{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33381243", "kind": "science-record", "revision": 8, "content_hash": "sha256:e867f86e1f8e9897524fe0af793452cf252b6843dfc4ed0df82e25fd44821dd1", "created_at": "2026-11-01T15:41:21Z", "updated_at": "2026-11-01T22:45:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of miRNAs as the Crosstalk in the Interaction between Neural Stem/Progenitor Cells and Endothelial Cells.", "doi": "10.1155/2020/6630659", "pmid": "33381243", "authors": ["Xin Wang", "Simin Li", "Yihong Ma", "Yuzhen Xu", "Anthony Chukwunonso Ogbuehi", "Xianda Hu", "Aneesha Acharya", "Rainer Haak", "Dirk Ziebolz", "Gerhard Schmalz", "Hanluo Li", "Sebastian Gaus", "Bernd Lethaus", "Vuk Savkovic", "Zhiqiang Su"], "journal": "Disease markers", "year": 2020, "abstract": "AIM: This study is aimed at identifying genetic and epigenetic crosstalk molecules and their target drugs involved in the interaction between neural stem/progenitor cells (NSPCs) and endothelial cells (ECs).\nMATERIALS AND METHODS: Datasets pertaining to reciprocal mRNA and noncoding RNA changes induced by the interaction between NSPCs and ECs were obtained from the GEO database. Differential expression analysis (DEA) was applied to identify NSPC-induced EC alterations by comparing the expression profiles between monoculture of ECs and ECs grown in EC/NSPC cocultures. DEA was also utilized to identify EC-induced NSPC alterations by comparing the expression profiles between monoculture of NSPCs and NSPCs grown in EC/NSPC cocultures. The DEGs and DEmiRNAs shared by NSPC-induced EC alterations and EC-induced NSPC alterations were then identified. Furthermore, miRNA crosstalk analysis and functional enrichment analysis were performed, and the relationship between DEmiRNAs and small molecular drug targets/environment chemical compounds was investigated.\nRESULTS: One dataset (GSE29759) was included and analyzed in this study. Six genes (i.e., MMP14, TIMP3, LOXL1, CCK, SMAD6, and HSPA2), three miRNAs (i.e., miR-210, miR-230a, and miR-23b), and three pathways (i.e., Akt, ERK1/2, and BMPs) were identified as crosstalk molecules. Six small molecular drugs (i.e., deptropine, fluphenazine, lycorine, quinostatin, resveratrol, and thiamazole) and seven environmental chemical compounds (i.e., folic acid, dexamethasone, choline, doxorubicin, thalidomide, bisphenol A, and titanium dioxide) were identified to be potential target drugs of the identified DEmiRNAs.\nCONCLUSION: To conclude, three miRNAs (i.e., miR-210, miR-230a, and miR-23b) were identified to be crosstalks linking the interaction between ECs and NSPCs by implicating in both angiogenesis and neurogenesis. These crosstalk molecules might provide a basis for devising novel strategies for fabricating neurovascular models in stem cell tissue engineering.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis was performed using the R package “limma” [13] for identifying differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) relevant to EC-induced NSPC changes and NSPC-induced EC changes, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33381243", "locator": "sections[4] \"2.2. Differential Expression Analysis\" paragraph 2", "quote": "Differential expression analysis was performed using the R package “limma” [13] for identifying differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) relevant to EC-induced NSPC changes and NSPC-induced EC changes, respectively."}], "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:33381243", "locator": "sections[25] \"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"}], "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:33381243"], "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:GSE29759"], "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:GSE29759"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33381243", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/6630659", "sha256": "sha256:06138368cb60e14e0dd0683eedfb2f95a3e1847b3507ff7f0afa612fd2412e36", "bytes": 52929, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2020/6630659", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7758130", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE29759", "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=GSE29759", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29759", "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": ["GSM737620", "GSM737621", "GSM737622", "GSM737623", "GSM737624", "GSM737625", "GSM737626", "GSM737627", "GSM737628", "GSM737629", "GSM737630", "GSM737631", "GSM737672", "GSM737673", "GSM737674", "GSM737675", "GSM737676", "GSM737677", "GSM737678", "GSM737679", "GSM737680", "GSM737681", "GSM737682", "GSM737683"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "1261;8786", "taxon": "synthetic construct; Mus musculus", "title": "The Role of microRNAs in Neural Stem Cell-supported Endothelial Morphogenesis", "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:33381243:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1ea8e6b61feca8bc6017ed01f2e2a1d64d68e8eac5b4bea8bfd61d63eaa467e6", "bytes": 666, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tab1", "version": null, "note": "The number of up- and downregulated DEGs and DEmiRNAs that are, respectively, involved in NSPC-induced EC alterations and EC-induced NSPC alterations.", "structure": {"pmcid": "PMC7758130", "section_index": 14, "section_title": "3.2. Identification of DEGs and DEmiRNAs", "row_count": 4, "column_count": 7}, "table": {"label": "Table 1", "caption": "The number of up- and downregulated DEGs and DEmiRNAs that are, respectively, involved in NSPC-induced EC alterations and EC-induced NSPC alterations.", "rows": [["Coculture-induced genetic and epigenetic alteration in one type of cells", "Number of DEmRNAs (DEGs)", "Number of DEmiRNAs"], ["Upregulated DEGs", "Downregulated DEGs", "Total", "Upregulated DEmiRNAs", "Downregulated DEmiRNAs", "Total"], ["NSPC-induced alterations in ECs", "399", "345", "744", "5", "13", "18"], ["EC-induced alterations in NSPCs", "425", "710", "1135", "5", "3", "8"]], "row_count": 4, "column_count": 7, "numeric_cells": 12, "header_rows": 2, "locator": "section[14]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:33381243:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8255be90f52faae27090c51518b3d0127f38b93275f4e191c218aeb56ab14d46", "bytes": 2962, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#tab2", "version": null, "note": "The top 30 DEGs involved in the NSPC-induced alterations in ECs, ranked by the ascending order of P value.", "structure": {"pmcid": "PMC7758130", "section_index": 14, "section_title": "3.2. 