Prediction of the molecular mechanisms and potential therapeutic targets for diabetic nephropathy by bioinformatics methods.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26986014", "kind": "science-record", "revision": 8, "content_hash": "sha256:69eea4a003d4e3b1ed5354da4290c0bf5ab769ab6822666a71acda9d301b7451", "created_at": "2026-11-01T15:40:17Z", "updated_at": "2026-11-01T21:58:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prediction of the molecular mechanisms and potential therapeutic targets for diabetic nephropathy by bioinformatics methods.", "doi": "10.3892/ijmm.2016.2527", "pmid": "26986014", "authors": ["Wan-Ning Wang", "Wen-Long Zhang", "Guang-Yu Zhou", "Fu-Zhe Ma", "Tao Sun", "Sen-Sen Su", "Zhong-Gao Xu"], "journal": "International journal of molecular medicine", "year": 2016, "abstract": "In this study, we aimed to explore the molecular mechanisms of and genetic factors influencing diabetic nephropathy (DN). Gene expression profiles associated with DN were obtained from the GEO database (Accession no. GSE20844). The differentially expressed genes (DEGs) between diabetic mice and non-diabetic mice were screened. Subsequently, the DEGs were subjected to functional and pathway analysis. The protein-protein interaction (PPI) network was constructed and the transcription factors (TFs) were screened among the DEGs. A total of 92 upregulated and 118 downregulated genes were screened. Pathway analysis revealed that the p53 signaling pathway, the transforming growth factor (TGF)-β signaling pathway and the mitogen-activated protein kinase (MAPK) signaling pathway were significantly enriched by upregulated genes. Serpine1 (also known as plasminogen activator inhibitor-1), early growth response 1 (Egr1) and Mdk were found to be significant nodes in the PPI network by three methods. A total of 12 TFs were found to be differentially expressed, of which nuclear receptor subfamily 4, group A, member 1 (Nr4a1) and peroxisome proliferator-activated receptor gamma (Pparg) were found to have multiple interactions with other DEGs. We demonstrated that the p53 signaling pathway, the TGF-β signaling pathway and the MAPK signaling pathway were dysregulated in the diabetic mice. The significant nodes (Serpine1, Egr1 and Mdk) and differentially expressed TFs (Nr4a1 and Pparg) may provide a novel avenue for the targeted therapy of DN.", "claims": [{"id": "claim-method", "statement": "The P-value for each gene was calculated using the Student's t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26986014", "locator": "sections[4] \"Analysis of DEGs\" paragraph 2", "quote": "The P-value for each gene was calculated using the Student's t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In the present study, we downloaded the same microarray data from the Gene Expression Omnibus (GEO) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26986014", "locator": "sections[1] \"Introduction\" paragraph 4", "quote": "In the present study, we downloaded the same microarray data from the Gene Expression Omnibus (GEO) database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using Bioconductor limma with a Student's t-test on GEO dataset GSE20844, the study identified 210 differentially expressed genes in diabetic mice, comprising 92 upregulated and 118 downregulated genes.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "According to values of p<0.05 and |log2FC(fold change)|≥0.58, a total of 210 genes were found to be differentially expressed in the diabetic group, including 92 upregulated and 118 downregulated genes."}, "evidence": [{"asset": "source:pmid:26986014", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Gene expression profiles associated with DN were obtained from the GEO database (Accession no. GSE20844)."