{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31545431", "kind": "science-record", "revision": 5, "content_hash": "sha256:40596f9657bf4e4bf093c62b57f6c695863541b8047cac262e357e2668c33ff0", "created_at": "2026-11-01T15:40:49Z", "updated_at": "2026-11-01T22:00:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "miR‑126a‑5p‑Dbp and miR‑31a‑Crot/Mrpl4 interaction pairs crucial for the development of hypertension and stroke.", "doi": "10.3892/mmr.2019.10679", "pmid": "31545431", "authors": ["Qini Zhao", "Huan Sun", "Liquan Yin", "Libo Wang"], "journal": "Molecular medicine reports", "year": 2019, "abstract": "The present study aimed to integrate the mRNA and microRNA (miRNA) expression profiles of spontaneously hypertensive rats (SHR rats) and stroke‑prone spontaneously hypertensive rats (SHRSP rats) to screen for potential therapeutic targets for hypertension and stroke. The datasets GSE41452, GSE31457, GSE41453 and GSE53363 were collected from the Gene Expression Omnibus (GEO) database to screen differentially expressed genes (DEGs). The GSE53361 dataset was obtained to analyze differentially expressed miRNAs (DEMs). The DEGs and DEMs were identified between SHR (or SHRSP) rats and normotensive Wistar‑Kyoto (WKY) rats using the Linear Models for Microarray (limma) data method. Venn diagrams were used to show the SHR‑specific, SHRSP‑specific and SHR‑SHRSP shared DEGs and DEMs, and these were utilized to construct the protein‑protein interaction (PPI) and miRNA‑mRNA regulatory networks. The Database for Annotation, Visualization and Integrated Discovery (DAVID) was used to explore the function of the genes. Subsequently, the connectivity Map (CMAP) database was searched to identify small‑molecule drugs. Comparisons between the GSE41452‑GSE31457‑GSE41453 merged and GSE53363 datasets identified 2 SHR‑specific, 8 SHRSP‑specific and 15 SHR‑SHRSP shared DEGs. Function enrichment analysis showed that SHRSP‑specific D‑box binding PAR bZIP transcription factor (Dbp) was associated with circadian rhythm, and SHR‑SHRSP shared carnitine O‑octanoyltransferase (Crot) was involved in fatty acid metabolic processes or the inflammatory response via interacting with epoxide hydrolase 2 (EPHX2). SHR‑SHRSP shared mitochondrial ribosomal protein L4 (Mrpl4) may exert roles by interacting with the threonine‑tRNA ligase, TARS2. The miRNA regulatory network predicted that upregulated Dbp could be regulated by rno‑miR‑126a‑5p, whereas downregulated Crot and Mrpl4 could be modulated by rno‑miR‑31a. The CMAP database predicted that small‑molecule drugs, including botulin, Gly‑His‑Lys, and podophyllotoxin, may possess therapeutic potential. In conclusion, the present study has identified Dbp, Crot and Mrpl4 as potential targets for the treatment of hypertension and stroke. Furthermore, the expression of these genes may be reversed by the above miRNAs or drugs.", "claims": [{"id": "claim-data-access", "statement": "The sequencing data GSE41452, GSE31457, GSE41453, GSE53363 and GSE53361 were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31545431", "locator": "sections[20] \"Availability of data and materials\" paragraph 2", "quote": "The sequencing data GSE41452, GSE31457, GSE41453, GSE53363 and GSE53361 were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/)."