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P value", "B value", "Regulation pattern"], ["Matn2", "-0.95204", "0.491256", "-10.0494", "3.86E − 06", "0.025782", "4.509474", "Down"], ["Fmod", "-1.02587", "0.511182", "-10.011", "3.98E − 06", "0.025782", "4.485352", "Down"], ["LOC102641248///Maf", "-1.1636", "0.572078", "-9.81371", "4.69E − 06", "0.025782", "4.359141", "Down"], ["Csf2", "0.946405", "-0.49723", "9.80391", "4.73E − 06", "0.025782", "4.352778", "Up"], ["Cyr61", "1.916043", "-0.90785", "9.163675", "8.19E − 06", "0.035735", "3.917772", "Up"], ["Rad54b", "0.884623", "-0.50864", "8.718932", "1.22E − 05", "0.038883", "3.591553", "Up"], ["Hmgb3", "1.027877", "-0.53931", "8.697135", "1.25E − 05", "0.038883", "3.575027", "Up"], ["Srpx2", "-1.03053", "0.491458", "-8.532", "1.45E − 05", "0.039663", "3.448146", "Down"], ["Ces1g", "-1.12288", "0.585271", "-8.39761", "1.65E − 05", "0.040014", "3.342658", "Down"], ["Glis3", "-0.82208", "0.370708", "-8.27324", "1.86E − 05", "0.040548", "3.243204", "Down"], ["Negr1", "-0.85748", "0.4562", "-8.03571", "2.34E − 05", "0.041325", "3.048246", "Down"], ["C1ra", "-0.80236", "0.398421", "-7.9815", "2.47E − 05", "0.041325", "3.002814", "Down"], ["Smarca1", "-0.90427", "0.471865", "-7.90938", "2.65E − 05", "0.041325", "2.941813", "Down"], ["Gmnn", "0.868301", "-0.43587", "7.834033", "2.86E − 05", "0.041325", "2.877409", "Up"], ["Tex30", "1.021454", "-0.5467", "7.64017", "3.48E − 05", "0.041325", "2.708438", "Up"], ["Steap4", "-0.90097", "0.356113", "-7.58391", "3.68E − 05", "0.041325", "2.658512", "Down"], ["Rbms3", "-0.79877", "0.399764", "-7.5764", "3.71E − 05", "0.041325", "2.651814", "Down"], ["Cdo1", "-0.87123", "0.459852", "-7.51396", "3.96E − 05", "0.041325", "2.595861", "Down"], ["Col3a1", "-0.72967", "0.358484", "-7.49893", "4.02E − 05", "0.041325", "2.582317", "Down"], ["3632451O06Rik", "-0.99083", "0.395715", "-7.37964", "4.55E − 05", "0.041325", "2.47378", "Down"], ["C3", "-0.8261", "0.446644", "-7.36875", "4.61E − 05", "0.041325", "2.463774", "Down"], ["Thsd7a", "-1.00741", "0.566198", "-7.34217", "4.74E − 05", "0.041325", "2.439301", "Down"], ["Mad2l1", "0.769878", "-0.43152", "7.272629", "5.10E − 05", "0.041325", "2.374807", "Up"], ["Ccne2", "0.891927", "-0.50969", "7.268195", "5.12E − 05", "0.041325", "2.370674", "Up"], ["Adamts2", "-0.9331", "0.460263", "-7.23757", "5.29E − 05", "0.041325", "2.342049", "Down"], ["AI506816", "0.79492", "-0.41645", "7.222375", "5.38E − 05", "0.041325", "2.327797", "Up"], ["Timm8a1", "0.742468", "-0.41919", "7.211119", "5.44E − 05", "0.041325", "2.317221", "Up"], ["Ccnb2", "0.6736", "-0.32421", "7.16572", "5.71E − 05", "0.041325", "2.274388", "Up"], ["Tyms///Tyms-ps", "0.676379", "-0.36727", "7.152192", "5.80E − 05", "0.041325", "2.26157", "Up"], ["5730414N17Rik", "-0.79662", "0.418908", "-7.14794", "5.82E − 05", "0.041325", "2.257534", "Down"]], "row_count": 31, "column_count": 8, "numeric_cells": 187, "header_rows": 1, "locator": "section[14]/table-wrap[2]#tab2"}}, {"id": "asset:table:pmid:33381243:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:00228cc9baeef2c915ad0cd97b1cbd332e97690b8ece29426c2e7fcd7e1598c3", "bytes": 2970, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[3]#tab3", "version": null, "note": "The top 30 DEGs involved in the EC-involved alterations in NSPCs, ranked by the ascending order of P value.", "structure": {"pmcid": "PMC7758130", "section_index": 14, "section_title": "3.2. Identification of DEGs and DEmiRNAs", "row_count": 31, "column_count": 8}, "table": {"label": "Table 3", "caption": "The top 30 DEGs involved in the EC-involved alterations in NSPCs, ranked by the ascending order of P value.", "rows": [["Gene", "logFC", "AveExpr", "t value", "P value", "Adj. P value", "B value", "Regulation pattern"], ["Pcolce2", "-3.29485", "1.6351", "-45.4871", "2.08E − 11", "4.55E − 07", "13.2377", "Down"], ["Dbp", "-2.00859", "1.062409", "-26.2015", "2.14E − 09", "2.34E − 05", "11.11723", "Down"], ["AU020206", "-1.63296", "0.821066", "-21.5827", "1.08E − 08", "7.32E − 05", "10.05187", "Down"], ["F3", "-1.6611", "0.850706", "-20.9105", "1.41E − 08", "7.32E − 05", "9.863187", "Down"], ["Tpi1", "-1.68121", "0.830618", "-20.4734", "1.68E − 08", "7.32E − 05", "9.73502", "Down"], ["Gm2115", "-1.53464", "0.719453", "-19.4163", "2.60E − 08", "9.46E − 05", "9.405935", "Down"], ["Ldha", "-1.78095", "0.900045", "-18.2662", "4.32E − 08", "0.000134", "9.014231", "Down"], ["Sorl1", "-1.45704", "0.706881", "-17.7044", "5.59E − 08", "0.000135", "8.808873", "Down"], ["Dct", "-1.30765", "0.669351", "-17.6998", "5.60E − 08", "0.000135", "8.807132", "Down"], ["Klf9", "-1.86306", "0.937896", "-17.4915", "6.17E − 08", "0.000135", "8.728473", "Down"], ["Pgk1", "-1.18385", "0.609345", "-16.5411", "9.78E − 08", "0.000194", "8.351213", "Down"], ["Gypc", "-1.22407", "0.595138", "-16.039", "1.26E − 07", "0.000207", "8.139031", "Down"], ["Aldoa", "-1.26041", "0.65786", "-15.9803", "1.30E − 07", "0.000207", "8.113603", "Down"], ["Plekhf1", "-1.317", "0.690027", "-15.8197", "1.41E − 07", "0.000207", "8.043409", "Down"], ["4-Sep", "-1.14394", "0.579925", "-15.6971", "1.50E − 07", "0.000207", "7.989137", "Down"], ["Aldh1a1", "-2.80632", "1.506176", "-15.6785", "1.52E − 07", "0.000207", "7.980857", "Down"], ["Plin3", "-1.2668", "0.589403", "-15.1096", "2.06E − 07", "0.000264", "7.720663", "Down"], ["Parp9", "-1.23876", "0.648245", "-14.7499", "2.50E − 07", "0.000303", "7.549197", "Down"], ["Cldn12", "-1.28813", "0.622674", "-14.0937", "3.63E − 07", "0.000408", "7.221524", "Down"], ["Gpi1", "-1.00716", "0.517518", "-14.0417", "3.74E − 07", "0.000408", "7.194653", "Down"], ["Htra1", "-1.19764", "0.56397", "-13.8878", "4.09E − 07", "0.000409", "7.114509", "Down"], ["Srd5a1", "-1.16578", "0.561656", "-13.8718", "4.13E − 07", "0.000409", "7.106129", "Down"], ["Dlx5", "1.127851", "-0.58715", "13.43145", "5.37E − 07", "0.000478", "6.87001", "Up"], ["ND5", "1.058484", "-0.52334", "13.36773", "5.58E − 07", "0.000478", "6.835023", "Up"], ["Rbp1", "-1.12775", "0.585747", "-13.3416", "5.67E − 07", "0.000478", "6.820608", "Down"], ["Atp1b2", "-1.03892", "0.500454", "-13.3344", "5.69E − 07", "0.000478", "6.816639", "Down"], ["Clybl", "-1.27083", "0.618039", "-13.1367", "6.42E − 07", "0.000519", "6.706417", "Down"], ["Sox8", "-1.02853", "0.485142", "-12.9808", "7.08E − 07", "0.000551", "6.617969", "Down"], ["Srprb///Trf", "-1.18478", "0.624131", "-12.8262", "7.80E − 07", "0.000586", "6.52904", "Down"], ["Hspb6", "-0.93188", "0.490732", "-12.7078", "8.40E − 07", "0.000594", "6.459985", "Down"]], "row_count": 31, "column_count": 8, "numeric_cells": 184, "header_rows": 1, "locator": "section[14]/table-wrap[3]#tab3"}}, {"id": "asset:table:pmid:33381243:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b2ca584a6b9c8d3cacb7809f094f456cd5fe93f41056eaf80a712a6c5250bd12", "bytes": 2520, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#tab4", "version": null, "note": "The topological characteristics of the top 30 nodes in the PPI network