AKT3 and related molecules as potential biomarkers responsible for cryptorchidism and cryptorchidism-induced azoospermia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34430428", "kind": "science-record", "revision": 8, "content_hash": "sha256:84a88fda159a0156a83c59b32f346dc5354a8553c46c661764a33d26532e5bfd", "created_at": "2026-11-01T15:41:49Z", "updated_at": "2026-11-01T22:04:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "AKT3 and related molecules as potential biomarkers responsible for cryptorchidism and cryptorchidism-induced azoospermia.", "doi": "10.21037/tp-21-31", "pmid": "34430428", "authors": ["Hongshuai Jia", "Tiantian Ma", "Shujing Jia", "Yuru Ouyang"], "journal": "Translational pediatrics", "year": 2021, "abstract": "BACKGROUND: Cryptorchidism is a common congenital malformation strongly related to future oligospermia and male infertility. Normally functioning early-stage spermatogonia are vital to ensure fertility. The present study aimed to identify new differentially expressed genes (DEGs) associated with signaling pathways related to spermatogonial stem cell (SSC) maintenance during early spermatogenesis.\nMETHODS: GEO2R was used to screen for genes differentially regulated in cryptorchidism using mRNA expression profiling data in the GEO database. DAVID was used to perform GO and KEGG enrichment analysis of DEGs to analyze their functions. A protein-protein interaction (PPI) network of DEGs was constructed using the STRING database. The hub genes in the PPI networks were identified using Maximal Clique Centrality (MCC) in Cytohubba, and the top 50 genes were displayed as hub genes using Cytoscape software. Then, the miRNAs targeting hub genes were predicted using miRWalk and an mRNA-miRNA interaction network was constructed using Cytoscape. We took the intersection of these target miRNAs and the differentially expressed miRNAs identified from a non-coding RNA sequencing dataset, GSE149084. Furthermore, the intersected miRNAs and their predicted target genes were validated in the testicular tissue of rats with cryptorchidism.\nRESULTS: A total of 474 DEGs were identified, most of which were annotated to the PI3K-AKT-mTOR signaling pathway. Hub genes related to the pathway were predicted to be targeted by 27 miRNAs. Further miRNA mining revealed that miRNA-7-5p and miRNA-519d-3p were both dysregulated in cryptorchidism patients. Further, we found that these two miRNAs were predicted with high confidence to share a common target gene, AKT3. In the testicular tissue of rats with cryptorchidism, miRNA-519d-3p was upregulated while miRNA-7-5p and AKT3 were downregulated. We also found that AKT3 plays an essential role in regulating SSC state through the PI3K-AKT-mTOR signaling pathway and that AKT3 is one of the key genes related to SSC self-renewal, proliferation, and differentiation.\nCONCLUSIONS: The PI3K-AKT-mTOR signaling pathway functions in SSC maintenance, and alterations in this pathway may explain defects in spermatogenesis. AKT3-related miRNAs, including hsa-miR-7-5p and hsa-miR-519d-3p, might be responsible for cryptorchidism and cryptorchidism-induced azoospermia and serve as potential biomarkers.", "claims": [{"id": "claim-data-access", "statement": "The GSE16191 dataset comprises gene expression data for 14 UDT and 4 contralateral descended testis (DT) tissue samples from testicular agenesis patients, while the GSE25518 is for 19 UDT and 4 contralateral DT tissue samples from testicular agenesis patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34430428", "locator": "sections[3] \"Microarray analysis of cryptorchidism patients\" paragraph 2", "quote": "The GSE16191 dataset comprises gene expression data for 14 UDT and 4 contralateral descended testis (DT) tissue samples from testicular agenesis patients, while the GSE25518 is for 19 UDT and 4 contralateral DT tissue samples from testicular agenesis patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34430428"], "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:GSE149084"], "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:GSE149084"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34430428", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tp-21-31", "sha256": "sha256:6a79d29481beab919fb47faee56aaaaa1ae4c2c03da3786289e9c02e2616f8de", "bytes": 40298, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tp-21-31", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8349953", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE149084", "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=GSE149084", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE149084", "version": null, "note": "The GSE16191 dataset comprises gene expression data for 14 UDT and 4 contralateral descended testis (DT) tissue samples from testicular agenesis patients, while the GSE25518 is for 19 UDT and 4 contralateral DT tissue samples from testicular agenesis patients.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The GSE16191 dataset comprises gene expression data for 14 UDT and 4 contralateral descended testis (DT) tissue samples from testicular agenesis patients, while the GSE25518 is for 19 UDT and 4 contralateral DT tissue samples from testicular agenesis patients.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM4490322", "GSM4490323", "GSM4490324", "GSM4490325", "GSM4490326", "GSM4490327", "GSM4490328", "GSM4490329", "GSM4490330", "GSM4490331", "GSM4490332", "GSM4490333", "GSM4490334", "GSM4490335", "GSM4490336", "GSM4490337", "GSM4490338", "GSM4490339"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "20795", "taxon": "Homo sapiens", "title": "Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomics in children with Cryptorchidism", "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:GSE16191", "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=GSE16191", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16191", "version": null, "note": "The GSE16191 dataset comprises gene expression data for 14 UDT and 4 contralateral descended testis (DT) tissue samples from testicular agenesis patients, while the GSE25518 is for 19 UDT and 4 contralateral DT tissue samples from testicular agenesis patients.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The GSE16191 dataset comprises gene expression data for 14 UDT and 4 contralateral descended testis (DT) tissue samples from testicular agenesis patients, while the GSE25518 is for 19 UDT and 4 contralateral DT tissue samples from testicular agenesis patients.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM406416", "GSM406417", "GSM406418", "GSM406419", "GSM406420", "GSM406421", "GSM406422", "GSM406423", "GSM406424", "GSM406425", "GSM406426", "GSM406427", "GSM406428", "GSM406429", "GSM406430", "GSM406431", "GSM406432", "GSM406433", "GSM406434", "GSM406435"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "EGR4 is a master gene responsible for fertility in cryptorchidism", "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:GSE25518", "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=GSE25518", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25518", "version": null, "note": "The GSE16191 dataset comprises gene expression data for 14 UDT and 4 contralateral descended testis (DT) tissue samples from testicular agenesis patients, while the GSE25518 is for 19 UDT and 4 contralateral DT tissue samples from testicular agenesis patients.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The GSE16191 dataset comprises gene expression data for 14 UDT and 4 contralateral descended testis (DT) tissue samples from testicular agenesis patients, while the GSE25518 is for 19 UDT and 4 contralateral DT tissue samples from testicular agenesis patients.