}], "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:31545431"], "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. 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"identifier": "section[12]/table-wrap[1]#tII-mmr-20-05-4151", "version": null, "note": "Differentially expressed miRNAs comparing between SHR (or SHRSP) and WKY rats.", "structure": {"pmcid": "PMC6797943", "section_index": 5, "section_title": "Differential expression analysis", "row_count": 36, "column_count": 4}, "table": {"label": "Table II.", "caption": "Differentially expressed miRNAs comparing between SHR (or SHRSP) and WKY rats.", "rows": [["A, SHR vs. WKY"], [""], ["", "SHR vs. WKY"], ["", ""], ["miRNA", "logFC", "P-value", "FDR"], ["rno-miR-31a-3p", "1.66", "3.99E-06", "2.87E-03"], ["rno-miR-31a-5p", "2.35", "4.15E-05", "1.49E-02"], ["rno-miR-150-5p", "−0.51", "2.87E-04", "6.88E−02"], ["rno-miR-511-3p", "0.77", "6.86E-04", "9.87E−02"], ["rno-miR-146b-5p", "0.84", "5.78E-03", "6.92E−01"], ["rno-miR-146a-5p", "−0.56", "8.54E-03", "7.62E−01"], ["rno-miR-672-5p", "−0.74", "1.67E-02", "7.62E−01"], ["rno-miR-132-3p", "0.76", "1.70E-02", "7.62E−01"], ["rno-miR-150-3p", "−0.68", 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"header_rows": 5, "locator": "section[12]/table-wrap[1]#tII-mmr-20-05-4151"}}, {"id": "asset:table:pmid:31545431:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9f7dd53a7ca6b6f03bfcd414232f939225d74a49774737370c71f57bf5aa8ac6", "bytes": 3512, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#tIII-mmr-20-05-4151", "version": null, "note": "Differentially expressed genes between SHR (or SHRSP) and WKY.", "structure": {"pmcid": "PMC6797943", "section_index": 5, "section_title": "Differential expression analysis", "row_count": 43, "column_count": 8}, "table": {"label": "Table III.", "caption": "Differentially expressed genes between SHR (or SHRSP) and WKY.", "rows": [["", "", "GSE31457-GSE41452-GSE41453", "GSE53363"], ["", "", "", ""], ["", "Gene", "logFC", "P-value", "FDR", "logFC", "P-value", "FDR"], ["SHR-specific", "Ch25h", "0.51", "4.25E-03", "3.40E−01", "0.62", "6.53E-03", "3.82E−01"], ["", "Sec16b", "0.67", "2.61E-02", "9.16E−01", "0.50", "5.58E-03", "3.71E−01"], ["SHRSP-specific", "RGD1310414", "0.57", "1.44E-06", "8.96E-04", "0.53", "2.70E-03", "1.64E−01"], ["", "Nr1d2", "0.58", "6.35E-04", "1.10E−01", "0.54", "2.69E-03", "1.64E−01"], ["", "Dbp", "0.97", "1.15E-03", "1.63E−01", "0.87", "4.76E-03", "2.05E−01"], ["", "LOC686388", "−0.53", "1.41E-03", "1.81E−01", "−0.60", "6.61E-04", "8.71E−02"], ["", "Mb", "−0.53", "3.18E-03", "3.05E−01", "0.54", "4.04E-04", "7.10E−02"], ["", "Pigzl1", "1.23", "4.50E-02", "1.00E−01", "0.63", "3.13E-02", "4.07E−01"], ["", "Tgfbi", "−0.57", "4.66E-02", "1.00E−01", "−0.62", "2.09E-02", "3.59E−01"], ["", "Tef", "0.822", "4.84E-02", "1.00E−01", "0.74", "1.53E-02", "3.20E−01"], ["SHR-SHRSP (SHRSP)", "Endog", "−1.52", "5.13E-09", "7.06E-06", "−0.94", "9.03E-06", "6.20E-03"], ["", "Tor1b", "1.29", "7.91E-09", "1.02E-05", "1.37", "1.69E-08", "7.75E-05"], ["", "Chmp1b", "−1.08", "1.16E-08", "1.40E-05", "−0.70", "8.21E-04", "9.27E−02"], ["", "Riok1", "0.96", "2.01E-06", "1.21E-03", "0.66", "4.15E-04", "7.14E−02"], ["", "Fkbp5", "1.25", "1.15E-05", "5.05E-03", "1.76", "7.83E-06", "5.70E-03"], ["", "Mrpl4", "−0.74", "4.99E-05", "1.58E-02", "−0.87", "5.28E-06", "5.00E-03"], ["", "RGD1562351", "−0.89", "3.21E-04", "6.80E−02", "−0.50", "7.14E-03", "2.42E−01"], ["", "Tars2", "−0.66", "5.01E-04", "9.04E−02", "−0.93", "4.27E-07", "7.32E-04"], ["", "Crot", "−0.77", "1.27E-03", "1.74E−01", "−0.52", "9.78E-03", "2.83E−01"], ["", "Zfp597", "1.37", "2.35E-03", "2.52E−01", "1.00", "2.64E-05", "1.32E-02"], ["", "Ms4a11", "0.76", "4.37E-03", "3.72E−01", "1.09", "7.76E-03", "2.52E−01"], ["", "Aldh5a1", "−0.59", "5.85E-03", "4.45E−01", "−0.51", "2.75E-03", "1.66 E−01"], ["", "Retsat", "−1.07", "1.10E-02", "6.08E−01", "−0.66", "4.09E-02", "4.45E−01"], ["", "Pxmp4", "−0.68", "1.42E-02", "7.07 E−01", "0.93", "1.02E-05", "6.67E-03"], ["", "Tmem14a", "0.67", "1.75E-02", "7.93E−01", "0.80", "6.04E-06", "5.00E-03"], ["SHR-SHRSP (SHR)", "Endog", "−1.54", "1.30E-09", "1.94E-06", "−0.71", "4.88E-04", "1.01E−01"], ["", "Tor1b", "1.27", "3.43E-08", "2.55E-05", "1.04", "1.01E-04", "4.38E-02"], ["", "Chmp1b", "−1.09", "7.64E-09", "7.37E-06", "−0.88", "4.82E-05", "2.81E-02"], ["", "Riok1", "0.98", "1.38E-07", "6.17E-03", "0.56", "3.63E-03", "3.00E−01"], ["", "Fkbp5", "1.20", "5.53E-06", "2.32E-03", "1.22", "9.36E-04", "1.67E−01"], ["", "Mrpl4", "−0.68", "1.82E-05", "6.17E-03", "−0.90", "1.93E-06", "4.40E-03"], ["", "RGD1562351", "−0.81", "1.163E-03", "1.45E−01", "−0.60", "8.74E-04", "1.60E−01"], ["", "Tars2", "−0.61", "8.61E-04", "1.18E−01", "−0.721", "1.21E-04", "4.54E-02"], ["", "Crot", "−0.61", "1.26E-02", "6.10E−01", "−0.53", "4.67E-03", "0.3.48E−01"], ["", "Zfp597", "1.35", "5.63E-03", "3.92E−01", "0.94", "6.49E-05", "3.07E-02"], ["", "Ms4a11", "0.80", "1.34E-02", "6.33E−01", "0.71", "2.24E-02", "5.98E−01"], ["", "Aldh5a1", "−0.55", "8.58E-03", "5.12E−01", "−0.58", "3.00E-04", "7.34E−02"], ["", "Retsat", "−0.96", "2.42E-02", "8.81E−01", "−0.61", "3.19E-02", "6.45E−01"], ["", "Pxmp4", "−0.79", "9.60E-03", "5.41E−01", "0.77", "2.78E-04", "6.95E−02"], ["", "Tmem14a", "0.81", "4.98E-03", "3.72E−01", "0.93", "1.14E-03", "1.84E−01"]], "row_count": 43, "column_count": 8, "numeric_cells": 254, "header_rows": 3, "locator": "section[12]/table-wrap[2]#tIII-mmr-20-05-4151"}}, {"id": "asset:table:pmid:31545431:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:95a074ae2c011a2b9ce13905fd81d2b5e089d49883205ed2cc1f5ce294232afa", "bytes": 1673, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tII-mmr-20-05-4151", "version": null, "note": "Differentially expressed miRNAs comparing between SHR (or SHRSP) and WKY rats.", "structure": {"pmcid": "PMC6797943", "section_index": 12, "section_title": "Differential expression analysis", "row_count": 36, "column_count": 4}, "table": {"label": "Table