Identification and validation of diagnostic signature genes in non-obstructive azoospermia by machine learning.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37227814", "kind": "science-record", "revision": 4, "content_hash": "sha256:baa5a4e4f9c43992ef11f3f6a93b00ee3454668da38182865d860fce1a053c70", "created_at": "2026-11-01T19:01:56Z", "updated_at": "2026-11-01T22:51:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of diagnostic signature genes in non-obstructive azoospermia by machine learning.", "doi": "10.18632/aging.204749", "pmid": "37227814", "authors": ["Lingxiang Ran", "Zhixiang Gao", "Qiu Chen", "Fengmei Cui", "Xiaolong Liu", "Boxin Xue"], "journal": "Aging", "year": 2023, "abstract": "Non-obstructive azoospermia (NOA) is a common cause of male infertility, and no specific diagnostic indicators exist. In this study, we used human testis datasets GSE45885, GSE45887, and GSE108886 from GEO database as training datasets, and screened 6 signature genes (all lowly expressed in the NOA group) using Boruta algorithm and Lasso regression: C12orf54, TSSK6, OR2H1, FER1L5, C9orf153, XKR3. The diagnostic efficacy of the above genes was examined by constructing models with LightGBM algorithm: the AUC (Area Under Curve) of both ROC and Precision-Recall curves for internal validation was 1.0 (p < 0.05). For the external validation dataset GSE145467 (human testis), the AUC of its ROC curve was 0.9 and that of its Precision-Recall curve was 0.833 (p < 0.05). Next, we confirmed the cellular localization of the above genes using human testis single-cell RNA sequencing dataset GSE149512, which were all located in spermatid. Besides, the downstream regulatory mechanisms of the above genes in spermatid were inferred by GSEA algorithm: C12orf54 may be involved in the repression of E2F-related and MYC-related pathways, TSSK6 and C9orf153 may be involved in the repression of MYC-related pathways, while FER1L5 may be involved in the repression of spermatogenesis pathway. Finally, we constructed a NOA model in mice using X-ray irradiation, and quantitative Real-time PCR results showed that C12orf54, TSSK6, OR2H1, FER1L5, and C9orf153 were all lowly expressed in NOA group. In summary, we have identified novel signature genes of NOA using machine learning methods and complete experimental validation, which will be helpful for its early diagnosis.", "claims": [{"id": "claim-method", "statement": "We used the above 6 signature genes to construct the LightGBM Model in the training dataset, and the results showed that the AUC (Area Under Curve) of both the ROC and Precision-Recall curves for internal validation was 1.0 (p < 0.05) (Figure 4A, 4B).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37227814", "locator": "sections[19] \"LightGBM model and model performance\" paragraph 2", "quote": "We used the above 6 signature genes to construct the LightGBM Model in the training dataset, and the results showed that the AUC (Area Under Curve) of both the ROC and Precision-Recall curves for internal validation was 1.0 (p < 0.05) (Figure 4A, 4B)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37227814", "locator": "sections[14] \"Data availability\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Both internal and external validation illustrated that these 6 genes perform well in diagnostic NOA.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "We used the above 6 signature genes to construct the LightGBM Model in the training dataset, and the results showed that the AUC (Area Under Curve) of both the ROC and Precision-Recall curves for internal validation was 1.0 (p < 0.05) (Figure 4A, 4B)."}, "evidence": [{"asset": "source:pmid:37227814", "locator": "sections[19] \"LightGBM model and model performance\" paragraph 2", "quote": "We used the above 6 signature genes to construct the LightGBM Model in the training dataset, and the results showed that the AUC (Area Under Curve) of both the ROC and Precision-Recall curves for internal validation was 1.0 (p < 0.05) (Figure 4A, 4B)."}, {"asset": "source:pmid:37227814", "locator": "sections[19] \"LightGBM model and model performance\" paragraph 2", "quote": "We then used these 6 genes to construct the LightGBM Model on the external validation dataset, and the results showed that the AUC of its ROC curve was 0.9 and that of its Precision-Recall curve was 0.833 (p < 0.05) (Figure 4C, 4D)."}, {"asset": "source:pmid:37227814", "locator": "sections[19] \"LightGBM model and model performance\" paragraph 2", "quote": "Both internal and external validation illustrated that these 6 genes perform well in diagnostic NOA."