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM627468", "GSM627469", "GSM627470", "GSM627471", "GSM627472", "GSM627473", "GSM627474", "GSM627475", "GSM627476", "GSM627477", "GSM627478", "GSM627479", "GSM627480", "GSM627481", "GSM627482", "GSM627483", "GSM627484", "GSM627485", "GSM627486", "GSM627487", "GSM627488", "GSM627489", "GSM627490"], "sample_count": 23, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Testis developmental gene expression in cryptorchid boys at risk of azoospermia", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34430428:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1324882e10be33b72d25d1d17e4525a9898127f083b72a54e040b309adc53078", "bytes": 1288, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#t1", "version": null, "note": "List of 24 upregulated miRNAs of testes tissue in cryptorchidism patients from database GSE149084", "structure": {"pmcid": "PMC8349953", "section_index": 20, "section_title": "Validation of the predicted miRNAs and mRNA-miRNA interaction network analysis", "row_count": 25, "column_count": 3}, "table": {"label": "Table 1", "caption": "List of 24 upregulated miRNAs of testes tissue in cryptorchidism patients from database GSE149084", "rows": [["miRNA", "P value", "FC"], ["hsa-miR-8085", "1.71×10−04", "20.36"], ["hsa-miR-3621", "4.20×10−04", "18.06"], ["hsa-miR-10524-5p", "5.06×10−03", "17.03"], ["hsa-miR-6789-3p", "4.66×10−03", "10.05"], ["hsa-miR-4712-3p", "5.43×10−03", "6.12"], ["hsa-miR-4680-5p", "7.11×10−03", "5.42"], ["hsa-miR-3976", "7.94×10−03", "4.31"], ["hsa-miR-4287", "4.29×10−04", "3.90"], ["hsa-miR-3141", "1.48×10−03", "3.62"], ["hsa-miR-4433a-3p", "3.95×10−03", "3.54"], ["hsa-miR-1199-5p", "2.97×10−03", "3.26"], ["hsa-miR-5588-5p", "3.47×10−04", "3.18"], ["hsa-miR-4700-5p", "5.61×10−04", "2.88"], ["hsa-miR-7108-3p", "8.04×10−04", "2.79"], ["hsa-miR-6872-3p", "2.65×10−04", "2.76"], ["hsa-miR-3611", "1.74×10−05", "2.70"], ["hsa-miR-3160-5p", "5.27×10−03", "2.62"], ["hsa-miR-3195", "2.03×10−03", "2.46"], ["hsa-miR-5088-5p", "2.42×10−04", "2.39"], ["hsa-miR-6748-5p", "9.24×10−03", "2.38"], ["hsa-miR-219a-1-3p", "6.14×10−03", "2.37"], ["hsa-miR-11401", "3.23×10−03", "2.34"], ["hsa-miR-615-3p", "3.43×10−03", "2.23"], ["hsa-miR-3150b-5p", "1.99×10−03", "2.00"]], "row_count": 25, "column_count": 3, "numeric_cells": 72, "header_rows": 1, "locator": "section[20]/table-wrap[1]#t1"}}, {"id": "asset:table:pmid:34430428:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:56321e8e838e603f6cbe1c168a8e6d799971b24c2a1bd22866d8bc39e6b29fcf", "bytes": 1331, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[2]#t2", "version": null, "note": "List of 25 downregulated miRNAs of testes tissue in cryptorchidism patients from database GSE149084", "structure": {"pmcid": "PMC8349953", "section_index": 20, "section_title": "Validation of the predicted miRNAs and mRNA-miRNA interaction network analysis", "row_count": 26, "column_count": 3}, "table": {"label": "Table 2", "caption": "List of 25 downregulated miRNAs of testes tissue in cryptorchidism patients from database GSE149084", "rows": [["miRNA", "P value", "FC"], ["hsa-miR-519b-5p", "1.82×10−03", "0.14"], ["hsa-miR-520f-3p", "8.10×10−04", "0.18"], ["hsa-miR-518e-3p", "3.55×10−05", "0.20"], ["hsa-miR-519a-3p", "7.26×10−03", "0.21"], ["hsa-miR-517c-3p", "5.98×10−04", "0.22"], ["hsa-miR-519d-3p", "6.17×10−05", "0.23"], ["hsa-miR-518a-3p", "7.93×10−03", "0.24"], ["hsa-miR-518c-3p", "5.28×10−03", "0.26"], ["hsa-miR-1283", "8.81×10−03", "0.26"], ["hsa-miR-515-3p", "6.75×10−03", "0.27"], ["hsa-miR-526b-5p", "5.39×10−03", "0.27"], ["hsa-miR-539-5p", "3.31×10−03", "0.27"], ["hsa-miR-517b-3p", "4.23×10−03", "0.27"], ["hsa-miR-1299", "2.33×10−03", "0.28"], ["hsa-miR-518b", "1.96×10−03", "0.28"], ["hsa-miR-516b-5p", "4.28×10−03", "0.28"], ["hsa-miR-515-5p", "3.23×10−03", "0.29"], ["hsa-miR-517a-3p", "1.63×10−03", "0.29"], ["hsa-miR-520c-3p", "2.85×10−03", "0.30"], ["hsa-miR-3059-5p", "1.60×10−03", "0.32"], ["hsa-miR-520a-3p", "5.16×10−03", "0.36"], ["hsa-miR-7-5p", "1.42×10−03", "0.40"], ["hsa-miR-155-5p", "1.64×10−03", "0.40"], ["hsa-miR-3529-3p", "2.41×10−03", "0.40"], ["hsa-miR-224-5p", "2.25×10−03", "0.48"]], "row_count": 