of NSPC-induced EC genetic alterations. NA means not overlapped between the EC-PPI and NSPC-PPI networks.", "structure": {"pmcid": "PMC7758130", "section_index": 16, "section_title": "3.4. EC-PPI Network and NSPC-PPI Network", "row_count": 31, "column_count": 8}, "table": {"label": "Table 4", "caption": "The topological characteristics of the top 30 nodes in the PPI network of NSPC-induced EC genetic alterations. NA means not overlapped between the EC-PPI and NSPC-PPI networks.", "rows": [["DEGs", "Overlap", "Regulate", "Degree", "Average shortest path length", "Betweenness centrality", "Closeness centrality", "Topological coefficient"], ["Cdk1", "NA", "Up", "72", "2.737069", "0.056051", "0.365354", "0.179894"], ["Mad2l1", "NA", "Up", "63", "2.844828", "0.019572", "0.351515", "0.211029"], ["Ccnb1", "NA", "Up", "60", "2.706897", "0.084386", "0.369427", "0.195539"], ["Il6", "NA", "Up", "58", "2.872845", "0.111663", "0.348087", "0.08938"], ["Rad51", "NA", "Up", "58", "2.855603", "0.04335", "0.350189", "0.232014"], ["Birc5", "NA", "Up", "56", "2.732759", "0.058321", "0.365931", "0.213803"], ["Ccnb2", "NA", "Up", "54", "2.922414", "0.006045", "0.342183", "0.255649"], ["Ncapg", "NA", "Up", "52", "3.032328", "0.008236", "0.32978", "0.282051"], ["Rrm2", "NA", "Up", "52", "2.931034", "0.018658", "0.341176", "0.262327"], ["Zwilch", "NA", "Up", "52", "2.974138", "0.008695", "0.336232", "0.26455"], ["Espl1", "NA", "Up", "51", "2.961207", "0.010195", "0.3377", "0.265609"], ["Hells", "NA", "Up", "51", "2.967672", "0.006265", "0.336964", "0.268318"], ["Cdca5", "NA", "Up", "49", "2.971983", "0.002445", "0.336476", "0.279941"], ["Cenpa", "NA", "Up", "49", "2.997845", "0.016442", "0.333573", "0.260875"], ["Cenpe", "NA", "Up", "49", "2.961207", "0.018044", "0.3377", "0.257355"], ["Hmmr", "NA", "Up", "49", "3.040948", "0.009178", "0.328845", "0.288843"], ["Pbk", "NA", "Up", "49", "3.006466", "0.002026", "0.332616", "0.287645"], ["Prim1", "NA", "Up", "49", "2.935345", "0.019553", "0.340675", "0.251913"], ["Nuf2", "NA", "Up", "48", "2.974138", "0.00309", "0.336232", "0.275905"], ["Sgol1", "NA", "Up", "48", "2.997845", "0.002882", "0.333573", "0.28125"], ["Cenpi", "NA", "Up", "47", "2.99569", "0.017411", "0.333813", "0.26534"], ["Kif20a", "NA", "Up", "47", "3.0625", "0.001547", "0.326531", "0.30589"], ["Orc1", "NA", "Up", "47", "2.989224", "0.022176", "0.334535", "0.25024"], ["Tacc3", "NA", "Up", "46", "2.939655", "0.025243", "0.340176", "0.287225"], ["H2afz", "NA", "Up", "45", "3.002155", "0.040379", "0.333094", "0.188816"], ["Cep55", "NA", "Up", "44", "3.071121", "0.000625", "0.325614", "0.323656"], ["Cks2", "NA", "Up", "43", "2.980603", "0.001636", "0.335503", "0.301077"], ["Lrr1", "NA", "Up", "43", "3.047414", "0.025254", "0.328147", "0.28961"], ["Spag5", "NA", "Up", "42", "3.096983", "0.000598", "0.322895", "0.327866"], ["Arhgap11a", "NA", "Up", "41", "3.090517", "0.043119", "0.32357", "0.316706"]], "row_count": 31, "column_count": 8, "numeric_cells": 154, "header_rows": 1, "locator": "section[16]/table-wrap[1]#tab4"}}, {"id": "asset:table:pmid:33381243:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:563665299389e26b13be20a2b31286d5d05f0b57c1a5ff57401b0dc3c5d41101", "bytes": 2557, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#tab5", "version": null, "note": "The topological characteristics of the top 30 nodes in the PPI network of EC-induced NSPC genetic alterations. NA means not overlapped between the EC-PPI and NSPC-PPI networks.", "structure": {"pmcid": "PMC7758130", "section_index": 16, "section_title": "3.4. EC-PPI Network and NSPC-PPI Network", "row_count": 31, "column_count": 8}, "table": {"label": "Table 5", "caption": "The topological characteristics of the top 30 nodes in the PPI network of EC-induced NSPC genetic alterations. NA means not overlapped between the EC-PPI and NSPC-PPI networks.", "rows": [["Gene", "Overlap", "Regulate", "Degree", "Average shortest path length", "Betweenness centrality", "Closeness centrality", "Topological coefficient"], ["Gapdh", "NA", "Down", "129", "2.303797", "0.21952", "0.434066", "0.040603"], ["Fn1", "NA", "Down", "83", "2.586881", "0.062983", "0.386566", "0.054676"], ["Vegfa", "NA", "Down", "64", "2.638665", "0.041079", "0.37898", "0.063087"], ["Decr1", "NA", "Down", "59", "2.609896", "0.066189", "0.383157", "0.059219"], ["Cd44", "NA", "Down", "57", "2.693901", "0.029026", "0.371209", "0.069522"], ["Ccnd1", "NA", "Down", "54", "2.703107", "0.040282", "0.369945", "0.065015"], ["Gfap", "NA", "Down", "51", "2.663982", "0.042334", "0.375378", "0.070175"], ["Gad1", "NA", "Up", "47", "2.837745", "0.023163", "0.352393", "0.075753"], ["Cxcr4", "NA", "Down", "45", "2.805524", "0.015376", "0.35644", "0.091761"], ["Pkm", "NA", "Down", "45", "2.780207", "0.042856", "0.359685", "0.072881"], ["Anxa5", "NA", "Down", "41", "2.817031", "0.007322", "0.354984", "0.091351"], ["Timp1", "NA", "Down", "41", "2.805524", "0.010114", "0.35644", "0.09083"], ["Agt", "NA", "Down", "40", "2.857307", "0.014755", "0.34998", "0.0945"], ["Cav1", "NA", "Down", "40", "2.788262", "0.021742", "0.358646", "0.081866"], ["H6pd", "Overlap", "Down", "39", "2.905639", "0.018002", "0.344158", "0.081197"], ["Calb1", "NA", "Up", "39", "2.827388", "0.022978", "0.353683", "0.082931"], ["Ctgf", "NA", "Down", "38", "2.79977", "0.019484", "0.357172", "0.08851"], ["Pdgfrb", "NA", "Down", "38", "2.840046", "0.010704", "0.352107", "0.092062"], ["Snap25", "NA", "Up", "38", "2.840046", "0.026457", "0.352107", "0.071554"], ["Fos", "NA", "Down", "37", "2.757192", "0.026678", "0.362688", "0.086654"], ["Gad2", "NA", "Up", "37", "2.842348", "0.016537", "0.351822", "0.0868"], ["Anxa1", "NA", "Down", "36", "2.912543", "0.010209", "0.343343", "0.091158"], ["Tpi1", "NA", "Down", "36", "2.905639", "0.015808", "0.344158", "0.086608"], ["Gria1", "NA", "Up", "35", "2.837745", "0.033782", "0.352393", "0.079529"], ["Ldha", "NA", "Down", "35", "2.933257", "0.010636", "0.340918", "0.096276"], ["Thy1", "NA", "Down", "35", "2.886076", "0.018426", "0.346491", "0.090796"], ["Tubb3", "NA", "Up", "35", "2.829689", "0.013785", "0.353396", "0.087982"], ["Npy", "NA", "Up", "34", "2.906789", "0.010344", "0.344022", "0.099831"], ["Sst", "NA", "Up", "34", "2.921749", "0.012787", "0.342261", "0.101852"], ["Gng3", "NA", "Up", "32", "3.179517", "0.007673", "0.314513", "0.107118"]], "row_count": 31, "column_count": 8, "numeric_cells": 152, "header_rows": 1, "locator": "section[16]/table-wrap[2]#tab5"}}, {"id": "asset:table:pmid:33381243:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9c64330d8972dce0c6a20c7d930484b9e18c711247528a8f33846ca175acc27f", "bytes": 2612, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[3]#tab6", "version": null, "note": "The topological characteristics of overlapped DEGs in the PPI network of NSPC-induced EC genetic alterations. The overlapped