This guide records the inspected source scope behind the annotation review. Genuine repository fetching has produced the FOXJ1 seed and all 18 qualified normal sources: six existing-main publications reused unchanged and twelve new source files. The reviewed annotations are applied to the genuine seed. Default validation and strict GOA matching passed; the computed status is DRAFT with one retained advisory about unrestricted versus cell-type-restricted epithelium-development contexts. Private rendering and local-link checks passed. Provider calls remain on the established credential hold; the evidence comes from the recorded manual primary-source research.
The genuine source capture preserves all 72 original human QuickGO objects, with 72 TSV records and 71 genuine seed records. Every exported column and seed machine field matches the approved private projection. The two ISS cilium-assembly observations at raw 55/56 differ only in source identity, assigned database and date; both remain in the source evidence, alongside the actual raw-to-TSV-to-stored joins and the separately retained original forecast. All raw, TSV data-row and stored indices are zero-based; TSV data-row positions are not file line numbers. The two original CL extensions are retained at raw 34 to stored 38 and raw 62 to stored 66.
The principal human activation source is study 23822649. Study 9096351 supplies mouse biochemical grounding. The four original binding rows name RFX2/P48378, whereas study 23822649 investigates RFX3; their evidence is kept separate.
Original study 9073514 · PubMed record
Original human raw contexts: 8, 10, 30, 34, 62.
Access and locators. Authentic indexed abstract: human cloning, genomic organization and tissue expression; original full text uninspected.
Interpretation and limits. Authentic PubMed metadata/abstract identifies human FKHL13 cloning, genomic organization and tissue expression. Original full text was not inspected; DNA-binding, spermatogenic and extended developmental claims are not newly verified.
Original study 9096351 · PubMed record
Original human raw contexts: 1, 35, 50, 59.
Access and locators. Original Methods: DNA-site selection, EMSA and reporter construction; Results and Figures 3–4 captions; developmental expression section. Mouse full-length 421-aa HFH-4 and GST 110–236 domain.
Interpretation and limits. Selected original Methods/Results/captions establish mouse 421-aa HFH-4 cDNA, purified GST 110–236 sequence recognition and reporter activation. Human HepG2 host and promoter fragments are not a human protein construct. Choroid-plexus expression is not a developmental perturbation.
Original study 9530170 · PubMed record
Original human raw contexts: 46, 60, 63.
Access and locators. Authentic indexed abstract: human cDNA, RNA blot and in-situ expression. Original developmental figures/Methods uninspected.
Interpretation and limits. Authentic abstract identifies human 421-aa FOXJ1 cloning and developmental pulmonary/renal RNA expression. Full Methods/Results and exact renal images remain uninspected; no loss-of-function or direct developmental mechanism is inferred from IEP.
Original study 14963332 · PubMed record
Auxiliary source: independent human functional evidence or original mouse donor provenance; no original human citation is replaced.
Access and locators. Authentic PubMed abstract only. Original full text/PDF inaccessible after bounded access attempts; exact Methods and constructs unresolved.
Interpretation and limits. Authentic abstract reports deficiency-associated T-cell proliferation and inflammatory/NF-kappaB phenotypes; original full/PDF remained inaccessible. Exact Methods, cell autonomy and construct identities are unresolved. The positive report and matched mouse IMP are retained without an exhaustive negative conclusion.
Original study 16002694 · PubMed record
Auxiliary source: independent human functional evidence or original mouse donor provenance; no original human citation is replaced.
Access and locators. Original publisher PDF selected Materials and Methods, B-cell intrinsic Results, NF-kappaB/IL6 Results, Figures 5–6 captions and Discussion. No figure pixels or full supplementary inspection.
Interpretation and limits. Selected original publisher PDF Methods/Results/Figures 5–6 captions/Discussion support mouse B-cell intrinsic immune-response restraint, I-kappaB-beta/NF-kappaB and IL6 effects. The authors distinguish amplification of existing responses from breaking B-cell tolerance. These experiments do not establish central B-cell tolerance or the NIK/p100 non-canonical branch, nor human direct immune assays. The repository publication cache remains abstract-only, but selected original publisher full-text sections were accessible and read; therefore the review does not mark the full text as unavailable. The cached source bytes are unchanged.
Original study 16339515 · PubMed record
Auxiliary source: independent human functional evidence or original mouse donor provenance; no original human citation is replaced.
Access and locators. Authentic PubMed/publisher abstract only. Full original Methods/Results inaccessible.
Interpretation and limits. Authentic abstract only: CD2-Foxj1 lupus-prone mice, reduced disease and peripheral T cells, mature thymocyte retention and impaired exit. Full original Methods/Results were inaccessible. Central tolerance and differentiation cannot be equated automatically with egress.
Original study 17008636 · PubMed record
Original human raw contexts: 71.
Access and locators. Authentic abstract: human airway ALI/xenograft differentiation with TFF3. Exact nuclear imaging remains uninspected.
Interpretation and limits. Authentic abstract reports TFF3-mediated human airway differentiation and FOXJ1-positive cells. Exact nuclear-localization imaging and construct details were not inspected. Independent nuclear function supports the gene-level location, without retroactive source verification.
