Phe mutagenesis and activity assays\",\n      \"pmids\": [\"19941817\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Exact stoichiometry and dimerization geometry not resolved here\", \"How CTD engagement is regulated in cells unclear\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Defining sequential CDK1-then-Plk1 activation of NEK9 and the NEK9-Nek6/7-Eg5 axis placed the cascade in the prophase centrosome-separation program.\",\n      \"evidence\": \"In vitro kinase reconstitution, phosphosite mapping (Eg5 Ser1033), siRNA epistasis, and live imaging\",\n      \"pmids\": [\"21642957\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Spatiotemporal coordination of the two upstream kinases not fully mapped\", \"Other Nek6/7 mitotic substrates unaccounted for\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Showing LC8/DYNLL binding promotes multimerization yet competes with Nek6 revealed an autophosphorylation-gated switch controlling cascade output.\",\n      \"evidence\": \"Reciprocal co-IP, motif mutagenesis, and in vitro kinase assays defining Ser944 regulation\",\n      \"pmids\": [\"21454704\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cellular trigger for Ser944 autophosphorylation timing unknown\", \"Whether LC8 links NEK9 to dynein-based transport untested\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identifying NEDD1 Ser377 as a direct NEK9 substrate explained how NEK9 drives gamma-tubulin recruitment independently of Nek6/7.\",\n      \"evidence\": \"In vitro kinase assay, phosphosite mutagenesis, and validation in Xenopus and mammalian cells\",\n      \"pmids\": [\"22818914\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Branch-point logic separating NEDD1 from Nek6/7 arms not fully defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Oocyte meiosis phenotypes confirmed NEK9 requirement for spindle organization, chromosome alignment, and checkpoint silencing in a physiological division.\",\n      \"evidence\": \"Morpholino knockdown in mouse oocytes with confocal imaging and checkpoint marker analysis\",\n      \"pmids\": [\"23159858\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct meiotic substrates not identified\", \"Single knockdown approach\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Structures of LC8 bound to phospho- and unphospho-Nek9 peptides established the atomic basis for Ser944-dependent affinity regulation of the cascade switch.\",\n      \"evidence\": \"X-ray crystallography of two peptide states plus ITC\",\n      \"pmids\": [\"23482567\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In-cell kinetics of the switch not measured\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Linking NEK9 to CHK1 activity defined a role in the replication stress response distinct from its mitotic functions.\",\n      \"evidence\": \"Co-IP, kinase activity assays, RNAi synthetic-lethal screen, and gemcitabine sensitivity\",\n      \"pmids\": [\"25217585\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether NEK9 directly phosphorylates CHK1 not established\", \"Single lab\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"The Nek7(Y97F)-Nek9 peptide structure showing back-to-back dimerization completed the mechanistic model for how the NEK9 CTD activates downstream kinases.\",\n      \"evidence\": \"X-ray crystallography, binding-domain mapping (Nek9 810-828), and structure-function mutagenesis\",\n      \"pmids\": [\"26522158\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Dynamics of dimer assembly in vivo not visualized\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identifying NEK9 as a viral-recruited transcriptional repressor at GADD45A revealed an unexpected chromatin-associated, infection-dependent activity.\",\n      \"evidence\": \"siRNA knockdown, ChIP, colocalization with viral E4 orf3, and replication assays\",\n      \"pmids\": [\"26676776\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of promoter recruitment unknown\", \"Relevance outside viral infection unclear\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Discovering activating somatic NEK9 mutations in nevus comedonicus established a direct disease link and showed NEK9 kinase activity regulates follicular differentiation.\",\n      \"evidence\": \"Whole-exome sequencing with pThr210 Western blot and differentiation-marker immunofluorescence\",\n      \"pmids\": [\"27153399\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream effectors in keratinocyte differentiation not identified\", \"Single study\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Showing NEK9 phosphorylates the TPX2 NLS to block importin binding explained how a centrosomal TPX2 pool is maintained for prophase aster organization.