II.", "caption": "Differentially expressed miRNAs comparing between SHR (or SHRSP) and WKY rats.", "rows": [["A, SHR vs. WKY"], [""], ["", "SHR vs. WKY"], ["", ""], ["miRNA", "logFC", "P-value", "FDR"], ["rno-miR-31a-3p", "1.66", "3.99E-06", "2.87E-03"], ["rno-miR-31a-5p", "2.35", "4.15E-05", "1.49E-02"], ["rno-miR-150-5p", "−0.51", "2.87E-04", "6.88E−02"], ["rno-miR-511-3p", "0.77", "6.86E-04", "9.87E−02"], ["rno-miR-146b-5p", "0.84", "5.78E-03", "6.92E−01"], ["rno-miR-146a-5p", "−0.56", "8.54E-03", "7.62E−01"], ["rno-miR-672-5p", "−0.74", "1.67E-02", "7.62E−01"], ["rno-miR-132-3p", "0.76", "1.70E-02", "7.62E−01"], ["rno-miR-150-3p", "−0.68", "2.63E-02", "8.42E−01"], ["rno-miR-3593-3p", "−0.56", "3.44E-02", "8.42E−01"], ["rno-miR-1224", "−0.89", "3.54E-02", "8.42E−01"], [""], ["B, SHRSP vs. WKY"], [""], ["", "SHRSP vs. WKY"], ["", ""], ["miRNA", "logFC", "P-value", "FDR"], [""], ["rno-miR-31a-3p", "1.65", "1.27E-03", "4.33 E−01"], ["rno-miR-126a-5p", "−0.58", "1.91E-03", "4.33 E−01"], ["rno-miR-196a-5p", "2.11", "2.52E-03", "4.33 E−01"], ["rno-miR-146a-5p", "−0.85", "2.98E-03", "4.33 E−01"], ["rno-miR-150-5p", "−0.51", "3.05E-03", "4.33 E−01"], ["rno-miR-31a-5p", "2.12", "3.61E-03", "4.33 E−01"], ["rno-miR-126a-3p", "−0.53", "1.57E-02", "1.00E−01"], ["rno-miR-511-3p", "0.73", "2.10E-02", "1.00E−01"], ["rno-miR-21-5p", "0.70", "2.39E-02", "1.00E−01"], ["rno-miR-1224", "−1.43", "2.57E-02", "1.00E−01"], ["rno-miR-672-5p", "−1.01", "2.60E-02", "1.00E−01"], ["rno-miR-196b-5p", "1.98", "2.76E-02", "1.00E−01"], ["rno-miR-483-3p", "−0.66", "4.14E-02", "1.00E−01"]], "row_count": 36, "column_count": 4, "numeric_cells": 96, "header_rows": 5, "locator": "section[12]/table-wrap[1]#tII-mmr-20-05-4151"}}, {"id": "asset:table:pmid:31545431:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9f7dd53a7ca6b6f03bfcd414232f939225d74a49774737370c71f57bf5aa8ac6", "bytes": 3512, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#tIII-mmr-20-05-4151", "version": null, "note": "Differentially expressed genes between SHR (or SHRSP) and WKY.", "structure": {"pmcid": "PMC6797943", "section_index": 12, "section_title": "Differential expression analysis", "row_count": 43, "column_count": 8}, "table": {"label": "Table III.", "caption": "Differentially expressed genes between SHR (or SHRSP) and WKY.", "rows": [["", "", "GSE31457-GSE41452-GSE41453", "GSE53363"], ["", "", "", ""], ["", "Gene", "logFC", "P-value", "FDR", "logFC", "P-value", "FDR"], ["SHR-specific", "Ch25h", "0.51", "4.25E-03", "3.40E−01", "0.62", "6.53E-03", "3.82E−01"], ["", "Sec16b", "0.67", "2.61E-02", "9.16E−01", "0.50", "5.58E-03", "3.71E−01"], ["SHRSP-specific", "RGD1310414", "0.57", "1.44E-06", "8.96E-04", "0.53", "2.70E-03", "1.64E−01"], ["", "Nr1d2", "0.58", "6.35E-04", "1.10E−01", "0.54", "2.69E-03", "1.64E−01"], ["", "Dbp", "0.97", "1.15E-03", "1.63E−01", "0.87", "4.76E-03", "2.05E−01"], ["", "LOC686388", "−0.53", "1.41E-03", "1.81E−01", "−0.60", "6.61E-04", "8.71E−02"], ["", "Mb", "−0.53", "3.18E-03", "3.05E−01", "0.54", "4.04E-04", "7.10E−02"], ["", "Pigzl1", "1.23", "4.50E-02", "1.00E−01", "0.63", "3.13E-02", "4.07E−01"], ["", "Tgfbi", "−0.57", "4.66E-02", "1.00E−01", "−0.62", "2.09E-02", "3.59E−01"], ["", "Tef", "0.822", "4.84E-02", "1.00E−01", "0.74", "1.53E-02", "3.20E−01"], ["SHR-SHRSP (SHRSP)", "Endog", "−1.52", "5.13E-09", "7.06E-06", "−0.94", "9.03E-06", "6.20E-03"], ["", "Tor1b", "1.29", "7.91E-09", "1.02E-05", "1.37", "1.69E-08", "7.75E-05"], ["", "Chmp1b", "−1.08", "1.16E-08", "1.40E-05", "−0.70", "8.21E-04", "9.27E−02"], ["", "Riok1", "0.96", "2.01E-06", "1.21E-03", "0.66", "4.15E-04", "7.14E−02"], ["", "Fkbp5", "1.25", "1.15E-05", "5.05E-03", "1.76", "7.83E-06", "5.70E-03"], ["", "Mrpl4", "−0.74", "4.99E-05", "1.58E-02", "−0.87", "5.28E-06", "5.00E-03"], ["", "RGD1562351", "−0.89", "3.21E-04", "6.80E−02", "−0.50", "7.14E-03", "2.42E−01"], ["", "Tars2", "−0.66", "5.01E-04", "9.04E−02", "−0.93", "4.27E-07", "7.32E-04"], ["", "Crot", "−0.77", "1.27E-03", "1.74E−01", "−0.52", "9.78E-03", "2.83E−01"], ["", "Zfp597", "1.37", "2.35E-03", "2.52E−01", "1.00", "2.64E-05", "1.32E-02"], ["", "Ms4a11", "0.76", "4.37E-03", "3.72E−01", "1.09", "7.76E-03", "2.52E−01"], ["", "Aldh5a1", "−0.59", "5.85E-03", "4.45E−01", "−0.51", "2.75E-03", "1.66 E−01"], ["", "Retsat", "−1.07", "1.10E-02", "6.08E−01", "−0.66", "4.09E-02", "4.45E−01"], ["", "Pxmp4", "−0.68", "1.42E-02", "7.07 E−01", "0.93", "1.02E-05", "6.67E-03"], ["", "Tmem14a", "0.67", "1.75E-02", "7.93E−01", "0.80", "6.04E-06", "5.00E-03"], ["SHR-SHRSP (SHR)", "Endog", "−1.54", "1.30E-09", "1.94E-06", "−0.71", "4.88E-04", "1.01E−01"], ["", "Tor1b", "1.27", "3.43E-08", "2.55E-05", "1.04", "1.01E-04", "4.38E-02"], ["", "Chmp1b", "−1.09", "7.64E-09", "7.37E-06", "−0.88", "4.82E-05", "2.81E-02"], ["", "Riok1", "0.98", "1.38E-07", "6.17E-03", "0.56", "3.63E-03", "3.00E−01"], ["", "Fkbp5", "1.20", "5.53E-06", "2.32E-03", "1.22", "9.36E-04", "1.67E−01"], ["", "Mrpl4", "−0.68", "1.82E-05", "6.17E-03", "−0.90", "1.93E-06", "4.40E-03"], ["", "RGD1562351", "−0.81", "1.163E-03", "1.45E−01", "−0.60", "8.74E-04", "1.60E−01"], ["", "Tars2", "−0.61", "8.61E-04", "1.18E−01", "−0.721", "1.21E-04", "4.54E-02"], ["", "Crot", "−0.61", "1.26E-02", "6.10E−01", "−0.53", "4.67E-03", "0.3.48E−01"], ["", "Zfp597", "1.35", "5.63E-03", "3.92E−01", "0.94", "6.49E-05", "3.07E-02"], ["", "Ms4a11", "0.80", "1.34E-02", "6.33E−01", "0.71", "2.24E-02", "5.98E−01"], ["", "Aldh5a1", "−0.55", "8.58E-03", "5.12E−01", "−0.58", "3.00E-04", "7.34E−02"], ["", "Retsat", "−0.96", "2.42E-02", "8.81E−01", "−0.61", "3.19E-02", "6.45E−01"], ["", "Pxmp4", "−0.79", "9.60E-03", "5.41E−01", "0.77", "2.78E-04", "6.95E−02"], ["", "Tmem14a", "0.81", "4.98E-03", "3.72E−01", "0.93", "1.14E-03", "1.84E−01"]], "row_count": 43, "column_count": 8, "numeric_cells": 254, "header_rows": 3, "locator": "section[12]/table-wrap[2]#tIII-mmr-20-05-4151"}}, {"id": "asset:table:pmid:31545431:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f451105755127de7234ea8d10a440bb9bffed3369bea8cd4db8ef7f40319a67c", "bytes": 3365, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tIV-mmr-20-05-4151", "version": null, "note": "Function enrichment analysis for