Aberrant overexpression of transcription factor Forkhead box D1 predicts poor prognosis and promotes cancer progression in HNSCC.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34772357", "kind": "science-record", "revision": 5, "content_hash": "sha256:9a10aee09adce3b57733ab02357bbb3b25cf7af28fc83ec6bb3bd026f9b081ad", "created_at": "2026-11-01T17:36:28Z", "updated_at": "2026-11-01T22:47:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Aberrant overexpression of transcription factor Forkhead box D1 predicts poor prognosis and promotes cancer progression in HNSCC.", "doi": "10.1186/s12885-021-08868-4", "pmid": "34772357", "authors": ["Jin Li", "Tingyuan Yan", "Xiang Wu", "Xueping Ke", "Xin Li", "Yumin Zhu", "Jianrong Yang", "Zhongwu Li"], "journal": "BMC cancer", "year": 2021, "abstract": "OBJECTIVES: Forkhead box D1, the core transcription factor member of FOX family, has gradually seen as a key cancerous regulatory. However, its expression and carcinogenicity in head and neck squamous cell carcinoma (HNSCC) have not been reported yet. This study was to investigate its expression pattern, clinicopathological significance and biological roles in HNSCC.\nMETHODS: HNSCC data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) was used to indicate the detailed expression pattern and outcome association of FOXD1, while Western Blot assay to detect FOXD1 level in a panel of HNSCC cell lines as well as immunocytochemistry to explore FOXD1 protein abundance and sublocation. Series of siRNA-mediated FOXD1 knock-down experiments to assess the proliferation, migration, invasion and anti- apoptosis ability after FOXD1 down-regulation. Bioinformatic analysis to find out which biological function and cancer-related pathways of FOXD1 associated genes involved in.\nRESULTS: FOXD1 mRNA was significantly overexpressed in TCGA-HNSCC, GSE6631, GSE12452, GSE25099 and GSE30784. Besides, IHC results shown that nuclear location FOXD1 protein was significantly higher in primary HNSCC specimens from cohort involved in this study. Also, FOXD1 abundance was significantly correlated with cervical node metastasis and poor over-all/disease-free survival after combination analysis with patient pathological information. siRNA-mediated FOXD1 knock-down significantly inhibited cell proliferation, migration and invasion and induced apoptosis in HNSCC cells. Further analysis of GSEA, GO and KEGG showed that FOXD1 expression was significantly associated with oncological function and cancer-related pathways.\nCONCLUSIONS: Taken together, our study implies that the potential oncogene, FOXD1, facilitates oncological behavior who can be identified as a brand-new HNSCC biomarker with diagnostic and prognostic significance.", "claims": [{"id": "claim-method", "statement": "Normally distributed data were analyzed using an unpaired Student’s t test (two-tailed); multiple comparisons used nonparametric one-way ANOVA. Median cutoff and Log-rank (Mantel-Cox) test was used for survival Kapler-Merier plot.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34772357", "locator": "sections[11] \"Statistical analyses\" paragraph 2", "quote": "Normally distributed data were analyzed using an unpaired Student’s t test (two-tailed); multiple comparisons used nonparametric one-way ANOVA. Median cutoff and Log-rank (Mantel-Cox) test was used for survival Kapler-Merier plot."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset used during the present study is available from the corresponding author upon a reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34772357", "locator": "sections[26] \"notes\" paragraph 1", "quote": "The dataset used during the present study is available from the corresponding author upon a reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Further, as the Kaplan-Meier plots shown, patients with high FOXD1 abundance had obviously shorter overall-survival and disease-free survival than patients with low FOXD1 abundance (Log-rank, P = 0.0014, 0.0025, Figure3 A, B).", "kind": "quantitative", "target": {"value": 0.0014, "unit": "p-value", "tolerance": null, "source": "Further, as the Kaplan-Meier plots shown, patients with high FOXD1 abundance had obviously shorter overall-survival and disease-free survival than patients with low FOXD1 abundance (Log-rank, P = 0.0014, 0.0025, Figure3 A, B)."