26, "column_count": 3, "numeric_cells": 75, "header_rows": 1, "locator": "section[20]/table-wrap[2]#t2"}}], "gaps": ["asset:data:geo:GSE149084 not downloaded", "asset:data:geo:GSE149084 licence not read", "asset:data:geo:GSE16191 not downloaded", "asset:data:geo:GSE16191 licence not read", "asset:data:geo:GSE25518 not downloaded", "asset:data:geo:GSE25518 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-3", "family": "network_analysis", "specific": "centrality", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "Centrality"}}], "targets": [], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE16191", "GSE25518", "GSE149084"], "resolved_accessions": ["GSE16191", "GSE25518", "GSE149084"], "statements": ["The GSE16191 dataset comprises gene expression data for 14 UDT and 4 contralateral descended testis (DT) tissue samples from testicular agenesis patients, while the GSE25518 is for 19 UDT and 4 contralateral DT tissue samples from testicular agenesis patients."], "basis": "The paper names GSE16191, GSE25518, GSE149084 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:34430428", "data:geo:GSE149084", "asset:table:pmid:34430428:1", "asset:table:pmid:34430428:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE149084"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:46:23Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": null}, "calls": 3, "usage": {"prompt_tokens": 32124, "completion_tokens": 1767, "cached_tokens": 784}}, "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:34430428", "type": "paper", "label": "pmid:34430428"}, {"id": "source:pmid:34430428", "type": "manuscript", "label": "PMID 34430428 full text"}, {"id": "data:geo:GSE149084", "type": "dataset", "label": "GEO GSE149084"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34430428", "type": "paper", "label": "pmid:34430428"}, {"id": "source:pmid:34430428", "type": "manuscript", "label": "PMID 34430428 full text"}, {"id": "data:geo:GSE149084", "type": "dataset", "label": "GEO GSE149084"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34430428", "type": "extraction", "used": ["source:pmid:34430428"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE149084", "type": "accession_resolution", "used": ["data:geo:GSE149084"], "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:34430428", "parent_hash": "sha256:0205351c363b705235a971c0bcc148993d19fa8c6ef185a8e5e61a0a5639cb8d", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE149084 licence not read", "asset:data:geo:GSE149084 not downloaded", "asset:data:geo:GSE16191 licence not read", "asset:data:geo:GSE16191 not downloaded", "asset:data:geo:GSE25518 licence not read", "asset:data:geo:GSE25518 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["xpressed miRNAs identified from a non-coding RNA sequencing dataset, GSE149084. Furthermore, the interse"], "order_basis": "paper_text_order:1242", "id": "assay:1"}, {"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": ["s were validated in the testicular tissue of rats with cryptorchidism. RESULTS: A total of 474", "rget gene, AKT3. In the testicular tissue of rats with cryptorchidism, miRNA-519d-3p was upreg", "l Technology Co., Ltd. (Beijing, China). All rats were maintained in a controlled environment set a", "hway profiles. Animals A total of 20 male SD rats, aged 3–4 weeks, were obtained from Beijing"], "order_basis": "paper_text_order:1389", "id": "assay:2"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Methods Microarray analysis of cryptorchidism patients The stud", "EO database [GSE16191 (18) and GSE25518 (6); Affymetrix GPL570 platform, Affymetrix Human Genome U13", "nd GSE25518 (6); Affymetrix GPL570 platform, Affymetrix Human Genome U133 Plus 2.0 Array]. The GSE16", "public database. Note that the probes of the Affymetrix GPL570 chip were automatically converted int"], "order_basis": "paper_text_order:2559", "id": "assay:3"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}