Original study 17488776 · PubMed record
Auxiliary source: independent human functional evidence or original mouse donor provenance; no original human citation is replaced.
Access and locators. Original Results: A role for Foxj1 in RhoA-mediated ciliogenesis, Figure 5 caption; Discussion on Foxj1/RhoA; Methods Cell culture, GTPase activation assays and Adenovirus vector transfection. No pixels/SI inspected.
Interpretation and limits. Selected original publisher Results/Methods/Discussion/captions support mouse Foxj1-null mTEC apical actin and docking defects plus AdFoxj1-associated RhoA/B activation. The mechanistic route is unresolved; no FOXJ1 actin-binding or GEF activity is inferred. Exact adenoviral coding sequence is deferred in the paper to an earlier source, so host species does not identify the construct. The repository publication cache remains abstract-only, but selected original publisher full-text sections were accessible and read; therefore the review does not mark the full text as unavailable. The cached source bytes are unchanged.
Original study 20539013 · PubMed record
Original human raw contexts: 66.
Access and locators. Original Methods and Results through the start of Figure 6: 1008-bp human FOXJ1 promoter EGFP/Cre tracing and IL13 intervention. Later Results and supplementary material unread; successful extraction was displayed but not retained locally.
Interpretation and limits. Selected original Methods/Results through the start of Figure 6 were displayed and read in a separate consultation. A 1008-bp human FOXJ1 promoter drives EGFP/Cre lineage reporters and IL13 is the intervention; these are distinct from FOXJ1 protein perturbation. Later Results/SI were not read, and the successful extraction was not retained locally. Independent human functional sources support the gene-level differentiation role.
Original study 23822649 · PubMed record
Auxiliary source: independent human functional evidence or original mouse donor provenance; no original human citation is replaced.
Access and locators. Original Methods: Gene transfer to primary human airway basal cells; FOXJ1–RFX3 interaction. Results: Effect of FOXJ1 gene transfer; Role of RFX3; coactivator section and interaction; Figures 3,5,6 captions.
Interpretation and limits. Selected original publisher Methods/Results and captions explicitly use human FOXJ1/RFX3 cDNAs in primary human basal cells for ciliary-gene RNA and promoter activation. RFX3 co-immunoprecipitation in 293A permits indirect complex recovery and does not verify the original RFX2 partner. No endogenous occupancy at every promoter or complete mature multiciliation from transfer alone is asserted.
Original study 25609649 · PubMed record
Original human raw contexts: 11.
Access and locators. Original Materials and Methods: Constructs and small hairpin RNAs; Cell culture, treatments and transfection; TAP of TF-associated protein complexes and MS analysis. Original pair-specific supplementary table not inspected.
Interpretation and limits. Selected original Methods in the exact-main cache support tagged human FOX constructs and soluble/chromatin fraction TAP-MS. The precise FOXJ1–RFX2 original supplementary pair remains unrecovered; current query absence does not refute it. Exact same-pair HuRI and later AP-MS data independently support partner-class refinement.
Original study 28514442 · PubMed record
Original human raw contexts: 12.
Access and locators. Original Online Experimental Methods: Clone Construction and Cell Culture; Affinity-Purification Mass Spectrometry; Identification of Interacting Proteins. Exact IntAct IM-25778-7145 refers to Supplementary Table 1, which was not independently opened.
Interpretation and limits. Selected original Methods and exact curated IntAct pair record support tagged human FOXJ1 bait/RFX2 prey AP-MS association in HEK293T. Original Supplementary Table1 was not independently opened. No purified direct interface, transcriptional direction or ciliary coregulator mechanism is claimed.
Original study 31630787 · PubMed record
Original human raw contexts: 31, 36, 39, 44, 58.
Access and locators. Original genetic/transcript Results; respiratory-cell HVMA, ALI and spheroid assays; Figures 3–5 captions, TEM and immunofluorescence Results.
Interpretation and limits. Selected original human genetic/transcript and respiratory-cell Methods/Results/captions support FOXJ1-associated motile ciliopathy, impaired differentiation/flow, basal-body positioning and PTK2 localization phenotypes. No universal ultrastructural defect or direct structural/docking activity is inferred.
Original study 32296183 · PubMed record
Original human raw contexts: 13.
Access and locators. Original Results: Generation and characterization of HuRI; selected Discussion. Exact IntAct IM-25472-973, IM-25472-26001 and IM-25472-111784 refer to Supplementary Table 9; original workbook/full Methods not separately inspected.
Interpretation and limits. Selected original Results/discussion and three exact curated human RFX2–FOXJ1 Y2H records support the pair. Source-specific fusion/assay configurations are retained; no purified affinity or exact-pair MAPPIT/GPCA validation is claimed. Complete Methods and the original Table9 workbook were not separately read.
Original study 33961781 · PubMed record
Original human raw contexts: 14.
Access and locators. Authentic abstract and selected Introduction/Discussion plus exact IntAct IM-29278-7879 and IM-29278-22269. Retained cache lacks Methods/Results despite its metadata full-text flag.
