Identification of hub genes associated with spermatogenesis by bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37891374", "kind": "science-record", "revision": 4, "content_hash": "sha256:dbd0c2879fd3989ddeb1e89d0b26947ed21c96ce799a520dd59e49627a6147ff", "created_at": "2026-11-01T19:02:45Z", "updated_at": "2026-11-01T22:52:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes associated with spermatogenesis by bioinformatics analysis.", "doi": "10.1038/s41598-023-45620-3", "pmid": "37891374", "authors": ["Shuang Liu", "Yan-Chao Bian", "Wan-Lun Wang", "Tong-Jia Liu", "Ting Zhang", "Yue Chang", "Rui Xiao", "Chuan-Ling Zhang"], "journal": "Scientific reports", "year": 2023, "abstract": "Spermatogenesis is a complex process related to male infertility. Till now, the critical genes and specific mechanisms have not been elucidated clearly. Our objective was to determine the hub genes that play a crucial role in spermatogenesis by analyzing the differentially expressed genes (DEGs) present in non-obstructive azoospermia (NOA) compared to OA and normal samples using bioinformatics analysis. Four datasets, namely GSE45885, GSE45887, GSE9210 and GSE145467 were used. Functional enrichment analyses were performed on the DEGs. Hub genes were identified based on protein-protein interactions between DEGs. The expression of the hub genes was further examined in the testicular germ cell tumors from the TCGA by the GEPIA and validated by qRT-PCR in the testes of lipopolysaccharide-induced acute orchitis mice with impaired spermatogenesis. A total of 203 DEGs including 34 up-regulated and 169 down-regulated were identified. Functional enrichment analysis showed DEGs were mainly involved in microtubule motility, the process of cell growth and protein transport. PRM2, TEKT2, FSCN3, UBQLN3, SPATS1 and GTSF1L were identified and validated as hub genes for spermatogenesis. Three of them (PRM2, FSCN3 and TEKT2) were significantly down-regulated in the testicular germ cell tumors and their methylation levels were associated with the pathogenesis. In summary, the hub genes identified may be related to spermatogenesis and may act as potential therapeutic targets for NOA and testicular germ cell tumors.", "claims": [{"id": "claim-method", "statement": "The limma package (version 3.52.1) was subsequently used for DEG identification. DEGs were screened based on the criteria of P adj < 0.05 and |log2(fold change, FC)|> 1.0.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37891374", "locator": "sections[14] \"Identification of DEGs\" paragraph 2", "quote": "The limma package (version 3.52.1) was subsequently used for DEG identification. DEGs were screened based on the criteria of P adj < 0.05 and |log2(fold change, FC)|> 1.0."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed for this study can be found in the GEO repository. GSE45885 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45885, GSE45887 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45887, GSE9210 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9210, GSE145467 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145467.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37891374", "locator": "sections[30] \"Data availability\" paragraph 2", "quote": "The datasets generated and/or analyzed for this study can be found in the GEO repository. GSE45885 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45885, GSE45887 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45887, GSE9210 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9210, GSE145467 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145467."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Thus, we analyzed three datasets and identified 203 DEGs including 34 up-regulated and 169 down-regulated genes in NOA compared to OA and normal samples exhibiting normal spermatogenesis (|log2Fold change (FC)|> 1.0, P adjusted(adj) < 0.05).", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "Thus, we analyzed three datasets and identified 203 DEGs including 34 up-regulated and 169 down-regulated genes in NOA compared to OA and normal samples exhibiting normal spermatogenesis (|log2Fold change (FC)|> 1.0, P adjusted(adj) < 0.05)."}, "evidence": [{"asset": "source:pmid:37891374", "locator": "sections[3] \"Identification of DEGs\" paragraph 2", "quote": "Thus, we analyzed three datasets and identified 203 DEGs including 34 up-regulated and 169 down-regulated genes in NOA compared to OA and normal samples exhibiting normal spermatogenesis (|log2Fold change (FC)|> 1.0, P adjusted(adj) < 0.05)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Thus, we analyzed three datasets and identified 203 DEGs including 34 up-regulated and 169 down-regulated genes in NOA compared to OA and normal samples exhibiting normal spermatogenesis (|log2Fold change (FC)|> 1.0, P adjusted(adj) < 0.05).", "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:37891374"], "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:GSE145467"], "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:GSE145467"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37891374", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-023-45620-3", "sha256": "sha256:e3294803100cf98d303088eb69635f5f1bc3b4f0b4e6b3a9179573b71433eb81", "bytes": 53685, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-023-45620-3", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10611713", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"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 datasets generated and/or analyzed for this study can be found in the GEO repository. 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GSE45885 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45885, GSE45887 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45887, GSE9210 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9210, GSE145467 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145467.", "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: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 datasets generated and/or analyzed for this study can be found in the GEO repository. GSE45885 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45885, GSE45887 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45887, GSE9210 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9210, GSE145467 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145467.