DEGs mean these DEGs were overlapped between the PPI network of NSPC-induced EC alteration and the PPI network of EC-induced NSPC alteration.", "structure": {"pmcid": "PMC7758130", "section_index": 16, "section_title": "3.4. EC-PPI Network and NSPC-PPI Network", "row_count": 33, "column_count": 7}, "table": {"label": "Table 6", "caption": "The topological characteristics of overlapped DEGs in the PPI network of NSPC-induced EC genetic alterations. The overlapped DEGs mean these DEGs were overlapped between the PPI network of NSPC-induced EC alteration and the PPI network of EC-induced NSPC alteration.", "rows": [["Overlapped DEGs", "Regulate", "Degree", "Average shortest path length", "Betweenness centrality", "Closeness centrality", "Topological coefficient"], ["Timp3", "Down", "21", "3.394397", "0.012355", "0.294603", "0.193591"], ["Mmp14", "Down", "15", "3.321121", "0.006668", "0.301103", "0.213333"], ["Col11a1", "Down", "14", "3.681034", "0.000966", "0.271663", "0.265873"], ["H3f3b", "Up", "13", "3.793103", "3.40E − 05", "0.263636", "0.329522"], ["Loxl1", "Down", "13", "3.568966", "0.001462", "0.280193", "0.254605"], ["Ccp110", "Up", "12", "3.497845", "0.007609", "0.28589", "0.324906"], ["Rpl30", "Up", "12", "3.715517", "0.001937", "0.269142", "0.208333"], ["Irs1", "Down", "11", "3.103448", "0.01987", "0.322222", "0.171937"], ["Aldh1a1", "Down", "9", "3.403017", "0.022894", "0.293857", "0.139918"], ["P4ha2", "Down", "9", "3.913793", "0.00226", "0.255507", "0.381313"], ["Cck", "Up", "8", "3.579741", "0.011327", "0.27935", "0.194444"], ["Plod2", "Down", "8", "4.118534", "7.55E − 06", "0.242805", "0.428977"], ["Rhoq", "Down", "8", "4.008621", "0.012817", "0.249462", "0.156863"], ["H6pd", "Down", "7", "3.534483", "0.017785", "0.282927", "0.159664"], ["Luc7l3", "Up", "7", "3.571121", "0.009536", "0.280024", "0.188065"], ["Dlx5", "Up", "6", "3.784483", "0.007836", "0.264237", "0.215278"], ["Rcn3", "Down", "6", "3.525862", "0.008417", "0.283619", "0.330247"], ["F3", "Down", "5", "3.56681", "7.31E − 06", "0.280363", "0.413514"], ["Hspa2", "Down", "5", "3.221983", "0.000827", "0.310368", "0.275229"], ["Tgm2", "Down", "5", "3.538793", "0.005005", "0.282582", "0.379221"], ["Aldh1a7", "Down", "4", "4.165948", "0.000317", "0.240041", "0.416667"], ["Irgm2", "Down", "4", "4.290948", "0.000557", "0.233049", "0.3125"], ["Smad6", "Down", "4", "3.928879", "0.002692", "0.254526", "0.289474"], ["Bmper", "Down", "3", "4.810345", "0.000753", "0.207885", "0.433333"], ["Daam2", "Down", "3", "3.87931", "0.008654", "0.257778", "0.333333"], ["Rras", "Down", "3", "4.3125", "0.000343", "0.231884", "0.439394"], ["Syde1", "Down", "3", "4.939655", "0.000344", "0.202443", "0.545455"], ["Tns1", "Down", "3", "4.286638", "0.002258", "0.233283", "0.355556"], ["Fcgrt", "Down", "2", "4.157328", "0", "0.240539", "0.576923"], ["Rin2", "Down", "2", "4.681034", "0.000218", "0.213628", "0.5"], ["Sdpr", "Down", "2", "4.275862", "0.000187", "0.233871", "0.5"], ["Slc2a10", "Down", "2", "4.176724", "0", "0.239422", "0.738095"]], "row_count": 33, "column_count": 7, "numeric_cells": 165, "header_rows": 1, "locator": "section[16]/table-wrap[3]#tab6"}}, {"id": "asset:table:pmid:33381243:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d7b0368b259d69a7b48d3dc166355b4d5f23d4fbf0255fe396992d61bc451e88", "bytes": 3362, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[4]#tab7", "version": null, "note": "The topological characteristics of overlapped DEGs in the PPI network of EC-induced NSPC genetic alterations. The overlapped DEGs mean these DEGs were overlapped between the PPI network of NSPC-induced EC alteration and the PPI network of EC-induced NSPC alteration.", "structure": {"pmcid": "PMC7758130", "section_index": 16, "section_title": "3.4. EC-PPI Network and NSPC-PPI Network", "row_count": 45, "column_count": 7}, "table": {"label": "Table 7", "caption": "The topological characteristics of overlapped DEGs in the PPI network of EC-induced NSPC genetic alterations. The overlapped DEGs mean these DEGs were overlapped between the PPI network of NSPC-induced EC alteration and the PPI network of EC-induced NSPC alteration.", "rows": [["Overlapped DEGs", "Regulate", "Degree", "Average shortest path length", "Betweenness centrality", "Closeness centrality", "Topological coefficient"], ["H6pd", "Down", "39", "2.905639", "0.018002", "0.344158", "0.081197"], ["Mmp2", "Down", "30", "2.905639", "0.009375", "0.344158", "0.111791"], ["Cck", "Up", "24", "3.161105", "0.002392", "0.316345", "0.14388"], ["Irs1", "Down", "24", "2.90794", "0.011375", "0.343886", "0.090661"], ["Igfbp5", "Down", "18", "3.002302", "0.001391", "0.333078", "0.145524"], ["Loxl1", "Down", "18", "3.331415", "0.002588", "0.300173", "0.154147"], ["Mmp14", "Down", "18", "2.958573", "0.006212", "0.338001", "0.147655"], ["Aldh1a1", "Down", "16", "3.079402", "0.008487", "0.324738", "0.124419"], ["Plod2", "Down", "16", "3.535098", "0.002197", "0.282878", "0.168269"], ["Col11a1", "Down", "15", "3.464902", "0.007219", "0.288608", "0.154386"], ["Timp3", "Down", "15", "3.065593", "0.004764", "0.326201", "0.152648"], ["Irgm2", "Down", "14", "3.910242", "4.82E − 05", "0.255739", "0.348397"], ["P4ha2", "Down", "14", "3.637514", "0.001633", "0.274913", "0.177721"], ["Rhoq", "Down", "13", "3.673188", "0.001094", "0.272243", "0.173382"], ["F3", "Down", "11", "3.150748", "0.00066", "0.317385", "0.188776"], ["Dlx5", "Up", "10", "3.500575", "0.001701", "0.285667", "0.221359"], ["Hspa2", "Down", "10", "3.356732", "0.009675", "0.297909", "0.113084"], ["Luc7l3", "Up", "9", "3.771001", "0.004972", "0.265182", "0.17284"], ["Syde1", "Down", "9", "3.562716", "0.005367", "0.280685", "0.202822"], ["Tgm2", "Down", "9", "3.103567", "0.002864", "0.32221", "0.194714"], ["Rras", "Down", "8", "3.651323", "0.00461", "0.273873", "0.227113"], ["Sdpr", "Down", "8", "3.372842", "0.002511", "0.296486", "0.180118"], ["Aldh1a7", "Down", "7", "3.686997", "0.000587", "0.271223", "0.221254"], ["Ccp110", "Up", "7", "3.982739", "0.002565", "0.251084", "0.159664"], ["Cdc7", "Up", "7", "3.821634", "0.000152", "0.261668", "0.313589"], ["Rcn3", "Down", "7", "3.697353", "0.000432", "0.270464", "0.249433"], ["Tns1", "Down", "7", "3.397008", "0.005802", "0.294377", "0.188729"], ["Zcchc12", "Up", "6", "3.775604", "0.006142", "0.264858", "0.217391"], ["Akap12", "Down", "5", "3.422325", "0.002599", "0.292199", "0.261111"], ["Daam2", "Down", "5", "3.658228", "0.000694", "0.273356", "0.303226"], ["H3f3b", "Up", "5", "4.362486", "6.29E − 05", "0.229227", "0.5125"], ["Rpl30", "Up", "5", "4.084005", "0.000687", "0.244858", "0.3"], ["Sema3c", "Down", "5", "3.528193", "0.002593", "0.283431", "0.2075"], ["Smad6", "Down", "5", "3.510932", "0.001004", "0.284825", "0.284848"], ["Bmper", "Down", "4", "4.210587", "0.00075", "0.237497", "0.26"], ["Rin2", "Down", "4", "3.874568", "0.002452", "0.258093", "0.25"], ["Gem", "Down", "3", "3.882624", "0.002302", "0.257558", "0.42735"], ["Selenbp1", "Down", "3", "4.462601", "0.000293", "0.224085", "0.458333"], ["Fcgrt", "Down", "2", "3.943613", "3.45E − 05", "0.253575", "0.5"], ["Slc2a10", "Down", "2", "3.864212", "6.35E − 05", "0.258785", "0.5"], ["Sytl2", "Down", "2", "3.759494", "0.000207", "0.265993", "0.5"], ["Fam102a", "Down", "1", "5.730725", "0", "0.174498", "0"], ["Macrod1", "Down", "1", "5.880322", "0", "0.170059", "0"], ["Pdgfrl", "Down", "1", "4.286536", "0", "0.233289", "0"]], "row_count": 45, "column_count": 7, "numeric_cells": 228, "header_rows": 1, "locator": "section[16]/table-wrap[4]#tab7"}}, {"id": "asset:table:pmid:33381243:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fbfc25844e5903710568f6834f2706b3ef6e98c05d2f783096ec0e3ce063e308", "bytes": 2837, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#tab8", "version": null, "note": "The topological characteristics of the top 30 nodes in the TF-target DEG interaction network involved in the NSPC-induced EC alteration.", "structure": {"pmcid": "PMC7758130", "section_index": 17, "section_title": "3.5. The Transcription Factor-Target DEG Interaction Network", "row_count": 31, "column_count": 7}, "table": {"label": "Table 8", "caption": "The topological characteristics of the top 30 nodes in the TF-target DEG interaction network involved in the NSPC-induced EC alteration.", "rows": [["Name", "Label", "Degree", "Average shortest path length", "Betweenness centrality", "Closeness centrality", "Topological coefficient"], ["Ptgs2", "Upregulated DEG", "30", "3.17073171", "0.25370241", "0.31538462", "0.07348485"], ["Il6", "Upregulated DEG", "20", "3.31300813", "0.16071429", "0.30184049", "0.10921053"], ["Serpine1", "Upregulated DEG", "19", "3.40650407", "0.10638454", "0.29355609", "0.09078947"], ["Mmp9", "Downregulated DEG", "18", "3.25203252", "0.16761464", "0.3075", "0.11243386"], ["Sp1", "TF", "15", "3.17479675", "0.15105709", "0.31498079", "0.10813008"], ["Nfkb1", "TF", "14", "2.99593496", "0.17606132", "0.33378562", "0.11316212"], ["Mmp2", "Downregulated DEG", "13", "3.45121951", "0.05861543", "0.28975265", "0.16008316"], ["Fgf10", "Downregulated DEG", "13", "4.18699187", "0.10945704", "0.23883495", "0.07692308"], ["Trp53", "TF", "13", "3.42276423", "0.10326907", "0.29216152", "0.10697115"], ["Jun", "TF", "13", "3.14634146", "0.14436348", "0.31782946", "0.12725546"], ["Twist1", "Downregulated DEG_TF", "12", "3.50406504", "0.13470851", "0.28538283", "0.13288288"], ["Col1a1", "Downregulated DEG", "12", "3.4796748", "0.11936909", "0.28738318", "0.13709677"], ["Birc5", "Upregulated DEG", "11", "3.53252033", "0.1098108", "0.283084", "0.13636364"], ["Csf2", "Upregulated DEG", "10", "3.51626016", "0.08268292", "0.28439306", "0.16071429"], ["Smad6", "Downregulated DEG", "9", "4.94715447", "0.04322026", "0.2021364", "0.12698413"], ["Stat3", "TF", "9", "3.43495935", "0.09055949", "0.29112426", "0.15065913"], ["Egr1", "TF", "9", "3.76829268", "0.05361397", "0.26537217", "0.13947991"], ["Nfe2l2", "Upregulated DEG_TF", "8", "3.89430894", "0.03472983", "0.25678497", "0.15972222"], ["Rela", "TF", "8", "3.33333333", "0.05841757", "0.3", "0.18382353"], ["Ep300", "TF", "8", "3.52439024", "0.04168611", "0.28373702", "0.19067797"], ["Upp1", "Upregulated DEG", "7", "3.58536585", "0.04680464", "0.27891156", "0.1978022"], ["Igf2", "Downregulated DEG", "7", "5.18292683", "0.04071495", "0.19294118", "0.14285714"], ["Ebf1", "Downregulated DEG_TF", "7", "4.57723577", "0.04361263", "0.21847247", "0.14285714"], ["Fos", "TF", "6", "3.82926829", "0.01974273", "0.2611465", "0.22727273"], ["Dcstamp", "Upregulated DEG", "6", "3.75203252", "0.02000123", "0.26652221", "0.25396825"], ["Nqo1", "Upregulated DEG", "5", "3.83333333", "0.02317522", "0.26086957", "0.21904762"], ["Ndrg1", "Downregulated DEG", "5", "3.83333333", "0.02104419", "0.26086957", "0.27142857"], ["Mmp14", "Downregulated DEG", "5", "3.81707317", "0.01378142", "0.26198083", "0.29"], ["Maf", "Downregulated DEG_TF", "5", "3.84146341", "0.0340471", "0.26031746", "0.28571429"], ["Hspa1b", "Downregulated DEG", "5", "3.88211382", "0.05662735", "0.25759162", "0.24545455"]], "row_count": 31, "column_count": 7, "numeric_cells": 154, "header_rows": 1, "locator": "section[17]/table-wrap[1]#tab8"}}, {"id": "asset:table:pmid:33381243:9", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:39d3a96de827ee8dc987622153032d252b34ff52c45b475dbaeade7eece8033c", "bytes": 2828, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[2]#tab9", "version": null, "note": "The topological characteristics of the top 30 nodes in the TF-target DEG interaction network involved in the EC-induced NSPC alteration.", "structure": {"pmcid": "PMC7758130", "section_index": 17, "section_title": "3.5. The Transcription Factor-Target DEG Interaction Network", "row_count": 31, "column_count": 7}, "table": {"label": "Table 9", "caption": "The topological characteristics of the top 30 nodes in the TF-target DEG interaction network involved in the EC-induced NSPC alteration.", "rows": [["Name", "Label", "Degree", "Average shortest path length", "Betweenness centrality", "Closeness centrality", "Topological coefficient"], ["Cdkn1a", "Downregulated DEG", "65", "2.73913043", "0.30858346", "0.36507937", "0.0283698"], ["Ccnd1", "Downregulated DEG_TF", "44", "2.90096618", "0.18721585", "0.34471274", "0.0390556"], ["Sp1", "TF", "38", "2.75120773", "0.18665254", "0.36347673", "0.04086687"], ["Fos", "Downregulated DEG_TF", "37", "2.89855072", "0.15489676", "0.345", "0.05012705"], ["Vegfa", "Downregulated DEG", "24", "3.09178744", "0.1032236", "0.3234375", "0.06904762"], ["Hes1", "Downregulated DEG_TF", "21", "3.26328502", "0.093159", "0.30643967", "0.06776557"], ["Cdkn2a", "Downregulated DEG", "20", "3.16183575", "0.06806015", "0.31627196", "0.0622093"], ["Nfkb1", "TF", "19", "2.83091787", "0.10896078", "0.35324232", "0.078356"], ["Cebpb", "Downregulated DEG_TF", "15", "3.01690821", "0.0630859", "0.33146517", "0.07979003"], ["Acta2", "Downregulated DEG", "14", "3.41062802", "0.04841393", "0.29320113", "0.10449735"], ["Trp53", "TF", "14", "3.23188406", "0.04815141", "0.30941704", "0.09895151"], ["Jun", "TF", "14", "3.25603865", "0.03607564", "0.30712166", "0.10204082"], ["Mmp2", "Downregulated DEG", "13", "3.08937198", "0.03126342", "0.32369038", "0.11609687"], ["Ep300", "TF", "12", "3.13043478", "0.05353532", "0.31944444", "0.11131841"], ["Cdkn2b", "Downregulated DEG", "12", "3.80917874", "0.03041314", "0.26252378", "0.10714286"], ["Nfe2l2", "Downregulated DEG_TF", "12", "3.26570048", "0.04141463", "0.30621302", "0.10585586"], ["Rela", "TF", "11", "3.21497585", "0.03799736", "0.31104433", "0.118411"], ["Nr3c1", "Downregulated DEG_TF", "11", "3.24637681", "0.03066868", "0.30803571", "0.11162255"], ["Smad6", "Downregulated