}, "evidence": [{"asset": "source:pmid:34772357", "locator": "sections[15] \"Aberrant overexpression of FOXD1 in HNSCC patients associated with poor outcome\" paragraph 2", "quote": "Further, as the Kaplan-Meier plots shown, patients with high FOXD1 abundance had obviously shorter overall-survival and disease-free survival than patients with low FOXD1 abundance (Log-rank, P = 0.0014, 0.0025, Figure3 A, B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Further, as the Kaplan-Meier plots shown, patients with high FOXD1 abundance had obviously shorter overall-survival and disease-free survival than patients with low FOXD1 abundance (Log-rank, P = 0.0014, 0.0025, Figure3 A, B).", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:34772357"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE12452"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE12452"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34772357", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-021-08868-4", "sha256": "sha256:25a9c3abc7e4c42e3780bb12fed70877a46e8f035be11aaa255feab7505cc921", "bytes": 31467, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12885-021-08868-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8588630", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12452", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12452", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12452", "version": null, "note": "The dataset used during the present study is available from the corresponding author upon a reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The dataset used during the present study is available from the corresponding author upon a reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM312896", "GSM312897", "GSM312898", "GSM312899", "GSM312900", "GSM312901", "GSM312902", "GSM312903", "GSM312904", "GSM312905", "GSM312906", "GSM312907", "GSM312908", "GSM312909", "GSM312910", "GSM312911", "GSM312912", "GSM312913", "GSM312914", "GSM312915", "GSM312916", "GSM312917", "GSM312918", "GSM312919", "GSM312920", "GSM312921", "GSM312922", "GSM312923", "GSM312924", "GSM312925", "GSM312926", "GSM312927", "GSM312928", "GSM312929", "GSM312930", "GSM312931", "GSM312932", "GSM312933", "GSM312934", "GSM312935", "GSM312936"], "sample_count": 41, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "mRNA expression profiling of nasopharyngeal carcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE25099", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25099", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25099", "version": null, "note": "The dataset used during the present study is available from the corresponding author upon a reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The dataset used during the present study is available from the corresponding author upon a reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM616583", "GSM616584", "GSM616585", "GSM616586", "GSM616587", "GSM616588", "GSM616589", "GSM616590", "GSM616591", "GSM616592", "GSM616593", "GSM616594", "GSM616595", "GSM616596", "GSM616597", "GSM616598", "GSM616599", "GSM616600", "GSM616601", "GSM616602", "GSM616603", "GSM616604", "GSM616605", "GSM616606", "GSM616607", "GSM616608", "GSM616609", "GSM616610", "GSM616611", "GSM616612", "GSM616613", "GSM616614", "GSM616615", "GSM616616", "GSM616617", "GSM616618", "GSM616619", "GSM616620", "GSM616621", "GSM616622", "GSM616623", "GSM616624", "GSM616625", "GSM616626", "GSM616627", "GSM616628", "GSM616629", "GSM616630", "GSM616631", "GSM616632", "GSM616633", "GSM616634", "GSM616635", "GSM616636", "GSM616637", "GSM616638", "GSM616639", "GSM616640", "GSM616641", "GSM616642", "GSM616643", "GSM616644", "GSM616645", "GSM616646", "GSM616647", "GSM616648", "GSM616649", "GSM616650", "GSM616651", "GSM616652", "GSM616653", "GSM616654", "GSM616655", "GSM616656", "GSM616657", "GSM616658", "GSM616659", "GSM616660", "GSM616661"], "sample_count": 79, "group_sizes": null, "group_sizes_basis": null, "platform": "5175", "taxon": "Homo sapiens", "title": "Expression data from 57 patients with oral cancer and 22 normal persons", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE30784", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30784", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30784", "version": null, "note": "The dataset used during the present study is available from the corresponding author upon a reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The dataset used during the present study is available from the corresponding author upon a reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM764749", "GSM764750", "GSM764751", "GSM764752", "GSM764753", "GSM764754", "GSM764755", "GSM764756", "GSM764757", "GSM764758", "GSM764759", "GSM764760", "GSM764761", "GSM764762", "GSM764763", "GSM764764", "GSM764765", "GSM764766", "GSM764767", "GSM764768", "GSM764769", "GSM764770", "GSM764771", "GSM764772", "GSM764773", "GSM764774", "GSM764775", "GSM764776", "GSM764777", "GSM764778", "GSM764779", "GSM764780", "GSM764781", "GSM764782", "GSM764783", "GSM764784", "GSM764785", "GSM764786", "GSM764787", "GSM764788", "GSM764789", "GSM764790", "GSM764791", "GSM764792", "GSM764793", "GSM764794", "GSM764795", "GSM764796", "GSM764797", "GSM764798", "GSM764799", "GSM764800", "GSM764801", "GSM764802", "GSM764803", "GSM764804", "GSM764805", "GSM764806", "GSM764807", "GSM764808", "GSM764809", "GSM764810", "GSM764811", "GSM764812", "GSM764813", "GSM764814", "GSM764815", "GSM764816", "GSM764817", "GSM764818", "GSM764819", "GSM764820", "GSM764821", "GSM764822", "GSM764823", "GSM764824", "GSM764825", "GSM764826", "GSM764827", "GSM764828", "GSM764829", "GSM764830", "GSM764831", "GSM764832", "GSM764833", "GSM764834", "GSM764835", "GSM764836", "GSM764837", "GSM764838", "GSM764839", "GSM764840", "GSM764841", "GSM764842", "GSM764843", "GSM764844", "GSM764845", "GSM764846", "GSM764847", "GSM764848", "GSM764849", "GSM764850", "GSM764851", "GSM764852", "GSM764853", "GSM764854", "GSM764855", "GSM764856", "GSM764857", "GSM764858", "GSM764859", "GSM764860", "GSM764861", "GSM764862", "GSM764863", "GSM764864", "GSM764865", "GSM764866", "GSM764867", "GSM764868", "GSM764869", "GSM764870", "GSM764871", "GSM764872", "GSM764873", "GSM764874", "GSM764875", "GSM764876", "GSM764877", "GSM764878", "GSM764879", "GSM764880", "GSM764881", "GSM764882", "GSM764883", "GSM764884", "GSM764885", "GSM764886", "GSM764887", "GSM764888", "GSM764889", "GSM764890", "GSM764891", "GSM764892", "GSM764893", "GSM764894", "GSM764895", "GSM764896", "GSM764897", "GSM764898", "GSM764899", "GSM764900", "GSM764901", "GSM764902", "GSM764903", "GSM764904", "GSM764905", "GSM764906", "GSM764907", "GSM764908", "GSM764909", "GSM764910", "GSM764911", "GSM764912", "GSM764913", "GSM764914", "GSM764915", "GSM764916", "GSM764917", "GSM764918", "GSM764919", "GSM764920", "GSM764921", "GSM764922", "GSM764923", "GSM764924", "GSM764925", "GSM764926", "GSM764927", "GSM764928", "GSM764929", "GSM764930", "GSM764931", "GSM764932", "GSM764933", "GSM764934", "GSM764935", "GSM764936", "GSM764937", "GSM764938", "GSM764939", "GSM764940", "GSM764941", "GSM764942", "GSM764943", "GSM764944", "GSM764945", "GSM764946", "GSM764947", "GSM764948", "GSM764949", "GSM764950", "GSM764951", "GSM764952", "GSM764953", "GSM764954", "GSM764955", "GSM764956", "GSM764957", "GSM764958", "GSM764959", "GSM764960", "GSM764961", "GSM764962", "GSM764963", "GSM764964", "GSM764965", "GSM764966", "GSM764967", "GSM764968", "GSM764969", "GSM764970", "GSM764971", "GSM764972", "GSM764973", "GSM764974", "GSM764975", "GSM764976", "GSM764977"], "sample_count": 229, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiling of oral squamous cell carcinoma (OSCC)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE6631", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6631", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6631", "version": null, "note": "The dataset used during the present study is available from the corresponding author upon a reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The dataset used during the present study is available from the corresponding author upon a reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM153813", "GSM153814", "GSM153815", "GSM153816", "GSM153817", "GSM153818", "GSM153819", "GSM153820", "GSM153821", "GSM153822", "GSM153823", "GSM153824", "GSM153825", "GSM153826", "GSM153827", "GSM153828", "GSM153829", "GSM153830", "GSM153831", "GSM153832", "GSM153833", "GSM153834", "GSM153835", "GSM153836", "GSM153837", "GSM153838", "GSM153839", "GSM153840", "GSM153841", "GSM153842", "GSM153843", "GSM153844", "GSM153845", "GSM153846", "GSM153847", "GSM153848", "GSM153849", "GSM153850", "GSM153851", "GSM153852", "GSM153853", "GSM153854", "GSM153855", "GSM153856"], "sample_count": 44, "group_sizes": null, "group_sizes_basis": null, "platform": "8300", "taxon": "Homo sapiens", "title": "Expression data from head and neck squamous cell carcinoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE12452 not downloaded", "asset:data:geo:GSE12452 licence not read", "asset:data:geo:GSE25099 not downloaded", "asset:data:geo:GSE25099 licence not read", "asset:data:geo:GSE30784 not downloaded", "asset:data:geo:GSE30784 licence not read", "asset:data:geo:GSE6631 not downloaded", "asset:data:geo:GSE6631 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Normally distributed data were analyzed using an unpaired Student’s t test (two-tailed); multiple comparisons used nonparametric one-way ANOVA. Median cutoff and Log-rank (Mantel-Cox) test was used for survival Kapler-Merier plot."