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed for this study can be found in the GEO repository. GSE45885 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45885, GSE45887 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45887, GSE9210 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9210, GSE145467 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145467.", "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 datasets generated and/or analyzed for this study can be found in the GEO repository. GSE45885 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45885, GSE45887 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45887, GSE9210 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9210, GSE145467 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145467.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed for this study can be found in the GEO repository. GSE45885 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45885, GSE45887 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45887, GSE9210 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9210, GSE145467 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145467.", "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}}, {"id": "data:geo:GSE9210", "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=GSE9210", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE9210", "version": null, "note": "The datasets generated and/or analyzed for this study can be found in the GEO repository. GSE45885 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45885, GSE45887 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45887, GSE9210 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9210, GSE145467 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145467.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed for this study can be found in the GEO repository. GSE45885 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45885, GSE45887 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45887, GSE9210 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9210, GSE145467 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145467.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM232970", "GSM232971", "GSM232972", "GSM232973", "GSM232974", "GSM232975", "GSM232976", "GSM232977", "GSM232978", "GSM232979", "GSM232980", "GSM232981", "GSM232982", "GSM232983", "GSM232984", "GSM232985", "GSM232986", "GSM232987", "GSM232988", "GSM232989", "GSM232990", "GSM232991", "GSM232992", "GSM232993", "GSM232994", "GSM232995", "GSM232996", "GSM232997", "GSM232998", "GSM232999", "GSM233000", "GSM233001", "GSM233002", "GSM233003", "GSM233004", "GSM233005", "GSM233006", "GSM233007", "GSM233008", "GSM233009", "GSM233010", "GSM233011", "GSM233012", "GSM233013", "GSM233014", "GSM233015", "GSM233016", "GSM233017", "GSM233018", "GSM233019", "GSM233020", "GSM233021", "GSM233022", "GSM233023", "GSM233024", "GSM233025", "GSM233026", "GSM233027"], "sample_count": 58, "group_sizes": null, "group_sizes_basis": null, "platform": "887", "taxon": "Homo sapiens", "title": "A testicular gene expression profile for NOA patients, and ART3 as a genetic susceptibility gene for NOA", "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:GSE145467 not downloaded", "asset:data:geo:GSE145467 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", "asset:data:geo:GSE9210 not downloaded", "asset:data:geo:GSE9210 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The limma package (version 3.52.1) was subsequently used for DEG identification. 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No tolerance is published because the paper states none."}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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", "GSE9210", "GSE145467"], "resolved_accessions": ["GSE45885", "GSE45887", "GSE9210", "GSE145467"], "statements": ["The datasets generated and/or analyzed for this study can be found in the GEO repository. GSE45885 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45885, GSE45887 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45887, GSE9210 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9210, GSE145467 is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145467."], "basis": "The paper names GSE45885, GSE45887, GSE9210, GSE145467 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:37891374", "data:geo:GSE145467"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE145467"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:57:43Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16537, "completion_tokens": 3055, "cached_tokens": 256}}, "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:37891374", "type": "paper", "label": "pmid:37891374"}, {"id": "source:pmid:37891374", "type": "manuscript", "label": "PMID 37891374 full text"}, {"id": "data:geo:GSE145467", "type": "dataset", "label": "GEO GSE145467"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37891374", "type": "paper", "label": "pmid:37891374"}, {"id": "source:pmid:37891374", "type": "manuscript", "label": "PMID 37891374 full text"}, {"id": "data:geo:GSE145467", "type": "dataset", "label": "GEO GSE145467"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37891374", "type": "extraction", "used": ["source:pmid:37891374"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE145467", "type": "accession_resolution", "used": ["data:geo:GSE145467"], "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:37891374", "parent_hash": "sha256:6a13c2c36a1119a2654eb31ed25068604c99f165c03a94f4d5131084571ad17d", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE145467 licence not read", "asset:data:geo:GSE145467 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", "asset:data:geo:GSE9210 licence not read", "asset:data:geo:GSE9210 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The limma package (version 3.52.1) was subsequently used for DEG identification. DEGs were screened based on the criteria of P adj < 0.05 and |log2(fold change, FC)|> 1.0."], "order_basis": "analysis_only", "id": "assay:1"}]}