DEG_TF", "11", "3.73671498", "0.02413405", "0.26761474", "0.11004785"], ["Sp3", "TF", "10", "3.35990338", "0.01668852", "0.29762761", "0.12268041"], ["Stat3", "TF", "10", "3.33816425", "0.03841092", "0.29956585", "0.13235294"], ["Id3", "Downregulated DEG", "10", "3.82125604", "0.02673839", "0.26169406", "0.10869565"], ["Smad3", "TF", "9", "3.72463768", "0.03330304", "0.26848249", "0.14403292"], ["Egr1", "TF", "9", "3.57004831", "0.03896833", "0.28010825", "0.12007168"], ["Mbp", "Downregulated DEG", "9", "3.52415459", "0.02687184", "0.283756", "0.13888889"], ["Srebf1", "TF", "8", "3.59903382", "0.0307691", "0.27785235", "0.13380282"], ["Myc", "TF", "8", "3.36231884", "0.02336862", "0.29741379", "0.14650538"], ["Id1", "Downregulated DEG_TF", "8", "3.2826087", "0.02185908", "0.30463576", "0.13903061"], ["Cebpd", "Downregulated DEG", "8", "3.43236715", "0.01679448", "0.29134412", "0.16163793"], ["Pdk4", "Downregulated DEG", "8", "3.61111111", "0.01282401", "0.27692308", "0.19396552"]], "row_count": 31, "column_count": 7, "numeric_cells": 152, "header_rows": 1, "locator": "section[17]/table-wrap[2]#tab9"}}, {"id": "asset:table:pmid:33381243:10", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:954ccb40064e73b3c675b77abf10e46b34123892cd0851b84125e06970e9ca27", "bytes": 1033, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#tab10", "version": null, "note": "The number of experimentally validated, computationally predicted, and total miRNA-target DEG interaction pairs during the NSPC-induced EC alteration and EC-induced NSPC alteration.", "structure": {"pmcid": "PMC7758130", "section_index": 18, "section_title": "3.6. The DEmiRNAs-Target DEGs and Their Functions", "row_count": 3, "column_count": 5}, "table": {"label": "Table 10", "caption": "The number of experimentally validated, computationally predicted, and total miRNA-target DEG interaction pairs during the NSPC-induced EC alteration and EC-induced NSPC alteration.", "rows": [["Coculture-induced alterations in one type of cells", "Validated miRNA-target DEG pairs", "Predicted miRNA-target DEG pairs", "Total miRNA-target DEG pairs (including validated and predicted)", "Overlapped miRNA-target DEG interaction pairs (overlapped between NSPC-induced EC alteration and EC-induced NSPC alteration)"], ["NSPC-induced EC alteration", "536", "391", "810", "The overlapped 14 interaction pairs are as follows: miR-21-Rhoq, miR-23a-Akap12, miR-23a-Aldh1a1, miR-23a-Exoc3l4, miR-23a-Gm5424, miR-23a-Mfhas1, miR-23a-Nfe2l2, miR-23a-Slc16a6, miR-23b-Akap12, miR-23b-Aldh1a1, miR-23b-Gm5424, miR-23b-Mfhas1, miR-23b-Nfe2l2, and miR-23b-Slc16a6."], ["EC-induced NSPC alteration", "571", "243", "711"]], "row_count": 3, "column_count": 5, "numeric_cells": 7, "header_rows": 1, "locator": "section[18]/table-wrap[1]#tab10"}}, {"id": "asset:table:pmid:33381243:11", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0ec4dcea4e2dcbc6e5a81f6d720d9ba81fe01dfe03cfd4bbb0355d99f55db95b", "bytes": 2667, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[2]#tab11", "version": null, "note": "The topological characteristics of the top 30 nodes in the DEmiRNA-target network involved in the NSPC-induced EC alteration.", "structure": {"pmcid": "PMC7758130", "section_index": 18, "section_title": "3.6. The DEmiRNAs-Target DEGs and Their Functions", "row_count": 31, "column_count": 7}, "table": {"label": "Table 11", "caption": "The topological characteristics of the top 30 nodes in the DEmiRNA-target network involved in the NSPC-induced EC alteration.", "rows": [["Name", "lab2", "Degree", "Average shortest path length", "Betweenness centrality", "Closeness centrality", "Topological coefficient"], ["mmu-miR-26a-2", "DEmiRNA", "2371", "2.195604", "0.216585", "0.455455", "0.221505"], ["mmu-miR-26a-1", "DEmiRNA", "2371", "2.195604", "0.216585", "0.455455", "0.221505"], ["mmu-let-7i", "DEmiRNA", "2244", "2.238546", "0.131513", "0.446719", "0.323641"], ["mmu-let-7c-2", "DEmiRNA", "2202", "2.252747", "0.110037", "0.443902", "0.332539"], ["mmu-let-7c-1", "DEmiRNA", "2202", "2.252747", "0.110037", "0.443902", "0.332539"], ["mmu-let-7a-2", "DEmiRNA", "1585", "2.461369", "0.051855", "0.406278", "0.376735"], ["mmu-let-7a-1", "DEmiRNA", "1585", "2.461369", "0.051855", "0.406278", "0.376735"], ["mmu-miR-23a", "DEmiRNA", "1297", "2.558749", "0.106936", "0.390816", "0.247494"], ["mmu-miR-23b", "DEmiRNA", "1269", "2.568216", "0.100185", "0.389375", "0.248916"], ["mmu-let-7d", "DEmiRNA", "1252", "2.573965", "0.063356", "0.388506", "0.353484"], ["mmu-miR-199a-2", "DEmiRNA", "839", "2.713609", "0.055721", "0.368513", "0.273838"], ["mmu-miR-199a-1", "DEmiRNA", "839", "2.713609", "0.055721", "0.368513", "0.273838"], ["mmu-miR-140", "DEmiRNA", "760", "2.740321", "0.114496", "0.364921", "0.175411"], ["mmu-miR-182", "DEmiRNA", "668", "2.771429", "0.088383", "0.360825", "0.194891"], ["mmu-miR-199b", "DEmiRNA", "660", "2.774134", "0.048537", "0.360473", "0.278883"], ["mmu-miR-210", "DEmiRNA", "468", "2.839053", "0.061318", "0.35223", "0.195913"], ["mmu-miR-99b", "DEmiRNA", "52", "2.979713", "0.006853", "0.335603", "0.234375"], ["Celf1", "Target gene", "16", "2.004227", "0.002733", "0.498946", "0.24026"], ["Taok1", "Target gene", "15", "2.179374", "0.001948", "0.458847", "0.263894"], ["Ubn2", "Target gene", "14", "2.137447", "0.001613", "0.467848", "0.279439"], ["Suco", "Target gene", "14", "2.137447", "0.001613", "0.467848", "0.279439"], ["Mtf2", "Target gene", "14", "2.186475", "0.001497", "0.457357", "0.28312"], ["Map3k2", "Target gene", "14", "2.162468", "0.001485", "0.462435", "0.282045"], ["Kdm6a", "Target gene", "14", "2.162468", "0.001485", "0.462435", "0.282045"], ["Ino80d", "Target gene", "14", "2.137109", "0.001824", "0.467922", "0.267984"], ["Celf2", "Target gene", "14", "2.090786", "0.001937", "0.478289", "0.265165"], ["Ankrd44", "Target gene", "14", "2.186475", "0.001497", "0.457357", "0.28312"], ["Tnpo1", "Target gene", "13", "2.196281", "0.001334", "0.455315", "0.291288"], ["Rfx7", "Target gene", "13", "2.144548", "0.001367", "0.466299", "0.28419"], ["Kmt2a", "Target gene", "13", "2.263567", "0.001442", "0.441781", "0.289898"]], "row_count": 31, "column_count": 7, "numeric_cells": 169, "header_rows": 1, "locator": "section[18]/table-wrap[2]#tab11"}}, {"id": "asset:table:pmid:33381243:12", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:90ca385bdcff709d28d8c0416748e266f9cbd05a6d9a6c7b401fa5e315417779", "bytes": 2610, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[3]#tab12", "version": null, "note": "The topological characteristics of the top 30 nodes in the DEmiRNA-target network involved in the EC-induced NSPC alteration.", "structure": {"pmcid": "PMC7758130", "section_index": 18, "section_title": "3.6. The DEmiRNAs-Target DEGs and Their Functions", "row_count": 31, "column_count": 7}, "table": {"label": "Table 