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Both internal and external validation illustrated that these 6 genes perform well in diagnostic NOA.", "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:37227814"], "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:GSE108886"], "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:GSE108886"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37227814", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.204749", "sha256": "sha256:39d9b186c55c30dc70b735f1123ada8f67a2dc48bd0470097c0930f6e0108f33", "bytes": 49956, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.204749", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10257997", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE108886", "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=GSE108886", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE108886", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2915444", "GSM2915445", "GSM2915446", "GSM2915447", "GSM2915448", "GSM2915449", "GSM2915450", "GSM2915451", "GSM2915452", "GSM2915453", "GSM2915454", "GSM2915455"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Spermatogenomics: correlating testicular gene expression to human male infertility", "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:GSE145467", "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=GSE145467", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE145467", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4318655", "GSM4318656", "GSM4318657", "GSM4318658", "GSM4318660", "GSM4318662", "GSM4318665", "GSM4318668", "GSM4318670", "GSM4318672", "GSM4318673", "GSM4318674", "GSM4318675", "GSM4318676", "GSM4318677", "GSM4318678", "GSM4318679", "GSM4318680", "GSM4318681", "GSM4318682"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "Transcriptome changes in patients with severely impaired spermatogenesis", "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:GSE149512", "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=GSE149512", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE149512", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4504181", "GSM4504182", "GSM4504183", "GSM4504184", "GSM4504185", "GSM4504186", "GSM4504187", "GSM4504188", "GSM4504189", "GSM4504190", "GSM4504191", "GSM4504192", "GSM4504193", "GSM4504194", "GSM4504195", "GSM4504196", "GSM4504197"], "sample_count": 17, "group_sizes": null, "group_sizes_basis": null, "platform": "24676;27644", "taxon": "Homo sapiens", "title": "Single-cell analysis of developing and azoospermia human testicles reveals central role of Sertoli cells", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE45885", "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=GSE45885", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45885", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1118241", "GSM1118242", "GSM1118243", "GSM1118244", "GSM1118245", "GSM1118246", "GSM1118247", "GSM1118248", "GSM1118249", "GSM1118250", "GSM1118251", "GSM1118252", "GSM1118253", "GSM1118254", "GSM1118255", "GSM1118256", "GSM1118257", "GSM1118258", "GSM1118259", "GSM1118260", "GSM1118261", "GSM1118262", "GSM1118263", "GSM1118264", "GSM1118265", "GSM1118266", "GSM1118267", "GSM1118268", "GSM1118269", "GSM1118270", "GSM1118271"], "sample_count": 31, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Potential biomarkers of non-obstructive azoospermia identified in microarray gene expression analysis", "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:GSE45887", "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=GSE45887", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45887", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1118281", "GSM1118282", "GSM1118283", "GSM1118284", "GSM1118285", "GSM1118286", "GSM1118287", "GSM1118288", "GSM1118289", "GSM1118290", "GSM1118291", "GSM1118292", "GSM1118293", "GSM1118294", "GSM1118295", "GSM1118296", "GSM1118297", "GSM1118298", "GSM1118299", "GSM1118300"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "The gene expression analysis of paracrine/autocrine factors in patients with spermatogenetic failure compared to normal spermatogenesis", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE108886 not downloaded", "asset:data:geo:GSE108886 licence not read", "asset:data:geo:GSE145467 not downloaded", "asset:data:geo:GSE145467 licence not read", "asset:data:geo:GSE149512 not downloaded", "asset:data:geo:GSE149512 licence not read", "asset:data:geo:GSE45885 not downloaded", "asset:data:geo:GSE45885 licence not read", "asset:data:geo:GSE45887 not downloaded", "asset:data:geo:GSE45887 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "machine_learning", "specific": "gradient_boosting", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We used the above 6 signature genes to construct the LightGBM Model in the training dataset, and the results showed that the AUC (Area Under Curve) of both the ROC and Precision-Recall curves for internal validation was 1.0 (p < 0.05) (Figure 4A, 4B)."