\",\n      \"evidence\": \"In vitro kinase assay, importin-binding assay, siRNA epistasis with RHAMM/HMMR, and live imaging\",\n      \"pmids\": [\"29276125\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Coordination with the Eg5 and NEDD1 arms not unified mechanistically\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Demonstrating EML4-ALK V3 recruitment of NEK9/NEK7 to microtubules implicated the cascade in oncogenic cell migration independent of ALK catalytic activity.\",\n      \"evidence\": \"Co-IP, constitutively-active mutants, siRNA epistasis, and live imaging\",\n      \"pmids\": [\"32184261\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Microtubule substrate of NEK9/NEK7 in this context not defined here\", \"Single lab\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identifying NEK9 as a LIR-motif selective autophagy adaptor for MYH9 required for ciliogenesis revealed a non-mitotic degradative function validated in vivo.\",\n      \"evidence\": \"Co-IP, LIR mutagenesis, mouse knock-in, and MYH9-depletion rescue of ciliogenesis\",\n      \"pmids\": [\"34078910\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How NEK9 selects MYH9 cargo signal is unresolved\", \"Relationship between kinase activity and adaptor function unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defining ARHGEF2 as a direct NEK9 substrate connected the kinase to RhoA activation and cancer cell motility.\",\n      \"evidence\": \"In vitro kinase assay, phosphoproteomics, GST pull-down, and migration assays\",\n      \"pmids\": [\"33500736\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"ARHGEF2 phosphosite not specified\", \"Single lab cancer model\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Linking NEK9 to PRLR-SF and Hippo/TEAD signaling extended its reach to metabolic gene regulation in pancreatic cancer.\",\n      \"evidence\": \"Co-IP, PLA, ChIP, and promoter luciferase assays\",\n      \"pmids\": [\"33664869\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the effect requires NEK9 kinase activity not established\", \"Single lab\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Mapping a NEK9-ROBO1 interaction and TRIM28/cortactin substrates placed NEK9 in SLIT2-ROBO1 signaling and transcriptional regulation of CTTN.\",\n      \"evidence\": \"Mass spectrometry, co-IP, in vitro kinase assay, and domain-deletion analysis\",\n      \"pmids\": [\"37443302\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Phosphosites on TRIM28/cortactin not defined here\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identifying USP19-mediated stabilization and NEK9 phosphorylation of Raptor Ser792 connected NEK9 abundance to mTORC1 inhibition and autophagic cell death.\",\n      \"evidence\": \"Co-IP, in vitro deubiquitylation and kinase assays defining Lys525 ubiquitination and Ser792 phosphorylation\",\n      \"pmids\": [\"39627360\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological signals controlling the USP19-NEK9 axis unclear\", \"Single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showing NEK7 phosphorylates cortactin in its actin-binding region links the NEK9/NEK7 cascade to actin-driven filopodia and migration.\",\n      \"evidence\": \"In vitro kinase assay with phospho-mimetic/null mutagenesis and live imaging (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.08.30.672807\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not yet peer-reviewed\", \"In vivo relevance of cortactin phosphorylation untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How NEK9 selects between its many distinct functional outputs—mitotic cascade, autophagy adaptor, replication stress, mTORC1, and cancer signaling—within a single cell remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unifying model for context-dependent substrate selection\", \"Relationship between kinase-dependent and adaptor functions not integrated\", \"Whether non-mitotic substrates require the same activation hierarchy unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 6, 8, 15, 19, 21]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [1, 8, 15]},\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [17]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [13]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [3, 9, 15]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2, 4]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [16]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [1, 3, 6, 8, 15]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [17, 21]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [19, 20, 21]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [11]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [17]}\n    ],\n    \"complexes\": [\"FACT (Spt16-Pob3)\", \"gamma-tubulin ring complex (associated)\"],\n    \"partners\": [\"NEK6\", \"NEK7\", \"DYNLL1\", \"PLK1\", \"RAN\", \"TPX2\", \"MYH9\", \"USP19\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":8,"faith_pct":87.5}}