12", "caption": "The topological characteristics of the top 30 nodes in the DEmiRNA-target network involved in the EC-induced NSPC alteration.", "rows": [["Name", "lab2", "Degree", "Average shortest path length", "Betweenness centrality", "Closeness centrality", "Topological coefficient"], ["mmu-let-7b", "DEmiRNA_up", "2362", "2.046362", "0.551173", "0.488672", "0.170618"], ["mmu-miR-124-1", "DEmiRNA_down", "1863", "2.247531", "0.154513", "0.444933", "0.394448"], ["mmu-miR-124-2", "DEmiRNA_down", "1863", "2.247531", "0.154513", "0.444933", "0.394448"], ["mmu-miR-124-3", "DEmiRNA_down", "1863", "2.247531", "0.154513", "0.444933", "0.394448"], ["mmu-miR-23a", "DEmiRNA_up", "1297", "2.475711", "0.158061", "0.403924", "0.306091"], ["mmu-miR-23b", "DEmiRNA_up", "1269", "2.486999", "0.14813", "0.402091", "0.309242"], ["mmu-miR-320", "DEmiRNA_up", "690", "2.720419", "0.141572", "0.36759", "0.217805"], ["mmu-miR-210", "DEmiRNA_up", "468", "2.809917", "0.093463", "0.355882", "0.206654"], ["Ino80d", "Target gene", "8", "1.998387", "0.0024", "0.500403", "0.294443"], ["Adam10", "Target gene", "8", "1.998387", "0.0024", "0.500403", "0.294443"], ["Mtf2", "Target gene", "8", "1.998387", "0.0024", "0.500403", "0.294443"], ["Pcdh19", "DEmRNA", "7", "2.085467", "0.001524", "0.479509", "0.337695"], ["Rora", "DEmRNA", "7", "2.545051", "0.001403", "0.392919", "0.369491"], ["Ago2", "Target gene", "7", "2.1282", "0.00156", "0.469881", "0.338576"], ["Ago3", "Target gene", "7", "2.1282", "0.00156", "0.469881", "0.338576"], ["Col4a1", "Target gene", "7", "2.085467", "0.001524", "0.479509", "0.337695"], ["Cpd", "Target gene", "7", "2.085467", "0.001524", "0.479509", "0.337695"], ["Map3k1", "Target gene", "7", "2.085467", "0.001524", "0.479509", "0.337695"], ["Mecp2", "Target gene", "7", "2.085467", "0.001524", "0.479509", "0.337695"], ["Etnk1", "Target gene", "7", "2.085467", "0.001524", "0.479509", "0.337695"], ["Kpna1", "Target gene", "7", "2.085467", "0.001524", "0.479509", "0.337695"], ["Yod1", "Target gene", "7", "2.085467", "0.001524", "0.479509", "0.337695"], ["Prtg", "Target gene", "7", "2.085467", "0.001524", "0.479509", "0.337695"], ["Slc36a1", "Target gene", "7", "2.1282", "0.00156", "0.469881", "0.338576"], ["Tet2", "Target gene", "7", "2.1282", "0.00156", "0.469881", "0.338576"], ["Ahctf1", "Target gene", "7", "2.1282", "0.00156", "0.469881", "0.338576"], ["Qser1", "Target gene", "7", "2.085467", "0.001524", "0.479509", "0.337695"], ["Wnk1", "Target gene", "7", "2.085467", "0.001524", "0.479509", "0.337695"], ["Slc7a2", "Target gene", "7", "2.085467", "0.001524", "0.479509", "0.337695"], ["Aldh1l2", "Target gene", "7", "2.545051", "0.001403", "0.392919", "0.369491"]], "row_count": 31, "column_count": 7, "numeric_cells": 162, "header_rows": 1, "locator": "section[18]/table-wrap[3]#tab12"}}, {"id": "asset:table:pmid:33381243:13", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:caf7d3a08c2735dabfbb2c80167b7226539cb479736af8a5a7647cee9b2176c1", "bytes": 954, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#tab13", "version": null, "note": "The 16 small molecular drugs that were overlapped between NSPC-induced EC genetic alteration and EC-induced NSPC genetic alteration.", "structure": {"pmcid": "PMC7758130", "section_index": 19, "section_title": "3.7. Identifying Significant Small Molecular Drugs", "row_count": 17, "column_count": 3}, "table": {"label": "Table 13", "caption": "The 16 small molecular drugs that were overlapped between NSPC-induced EC genetic alteration and EC-induced NSPC genetic alteration.", "rows": [["Small molecular drugs", "Enrichment in the NSPC-induced EC alteration", "Enrichment in the EC-induced NSPC alteration"], ["2-Aminobenzenesulfonamide", "0.629", "-0.682"], ["Adiphenine", "0.748", "-0.693"], ["Deptropine", "-0.677", "-0.672"], ["Diphenhydramine", "0.67", "-0.573"], ["Felbinac", "0.719", "-0.697"], ["Fludrocortisone", "0.503", "-0.496"], ["Fluphenazine", "-0.357", "-0.378"], ["Ikarugamycin", "0.811", "-0.838"], ["Lycorine", "0.633", "0.776"], ["Milrinone", "-0.779", "0.73"], ["PHA-00745360", "0.567", "-0.514"], ["Podophyllotoxin", "0.661", "-0.933"], ["Quinostatin", "-0.992", "-0.954"], ["Resveratrol", "-0.479", "-0.504"], ["Thiamazole", "0.726", "0.543"], ["Triflupromazine", "0.694", "-0.71"]], "row_count": 17, "column_count": 3, "numeric_cells": 34, "header_rows": 1, "locator": "section[19]/table-wrap[1]#tab13"}}, {"id": "asset:table:pmid:33381243:14", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6eee76bae85ec6afb9b6ba0332997ba3af2cf3c3fd69748908d4a9950ec2c9f2", "bytes": 5039, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[1]#tab14", "version": null, "note": "The scores of the crosstalk miRNA interaction pairs under five conditions including the target genes, small molecular drugs, chemical compounds, signaling pathways, and biological processes. These crosstalk miRNAs link the EC-induced NSPC alteration process and NSPC-induced EC alteration process. The scores were calculated by the “Meet/Min” formula.", "structure": {"pmcid": "PMC7758130", "section_index": 21, "section_title": "3.9. Crosstalk miRNAs Linking the EC-Induced NSPC Alteration Process and NSPC-Induced EC Alteration Process", "row_count": 55, "column_count": 7}, "table": {"label": "Table 14", "caption": "The scores of the crosstalk miRNA interaction pairs under five conditions including the target genes, small molecular drugs, chemical compounds, signaling pathways, and biological processes. These crosstalk miRNAs link the EC-induced NSPC alteration process and NSPC-induced EC alteration process. The scores were calculated by the “Meet/Min” formula.", "rows": [["miRNAs involved in the NSPC-induced EC alteration", "miRNAs involved in the EC-induced NSPC alteration", "Score_target", "Score_molecular", "Score_chemical", "Score_pathway", "Score_bp"], ["mmu-miR-210", "mmu-miR-210", "1", "0.166667", "1", "1", "1"], ["mmu-miR-23b", "mmu-miR-23b", "1", "0.075", "1", "1", "1"], ["mmu-miR-23b", "mmu-miR-23a", "0.966903", "0.022222", "1", "0.946667", "0.931284"], ["mmu-miR-23a", "mmu-miR-23b", "0.966903", "0.05", "0.95", "0.946667", "0.931284"], ["mmu-let-7d", "mmu-let-7b", "0.834665", "0.021739", "0.2", "1", "0.862256"], ["mmu-miR-26a-1", "mmu-miR-23a", "0.393215", "0.05", "0.321429", "0.936709", "0.614696"], ["mmu-miR-26a-2", "mmu-miR-23a", "0.393215", "0.05", "0.321429", "0.936709", "0.614696"], ["mmu-miR-26a-1", "mmu-miR-23b", "0.389283", "0.025", "0.307692", "0.946667", "0.615335"], ["mmu-miR-26a-2", "mmu-miR-23b", "0.389283", "0.025", "0.307692", "0.946667", "0.615335"], ["mmu-miR-26a-1", "mmu-miR-210", "0.344017", "0.027778", "0.333333", "0.8", "0.689956"], ["mmu-miR-26a-2", "mmu-miR-210", "0.344017", "0.027778", "0.333333", "0.8", "0.689956"], ["mmu-miR-26a-1", "mmu-miR-320", "0.337681", "0.05", "0.4", "0.885714", "0.708661"], ["mmu-