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "cox proportional hazards"}}, {"id": "method-4", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Log-rank"}}, {"id": "method-5", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-6", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi-square"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 0.0014, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE6631", "GSE12452", "GSE25099", "GSE30784"], "resolved_accessions": ["GSE6631", "GSE12452", "GSE25099", "GSE30784"], "statements": ["The dataset used during the present study is available from the corresponding author upon a reasonable request."], "basis": "The paper names GSE6631, GSE12452, GSE25099, GSE30784 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:34772357", "data:geo:GSE12452"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE12452"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:07:42Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9637, "completion_tokens": 2794, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:34772357", "type": "paper", "label": "pmid:34772357"}, {"id": "source:pmid:34772357", "type": "manuscript", "label": "PMID 34772357 full text"}, {"id": "data:geo:GSE12452", "type": "dataset", "label": "GEO GSE12452"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34772357", "type": "paper", "label": "pmid:34772357"}, {"id": "source:pmid:34772357", "type": "manuscript", "label": "PMID 34772357 full text"}, {"id": "data:geo:GSE12452", "type": "dataset", "label": "GEO GSE12452"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34772357", "type": "extraction", "used": ["source:pmid:34772357"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE12452", "type": "accession_resolution", "used": ["data:geo:GSE12452"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:34772357", "parent_hash": "sha256:cc1f3dd4d930286ea96281f65f255ffc167269d11ebe01b84b1773af30f54d26", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE12452 licence not read", "asset:data:geo:GSE12452 not downloaded", "asset:data:geo:GSE25099 licence not read", "asset:data:geo:GSE25099 not downloaded", "asset:data:geo:GSE30784 licence not read", "asset:data:geo:GSE30784 not downloaded", "asset:data:geo:GSE6631 licence not read", "asset:data:geo:GSE6631 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["tern and outcome association of FOXD1, while Western Blot assay to detect FOXD1 level in a panel of HN"], "order_basis": "paper_text_order:638", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["sublocation. Series of siRNA-mediated FOXD1 knock-down experiments to assess the proliferation, mig", "thological information. siRNA-mediated FOXD1 knock-down significantly inhibited cell proliferation,", "protein abundance and sublocation. Series of siRNA-mediated FOXD1 knock-down experiments to ass", "lysis with patient pathological information. siRNA-mediated FOXD1 knock-down significantly inhi"], "order_basis": "paper_text_order:803", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["proliferation, migration, invasion and anti- apoptosis ability after FOXD1 down-regulation. Bioinfo", "feration, migration and invasion and induced apoptosis in HNSCC cells. Further analysis of GSEA, GO", "(Fig. 6D), KEGG Focal adhesion (Fig. 6E) and Apoptosis (Fig. 6F). In conclusion, combined with cell"], "order_basis": "paper_text_order:906", "id": "assay:3"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["1, GSE12452, GSE25099 and GSE30784. Besides, IHC results shown that nuclear location FOXD1 pr", "s ClusterProfiler [13]. Clinical samples and immunohistochemical staining (IHC) This study protocol was appro", "attern in 110 patients with primary HNSCC by immunohistochemical staining. All clinical data of these patient", "al samples and immunohistochemical staining (IHC) This study protocol was approved by the Res"], "order_basis": "paper_text_order:1199", "id": "assay:4"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Normally distributed data were analyzed using an unpaired Student’s t test (two-tailed); multiple comparisons used nonparametric one-way ANOVA. Median cutoff and Log-rank (Mantel-Cox) test was used for survival Kapler-Merier plot."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}