genes of the SHR-specific group of the PPI network.", "structure": {"pmcid": "PMC6797943", "section_index": 13, "section_title": "PPI network and function enrichment analyses", "row_count": 31, "column_count": 4}, "table": {"label": "Table IV.", "caption": "Function enrichment analysis for genes of the SHR-specific group of the PPI network.", "rows": [["Category", "Term", "P-value", "Genes"], ["GO BP", "GO:0008584~male gonad development", "2.69E−04", "TEX19.1, ADAM6, CYP11A1, RXFP2, CST3, UBB, INSL6"], ["GO BP", "GO:0050728~negative regulation of inflammatory response", "1.76E−03", "CXCL17, IER3, TNFAIP6, PPARD, SMAD3"], ["GO BP", "GO:0043066~negative regulation of apoptotic process", "4.11E−03", "IER3, PPARD, SGK1, PLK3, DUSP1, RXFP2, SMAD3, PALB2, INSL6, HIGD1A"], ["GO BP", "GO:0031640~killing of cells of other organism", "1.80E−02", "DEFA5, NP4"], ["GO BP", "GO:0030513~positive regulation of BMP signaling pathway", "2.00E−02", "HES1, TWSG1, GDF5"], ["GO BP", "GO:0006955~immune response", "2.30E−02", "CXCL1, CD244, CD36, SMAD3, COLEC12, CCL4"], ["GO BP", "GO:0001562~response to protozoan", "2.40E−02", "IER3, CYSS"], ["GO BP", "GO:0030174~regulation of DNA-dependent DNA replication initiation", "2.40E−02", "TEX10, CDT1"], ["GO BP", "GO:0014070~response to organic cyclic compound", "2.47E−02", "HES1, CYP2B2, CYP11A1, CYSS, CST3, FOSL1"], ["GO BP", "GO:0001701~in utero embryonic development", "2.76E−02", "HES1, MAFF, SMAD3, LIG4, PALB2, FOSL1"], ["GO BP", "GO:0007431~salivary gland development", "3.00E−02", "CYSS, CST3"], ["GO BP", "GO:0033262~regulation of nuclear cell cycle DNA replication", "3.00E−02", "TIPIN, CDT1"], ["GO BP", "GO:0010332~response to gamma radiation", "3.10E−02", "CXCL1, CYP11A1, LIG4"], ["GO BP", "GO:0046677~response to antibiotic", "3.28E−02", "CYP11A1, CYSS, SKIL"], ["GO BP", "GO:0006952~defense response", "3.41E−02", "CXCL1, NP4, CST3"], ["GO BP", "GO:0006954~inflammatory response", "3.43E−02", "CXCL1, IL17B, KNG2, LTB4R, CCL4, TLR7"], ["GO BP", "GO:0032755~positive regulation of interleukin-6 production", "3.67E−02", "CD36, IL33, TLR7"], ["GO BP", "GO:0042493~response to drug", "4.10E−02", "CD36, CYP11A1, CYSS, CST3, FABP3, NDUFA10, CDH3, FOSL1"], ["GO BP", "GO:0000076~DNA replication checkpoint", "4.16E−02", "TIPIN, CDT1"], ["GO BP", "GO:0044539~long-chain fatty acid import", "4.16E−02", "CD36, FABP3"], ["GO BP", "GO:0001756~somitogenesis", "4.39E−02", "SMAD3, ZEB2, PALB2"], ["GO BP", "GO:0071356~cellular response to tumor necrosis factor", "4.68E−02", "HES1, MAP3K5, CYP11A1, CCL4"], ["GO MF", "GO:0003677~DNA binding", "6.91E−04", "BATF3, POLL, RCOR3, PTF1A, TIPIN, SMAD3, ZEB2, LIG4, CDT1, HES1, POU2F1, H2AFX, SP7, SKIL, PALB2, FOSL1"], ["", "GO:0070538~oleic acid binding", "1.63E−02", "CD36, FABP3"], ["", "GO:0004869~cysteine-type endopeptidase inhibitor activity", "2.31E−02", "KNG2, CYSS, CST3"], ["", "GO:0001078~transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding", "2.69E−02", "BATF3, HES1, PRDM5, SKIL"], ["", "GO:0004559~alpha-mannosidase activity", "4.29E−02", "MAN2B2, MANEA"], ["GO CC", "GO:0005615~extracellular