}}, {"id": "method-2", "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-3", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "classification_metrics", "expected_value": 0.05, "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": ["method.reader_differs_from_extractor"]}, "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": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: gradient_boosting."}, "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": ["GSE45885", "GSE45887", "GSE108886", "GSE145467", "GSE149512"], "resolved_accessions": ["GSE45885", "GSE45887", "GSE108886", "GSE145467", "GSE149512"], "statements": ["The data used to support the findings of this study are available from the corresponding author upon request."], "basis": "The paper names GSE45885, GSE45887, GSE108886, GSE145467, GSE149512 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "assets": ["source:pmid:37227814", "data:geo:GSE108886"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE108886"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:41:29Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14548, "completion_tokens": 2028, "cached_tokens": 264}}, "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:37227814", "type": "paper", "label": "pmid:37227814"}, {"id": "source:pmid:37227814", "type": "manuscript", "label": "PMID 37227814 full text"}, {"id": "data:geo:GSE108886", "type": "dataset", "label": "GEO GSE108886"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37227814", "type": "paper", "label": "pmid:37227814"}, {"id": "source:pmid:37227814", "type": "manuscript", "label": "PMID 37227814 full text"}, {"id": "data:geo:GSE108886", "type": "dataset", "label": "GEO GSE108886"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37227814", "type": "extraction", "used": ["source:pmid:37227814"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE108886", "type": "accession_resolution", "used": ["data:geo:GSE108886"], "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:37227814", "parent_hash": "sha256:048e0c4e7242aba5d5091400e0962b209278bcdebb6a852a38fefe8702e813a9", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE108886 licence not read", "asset:data:geo:GSE108886 not downloaded", "asset:data:geo:GSE145467 licence not read", "asset:data:geo:GSE145467 not downloaded", "asset:data:geo:GSE149512 licence not read", "asset:data:geo:GSE149512 not downloaded", "asset:data:geo:GSE45885 licence not read", "asset:data:geo:GSE45885 not downloaded", "asset:data:geo:GSE45887 licence not read", "asset:data:geo:GSE45887 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["zation of the above genes using human testis single-cell RNA sequencing dataset GSE149512, which were all located in"], "order_basis": "paper_text_order:921", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["e above genes using human testis single-cell RNA sequencing dataset GSE149512, which were all located in"], "order_basis": "paper_text_order:933", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["pathway. Finally, we constructed a NOA model in mice using X-ray irradiation, and quantitative Re", ". China. The experimental procedures for all mice were performed in accordance with the Regulations", "nstruct NOA animal models [9], 8 BALB/c male mice were randomly divided into control and irradiated", "med daily with a total of 5 times. After the mice were euthanized, the abdominal cavity was cut ope"], "order_basis": "paper_text_order:1388", "id": "assay:3"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ce using X-ray irradiation, and quantitative Real-time PCR results showed that C12orf54, TSSK6, OR2H1,", "we designed primers to perform quantitative Real-time PCR experiments on the above 5 of 6 signature ge", "of the two groups, we performed quantitative Real-time PCR experiments on the above 5 of 6 signature ge"], "order_basis": "paper_text_order:1438", "id": "assay:4"}, {"role": "analysis", "definition_id": "machine_learning", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["train_classifier", "cross_validate", "roc_auc"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We used the above 6 signature genes to construct the LightGBM Model in the training dataset, and the results showed that the AUC (Area Under Curve) of both the ROC and Precision-Recall curves for internal validation was 1.0 (p < 0.05) (Figure 4A, 4B)."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}