Interpretation and limits. Authentic abstract/selected introduction and discussion plus exact IntAct pair records support FOXJ1–RFX2 associations in HEK293T and HCT116. The cache full-text flag does not mean its extraction contains Methods/Results; these were not read. Cellular AP-MS associations remain distinct from binary HuRI evidence.
Official reviewed human protein identifies FOXJ1/Q92949 as a 421-aa protein. The retained complete response contains no alternative-product comments or VAR_SEQ records. Historical mouse full-length protein and purified fragments are not assigned to invented human natural products. Direct UniProt REST endpoints failed during intake; the successful official EBI response is identified separately. Current official UniProt JSON and text were later retrieved during genuine acquisition and match the same 421-aa human sequence.
The official PANTHER19 family download supplies the actual tree and MSA used with the official AN/PTN mapping. Human AN11/PTN002483655 has an exact 421-aa match in the retained tree.mia ancestral-and-leaf alignment, the separate cluster.pir leaf alignment, cluster.fasta, and the current official EBI sequence. All four original IBA nodes are AN1/PTN002929598 on its actual lineage, with original literal rows and donors from the official PAINT IBD GAF preserved. The retained GAF was fetched on 2026-10-28 and reports a 2026-08-28 modification date. Human self-donor evidence is valid descendant grounding.
These are explicitly dated PANTHER19 downloads; the current service endpoints returned 403. An off-target spotted-gar W5MLL2 alignment/FASTA discrepancy is recorded in the evidence without altering either source. It does not affect the exact human sequence or node joins, and no biological action is inferred merely from a sequence match.
The original two cell-type extensions are occurs_in CL:0000706, choroid plexus epithelial cell, on raw 34 and 62. They are separate singleton conjunctive groups, not an OR expression. Choroid-plexus epithelium is not silently replaced by another ependymal/ciliated-cell population.
The proposal separates a source-access limitation from a mechanistic gap. Original spermatogenic/renal developmental assays, exact central-tolerance and thymic differentiation evidence, and the specific choroid-plexus developmental conjunction remain unresolved where the available sources do not settle them. The B-cell study supports peripheral immune restraint but explicitly cautions about tolerance; its RELA/I-kappaB-beta data also do not identify the NIK/p100 non-canonical branch.
The mechanistic questions and proportionate experiments remain the ones in the proposed synthesis: endogenous human ciliary targets and stage transitions; RFX2 versus RFX3 complexes; human immune-cell conservation with branch-specific signaling measurements; and causal choroid-plexus epithelial maturation. No new process annotation is manufactured from necessity or expression alone.
Genuine acquisition now covers all 18 normal paths: 15 publication sources and three PTHR46805 family files. Six existing-main publications were reused unchanged; twelve qualified absent paths were acquired through the repository workflow. All 72 original contexts and 72 exported rows match the approved source capture, and the untouched genuine seed contains 71 records. Both originals at raw55/56 and both CL extensions are preserved in the evidence. The reviewed annotations, validation and private rendering are complete for this local candidate; the retained advisory and source-specific uncertainties are recorded in the notes. Provider calls remain on the established credential hold; manual primary research supplies the evidence.
The native PANTHER workflow produced four node-level assertions from 55 resolved nodes. Each assertion matches the retained literal IBD fields after the native writer sorts donor identifiers; the original literal donor order remains archived. The genuine InterPro entries file lists ten members including the exact human Q92949 record. These new source files are distinct from the dated 28-leaf PANTHER19 tree/MSA used for the target-path proof. The existing global PAINT cache was reused byte for byte.
Normal-cache availability and the selected original reading scope are separate. The following cache flags describe the acquired files; the source-specific sections above remain the record of what was actually inspected.
| PMID | Normal cache full-text flag |
|---|---|
| 9073514 | false |
| 9096351 | true |
| 9530170 | false |
| 14963332 | false |
| 16002694 | false |
| 16339515 | false |
| 17008636 | false |
| 17488776 | false |
| 20539013 | false |
| 23822649 | true |
| 25609649 | true |
| 28514442 | true |
| 31630787 | true |
| 32296183 | true |
| 33961781 | true |
The single nuclear activator core also represents the existing accepted motile-cilium assembly and positive regulation of lung ciliated-cell differentiation terms. The first names organelle formation; the second names promotion of a lung epithelial cell fate. They are not an is_a ancestor/descendant pair. Human ciliary-gene induction and promoter activation in study 23822649 and patient respiratory-cell ciliogenesis/differentiation defects in study 31630787 jointly support these scopes. The original study 20539013 remains a partially inspected promoter-lineage-tracing source; it is not retroactively described as a FOXJ1 coding perturbation.
The brain-development judgments remain unresolved because choroid-plexus expression and hydrocephalus do not settle a primary developmental role in the original cell-type context. The clinical left/right randomization is itself a developmental patterning outcome; its non-core judgment retains the limits of the human respiratory-cell assays. Both raw 55/56 source observations have the same explicit TOO_GENERAL judgment in the evidence and join one stored annotation.