}, {"asset": "source:pmid:26986014", "locator": "sections[9] \"Identification of DEGs\" paragraph 2", "quote": "According to values of p<0.05 and |log2FC(fold change)|≥0.58, a total of 210 genes were found to be differentially expressed in the diabetic group, including 92 upregulated and 118 downregulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using Bioconductor limma with a Student's t-test on GEO dataset GSE20844, the study identified 210 differentially expressed genes in diabetic mice, comprising 92 upregulated and 118 downregulated genes.", "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:26986014"], "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:GSE20844"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE20844"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26986014", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/ijmm.2016.2527", "sha256": "sha256:2a51bf5f84f2d89b68f8fe8933f57f0c699ac27123a15b8f7bf8366bc58e8a36", "bytes": 24069, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/ijmm.2016.2527", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4829133", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20844", "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=GSE20844", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20844", "version": null, "note": "In the present study, we downloaded the same microarray data from the Gene Expression Omnibus (GEO) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "In the present study, we downloaded the same microarray data from the Gene Expression Omnibus (GEO) database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM519444", "GSM519445", "GSM519766", "GSM519813", "GSM519814", "GSM519815", "GSM519816"], "sample_count": 7, "group_sizes": null, "group_sizes_basis": null, "platform": "1261", "taxon": "Mus musculus", "title": "Differential Expression of Ove26(Diabetic) vs FVB(Nondiabetic) mice", "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:26986014:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3b16233a28a4da1751bdce631bcac1b2d6017195a39d3b6b007a34e7de3ace32", "bytes": 2079, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#tI-ijmm-37-05-1181", "version": null, "note": "The significant GO terms enriched by DEGs.", "structure": {"pmcid": "PMC4829133", "section_index": 10, "section_title": "GO and pathway analysis", "row_count": 39, "column_count": 3}, "table": {"label": "Table I", "caption": "The significant GO terms enriched by DEGs.", "rows": [["Term", "Count", "P-value"], ["Upregulated genes"], ["BP"], ["GO:0042127 - regulation of cell proliferation", "13", "2.30E-05"], ["GO:0045765 - regulation of angiogenesis", "5", "9.16E-05"], ["GO:0016525 - negative regulation of angiogenesis", "4", "2.04E-04"], ["GO:0008285 - negative regulation of cell proliferation", "7", "0.001184688"], ["GO:0009611 - response to wounding", "8", "0.002365745"], ["CC"], ["GO:0005576 - extracellular region", "20", "5.60E-05"], ["GO:0044421 - extracellular region part", "11", "0.001793488"], ["GO:0046658 - anchored to plasma membrane", "3", "0.002476471"], ["GO:0005615 - extracellular space", "8", "0.006777968"], ["GO:0044459 - plasma membrane part", "14", "0.022475418"], ["MF"], ["GO:0005172 - vascular endothelial growth factor receptor binding", "3", "2.41E-04"], ["GO:0005539 - glycosaminoglycan binding", "5", "0.002459879"], ["GO:0030247 - polysaccharide binding", "5", "0.00373434"], ["GO:0001871 - pattern binding", "5", "0.00373434"], ["GO:0030246 - carbohydrate binding", "7", "0.00480543"], ["Downregulated genes"], ["BP"], ["GO:0006873 - cellular ion homeostasis", "7", "0.002754032"], ["GO:0055082 - cellular chemical homeostasis", "7", "0.003139335"], ["GO:0048878 - chemical homeostasis", "8", "0.003390517"], ["GO:0050801 - ion homeostasis", "7", "0.004850765"], ["GO:0019725 - cellular homeostasis", "7", "0.010204447"], ["CC"], ["GO:0016324 - apical plasma membrane", "6", "3.76E-04"], ["GO:0005576 - extracellular region", "22", "0.001139987"], ["GO:0045177 - apical part of cell", "6", "0.001580783"], ["GO:0005615 - extracellular space", "9", "0.014078693"], ["GO:0005903 - brush border", "3", "0.020010741"], ["MF"], ["GO:0015293 - symporter activity", "5", "0.008223849"], ["GO:0019807 - aspartoacylase activity", "2", "0.012005144"], ["GO:0008201 - heparin