miR-26a-2", "mmu-miR-320", "0.337681", "0.05", "0.4", "0.885714", "0.708661"], ["mmu-miR-23a", "mmu-let-7b", "0.312259", "0.021739", "0.25", "0.772152", "0.595539"], ["mmu-let-7i", "mmu-miR-23b", "0.3026", "0.074074", "0.318182", "0.693333", "0.592737"], ["mmu-let-7i", "mmu-miR-23a", "0.302236", "0.074074", "0.363636", "0.708861", "0.590143"], ["mmu-miR-199a-1", "mmu-let-7b", "0.299166", "0.022222", "0.142857", "0.728395", "0.65798"], ["mmu-miR-199a-2", "mmu-let-7b", "0.299166", "0.022222", "0.142857", "0.728395", "0.65798"], ["mmu-let-7c-1", "mmu-miR-23b", "0.29866", "0.071429", "0.32", "0.72", "0.587937"], ["mmu-let-7c-2", "mmu-miR-23b", "0.29866", "0.071429", "0.32", "0.72", "0.587937"], ["mmu-let-7i", "mmu-miR-210", "0.297009", "0.037037", "0.222222", "0.8", "0.609898"], ["mmu-miR-210", "mmu-let-7b", "0.292735", "0.073171", "0.875", "0.8", "0.63901"], ["mmu-let-7c-1", "mmu-miR-124-1", "0.285561", "0.035714", "0.72", "0.709302", "0.623492"], ["mmu-let-7c-1", "mmu-miR-124-2", "0.285561", "0.035714", "0.72", "0.709302", "0.623492"], ["mmu-let-7c-1", "mmu-miR-124-3", "0.285561", "0.035714", "0.72", "0.709302", "0.623492"], ["mmu-let-7c-2", "mmu-miR-124-1", "0.285561", "0.035714", "0.72", "0.709302", "0.623492"], ["mmu-let-7c-2", "mmu-miR-124-2", "0.285561", "0.035714", "0.72", "0.709302", "0.623492"], ["mmu-let-7c-2", "mmu-miR-124-3", "0.285561", "0.035714", "0.72", "0.709302", "0.623492"], ["mmu-let-7a-1", "mmu-miR-23b", "0.239559", "0.041667", "0.619048", "0.706667", "0.616536"], ["mmu-let-7a-2", "mmu-miR-23b", "0.239559", "0.041667", "0.619048", "0.706667", "0.616536"], ["mmu-let-7a-1", "mmu-miR-23a", "0.2367", "0.041667", "0.666667", "0.721519", "0.610834"], ["mmu-let-7a-2", "mmu-miR-23a", "0.2367", "0.041667", "0.666667", "0.721519", "0.610834"], ["mmu-miR-23b", "mmu-miR-124-1", "0.230102", "0.028571", "0.666667", "0.8", "0.527677"], ["mmu-miR-23b", "mmu-miR-124-2", "0.230102", "0.028571", "0.666667", "0.8", "0.527677"], ["mmu-miR-23b", "mmu-miR-124-3", "0.230102", "0.028571", "0.666667", "0.8", "0.527677"], ["mmu-miR-23a", "mmu-miR-124-1", "0.229761", "0.028571", "0.75", "0.759494", "0.523207"], ["mmu-miR-23a", "mmu-miR-124-2", "0.229761", "0.028571", "0.75", "0.759494", "0.523207"], ["mmu-miR-23a", "mmu-miR-124-3", "0.229761", "0.028571", "0.75", "0.759494", "0.523207"], ["mmu-miR-23a", "mmu-miR-320", "0.226087", "0.04", "0.2", "0.714286", "0.755906"], ["mmu-miR-23b", "mmu-miR-320", "0.22029", "0.043478", "0.2", "0.628571", "0.76378"], ["mmu-miR-199a-1", "mmu-miR-23a", "0.212157", "0.066667", "0.142857", "0.594937", "0.619707"], ["mmu-miR-199a-2", "mmu-miR-23a", "0.212157", "0.066667", "0.142857", "0.594937", "0.619707"], ["mmu-miR-199a-1", "mmu-miR-23b", "0.205006", "0.05", "0.142857", "0.626667", "0.618078"], ["mmu-miR-199a-2", "mmu-miR-23b", "0.205006", "0.05", "0.142857", "0.626667", "0.618078"], ["mmu-miR-210", "mmu-miR-23a", "0.202991", "0.170732", "0.25", "0.8", "0.660844"], ["mmu-miR-210", "mmu-miR-23b", "0.196581", "0.075", "0.125", "0.8", "0.672489"], ["mmu-let-7d", "mmu-miR-23b", "0.183706", "0.025", "0.64", "0.666667", "0.675705"], ["mmu-let-7d", "mmu-miR-23a", "0.182109", "0.022222", "0.64", "0.717949", "0.671367"], ["mmu-let-7d", "mmu-miR-320", "0.176812", "0.057692", "0.2", "0.485714", "0.531496"], ["mmu-miR-199a-1", "mmu-miR-320", "0.127536", "0.022222", "0.2", "0.771429", "0.616142"], ["mmu-miR-199a-2", "mmu-miR-320", "0.127536", "0.022222", "0.2", "0.771429", "0.616142"], ["mmu-miR-182", "mmu-miR-320", "0.115269", "0.093023", "0.666667", "0.828571", "0.555118"], ["mmu-miR-199b", "mmu-miR-320", "0.109091", "0.090909", "0.6", "0.714286", "0.543307"], ["mmu-miR-210", "mmu-miR-320", "0.087607", "0.121951", "0.2", "0.2", "0.358268"]], "row_count": 55, "column_count": 7, "numeric_cells": 378, "header_rows": 1, "locator": "section[21]/table-wrap[1]#tab14"}}], "gaps": ["asset:data:geo:GSE29759 not downloaded", "asset:data:geo:GSE29759 licence not read"]}, "analysis": {"state": "complete", "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": "Differential expression analysis was performed using the R package “limma” [13] for identifying differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) relevant to EC-induced NSPC changes and NSPC-induced EC changes, respectively."}}], "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": ["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": ["GSE29759"], "resolved_accessions": ["GSE29759"], "statements": ["The data used to support the findings of this study are available from the corresponding author upon request."], "basis": "The paper names GSE29759 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:33381243", "data:geo:GSE29759", "asset:table:pmid:33381243:1", "asset:table:pmid:33381243:2", "asset:table:pmid:33381243:3", "asset:table:pmid:33381243:4", "asset:table:pmid:33381243:5", "asset:table:pmid:33381243:6", "asset:table:pmid:33381243:7", "asset:table:pmid:33381243:8", "asset:table:pmid:33381243:9", "asset:table:pmid:33381243:10", "asset:table:pmid:33381243:11", "asset:table:pmid:33381243:12", "asset:table:pmid:33381243:13", "asset:table:pmid:33381243:14"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE29759"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:41Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 42023, "completion_tokens": 1239, "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:33381243", "type": "paper", "label": "pmid:33381243"}, {"id": "source:pmid:33381243", "type": "manuscript", "label": "PMID 33381243 full text"}, {"id": "data:geo:GSE29759", "type": "dataset", "label": "GEO GSE29759"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33381243", "type": "paper", "label": "pmid:33381243"}, {"id": "source:pmid:33381243", "type": "manuscript", "label": "PMID 33381243 full text"}, {"id": "data:geo:GSE29759", "type": "dataset", "label": "GEO GSE29759"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33381243", "type": "extraction", "used": ["source:pmid:33381243"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE29759", "type": "accession_resolution", "used": ["data:geo:GSE29759"], "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:33381243", "parent_hash": "sha256:43932a3ba62e09b52e2d89eb9c18032884353310c4e43070d96f59d504e4368e", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE29759 licence not read", "asset:data:geo:GSE29759 not downloaded", "execution.not_run", "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": ["Differential expression analysis was performed using the R package “limma” [13] for identifying differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) relevant to EC-induced NSPC changes and NSPC-induced EC changes, respectively."], "order_basis": "analysis_only", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T03:48:54+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}