binding", "4", "0.013672168"], ["GO:0004046 - aminoacylase activity", "2", "0.023867944"], ["GO:0031402 - sodium ion binding", "4", "0.024166754"]], "row_count": 39, "column_count": 3, "numeric_cells": 90, "header_rows": 1, "locator": "section[10]/table-wrap[1]#tI-ijmm-37-05-1181"}}, {"id": "asset:table:pmid:26986014:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d7fe5072f66c427f68a6497530f74f0c3d50fb708b11afd70b094d9335ce1284", "bytes": 693, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#tII-ijmm-37-05-1181", "version": null, "note": "Pathways significantly enriched by differentially expressed genes.", "structure": {"pmcid": "PMC4829133", "section_index": 10, "section_title": "GO and pathway analysis", "row_count": 10, "column_count": 3}, "table": {"label": "Table II", "caption": "Pathways significantly enriched by differentially expressed genes.", "rows": [["Term", "Count", "P-value"], ["Upregulation"], ["mmu04115: p53 signaling pathway", "5", "7.57E-04"], ["mmu04110: Cell cycle", "5", "0.007243672"], ["mmu04060: Cytokine-cytokine receptor interaction", "6", "0.015248477"], ["mmu04350: TGF-β signaling pathway", "4", "0.015533727"], ["mmu04010: MAPK signaling pathway", "6", "0.021089527"], ["mmu05219: Bladder cancer", "3", "0.026718766"], ["Downregulation"], ["mmu00040: Pentose and glucuronate interconversions", "3", "0.003652816"]], "row_count": 10, "column_count": 3, "numeric_cells": 21, "header_rows": 1, "locator": "section[10]/table-wrap[2]#tII-ijmm-37-05-1181"}}, {"id": "asset:table:pmid:26986014:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:53ea3ae386e53576dbb4f7cf611c0db29def21292e7812060fe763842b092369", "bytes": 1143, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#tIII-ijmm-37-05-1181", "version": null, "note": "Top 15 significant nodes in the protein-protein interaction network based on degree, betweenness and subgraph centralities.", "structure": {"pmcid": "PMC4829133", "section_index": 11, "section_title": "PPI network", "row_count": 16, "column_count": 6}, "table": {"label": "Table III", "caption": "Top 15 significant nodes in the protein-protein interaction network based on degree, betweenness and subgraph centralities.", "rows": [["Node", "Degree", "Node betweenness", "Betweenness", "Node subgragh", "Subgragh"], ["Serpine1", "16", "Serpine1", "2905.323", "Egr1", "337.665"], ["Egr1", "15", "Egr1", "2433.539", "Serpine1", "337.1419"], ["Mdk", "14", "Mdk", "2319.191", "Mdk", "285.9198"], ["Nr4a1", "12", "Pparg", "2105.681", "Icam1", "209.8053"], ["Icam1", "12", "Lrp2", "2064.846", "Cdkn1a", "187.7399"], ["Cdkn1a", "12", "Cdh16", "1583.724", "Nr4a1", "178.7159"], ["Tlr4", "11", "Umod", "1440.558", "Tlr4", "147.8937"], ["Cdk1", "10", "Ltf", "1421.087", "Dusp1", "119.8608"], ["Bmp2", "10", "Ggt1", "1384.699", "Bmp2", "117.067"], ["Dusp1", "9", "Tlr4", "1286.763", "Cyr61", "104.8729"], ["Pparg", "8", "Slc12a1", "1250.098", "Pparg", "85.67106"], ["Ltf", "7", "Nr4a1", "1248.253", "Cybb", "68.2394"], ["Egf", "7", "Icam1", "1223.037", "Smad6", "63.11027"], ["Cybb", "7", "Cdk1", "1119.84", "Cdk1", "56.22912"], ["Tgfb3", "7", "Wfdc15b", "1082.356", "Map3k8", "52.32016"]], "row_count": 16, "column_count": 6, "numeric_cells": 49, "header_rows": 1, "locator": "section[11]/table-wrap[1]#tIII-ijmm-37-05-1181"}}, {"id": "asset:table:pmid:26986014:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:02e9bf67ddd5b8d5d9f5c7bb584f45024971711a94033e046f6020203a4b711d", "bytes": 671, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#tIV-ijmm-37-05-1181", "version": null, "note": "The significant pathways enriched by 24 significant nodes in the protein-protein interaction network.", "structure": {"pmcid": "PMC4829133", "section_index": 11, "section_title": "PPI network", "row_count": 6, "column_count": 3}, "table": {"label": "Table IV", "caption": "The significant pathways enriched by 24 significant nodes in the protein-protein interaction network.", "rows": [["Term", "P-value", "Genes"], ["mmu04010: MAPK signaling pathway", "0.005210429", "Dusp1, Map3K8, Tgfb3, Nr4A1, Egf"], ["mmu05200: Pathways in cancer", "0.010457331", "Cdkn1A, Bmp2, Pparg, Tgfb3, Egf"], ["mmu04115: p53 signaling pathway", "0.015340116", "Cdk1, Cdkn1A, Serpine1"], ["mmu04350: TGF-β signaling pathway", "0.023759324", "Bmp2, Smad6, Tgfb3"], ["mmu04110: Cell cycle", "0.048314969", "Cdk1, Cdkn1A, Tgfb3"]], "row_count": 6, "column_count": 3, "numeric_cells": 10, "header_rows": 1, "locator": "section[11]/table-wrap[2]#tIV-ijmm-37-05-1181"}}, {"id": "asset:table:pmid:26986014:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f0a7f7756786626b10b76697b775e78f561ffd3b6470734d2efd3a20ec25f588", "bytes": 517, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tV-ijmm-37-05-1181", "version": null, "note": "Differentially expressed transcription factors in diabetic samples.", "structure": {"pmcid": "PMC4829133", "section_index": 12, "section_title": "Analysis of TFs", "row_count": 13, "column_count": 2}, "table": {"label": "Table V", "caption": "Differentially expressed transcription factors in diabetic samples.", "rows": [["TF family", "TF gene symbol"], ["bHLH", "Atoh8"], ["bHLH", "Hey1"], ["HMG", "Tox2"], ["Homeobox", "Meox1"], ["Homeobox", "Six4"], ["IRF", "Irf6"], ["MH1", "Smad6"], ["Nuclear orphan receptor", "Nr4a1"], ["PPAR receptor", "Pparg"], ["Thyroid hormone receptor", "Vdr"], ["zf-C2H2", "Klf6"], ["zf-C2H2", "Egr1"]], "row_count": 13, "column_count": 2, "numeric_cells": 0, "header_rows": 1, "locator": "section[12]/table-wrap[1]#tV-ijmm-37-05-1181"}}], "gaps": ["asset:data:geo:GSE20844 not downloaded", "asset:data:geo:GSE20844 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The P-value for each gene was calculated using the Student's t-test."}}, {"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": "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"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "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.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE20844"], "resolved_accessions": ["GSE20844"], "statements": ["In the present study, we downloaded the same microarray data from the Gene Expression Omnibus (GEO) database."], "basis": "The paper names GSE20844 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26986014", "data:geo:GSE20844", "asset:table:pmid:26986014:1", "asset:table:pmid:26986014:2", "asset:table:pmid:26986014:3", "asset:table:pmid:26986014:4", "asset:table:pmid:26986014:5"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE20844"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:10Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 52847, "completion_tokens": 2857, "cached_tokens": 2096}}, "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:26986014", "type": "paper", "label": "pmid:26986014"}, {"id": "source:pmid:26986014", "type": "manuscript", "label": "PMID 26986014 full text"}, {"id": "data:geo:GSE20844", "type": "dataset", "label": "GEO GSE20844"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26986014", "type": "paper", "label": "pmid:26986014"}, {"id": "source:pmid:26986014", "type": "manuscript", "label": "PMID 26986014 full text"}, {"id": "data:geo:GSE20844", "type": "dataset", "label": "GEO GSE20844"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26986014", "type": "extraction", "used": ["source:pmid:26986014"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE20844", "type": "accession_resolution", "used": ["data:geo:GSE20844"], "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:26986014", "parent_hash": "sha256:f2e82dfaab204bd82d5acf046ae1f2d01686e135343dee32fd000e03cf4c5e13", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE20844 licence not read", "asset:data:geo:GSE20844 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["DEGs) between diabetic mice and non-diabetic mice were screened. Subsequently, the DEGs were subjec"], "order_basis": "paper_text_order:389", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The P-value for each gene was calculated using the Student's t-test."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}