space", "7.23E−04", "CXCL1, TWSG1, KNG2, DEFB14, GDF5, CST3, IL33, CCL4, CXCL17, TNFAIP6, CTSK, CD36, IL17B, DEFA5, SERPINA4, NP4, CYSS, FABP3, UBB"], ["", "GO:0043231~intracellular membrane-bounded organelle", "7.83E−03", "SEC16B, CYP2B2, GLUL, ATP2B3, KNG2, CD36, POU2F1, TIPIN, TREM2, FOSL1, PKD2L1"], ["", "GO:0000785~chromatin", "3.77E−02", "HES1, PLK3, MTBP, H2AFX"]], "row_count": 31, "column_count": 4, "numeric_cells": 75, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tIV-mmr-20-05-4151"}}, {"id": "asset:table:pmid:31545431:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:209ce3a8aa8d1fb966f241dc647b3fe658a1e010f7a9eb7268d39759e4d90ce1", "bytes": 5893, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#tV-mmr-20-05-4151", "version": null, "note": "Function enrichment analysis for the genes of the SHRSP group of the PPI network.", "structure": {"pmcid": "PMC6797943", "section_index": 13, "section_title": "PPI network and function enrichment analyses", "row_count": 36, "column_count": 4}, "table": {"label": "Table V.", "caption": "Function enrichment analysis for the genes of the SHRSP group of the PPI network.", "rows": [["Category", "Term", "P-value", "Genes"], ["GO BP", "GO:0032570~response to progesterone", "1.00E−05", "CCNE1, FOS, PTGER2, NCF2, ERBB4, ADH1, HSPA8, JUNB, TGFB1"], ["GO BP", "GO:0010033~response to organic substance", "1.69E−05", "TNF, CYP2D1, MGP, TGFB1, AMPD1, AFP, C1QB, PLA2G4A, BTG2, DUSP1, ALB, SQLE, SPP1"], ["GO BP", "GO:0007067~mitotic nuclear division", "7.62E−05", "ITGB3BP, SPC25, CDK1, PLK1, NUF2, CENPW, MAPRE2, FABP1, CEP55, CCNG1, WEE1"], ["GO BP", "GO:0000122~negative regulation of transcription from RNA polymerase II promoter", "7.95E−04", "TNF, PRRX1, ZEB2, AURKB, ZBTB16, TGFB1, CCNE1, EZR, NR1D1, SOX18, CRY1, TBX6, ISL1, PROX2, JUNB, NKX6-1, SHOX2, HHEX, ATF3, BTG2, PLK1, IRF2BPL, TRPS1, BCL6B, NELFE, NFIA, CRYM"], ["GO BP", "GO:0051301~cell division", "1.34E−03", "ITGB3BP, SPC25, CDK1, CCNE1, CHMP1B, DSN1, NUF2, CENPW, MAPRE2, CCNG1, WEE1"], ["GO BP", "GO:0032496~response to lipopolysaccharide", "1.50E−03", "FOS, SLC11A1, TNFRSF11B, PLA2G4A, PTGER2, TNF, RELT, NCF2, SERPINE1, ACP5, C2, LOXL1, JUNB, TRIB1"], ["GO BP", "GO:0030198~extracellular matrix organization", "1.67E−03", "COL18A1, TNFRSF11B, TNF, ADAMTSL2, OLFML2B, TGFBI, NID1, POSTN"], ["GO BP", "GO:0001755~neural crest cell migration", "1.69E−03", "ERBB4, SEMA3D, ZEB2, ISL1, HTR2B, GDNF"], ["GO BP", "GO:0045880~positive regulation of smoothened signaling pathway", "1.83E−03", "SHOX2, SCUBE3, PRRX1, GAS1, POR"], ["GO BP", "GO:0030316~osteoclast differentiation", "2.07E−03", "TF, TNF, ACP5, DCSTAMP, JUNB"], ["GO BP", "GO:0002062~chondrocyte differentiation", "8.72E−03", "SHOX2, TRPS1, TGFBI, CYTL1, TGFB1"], ["GO BP", "GO:0001889~liver development", "1.47E−02", "AFP, CCNE1, HHEX, COBL, BAAT, HMGCS2, DBP, TK1"], ["GO BP", "GO:0007623~circadian rhythm", "2.06E−02", "DHX9, TNF, NR1D1, DBP, NTRK2, CRY1, TPH1"], ["GO BP", "GO:0045944~positive regulation of transcription from RNA polymerase II promoter", "2.50E−02", "TNF, HEXB, PRRX1, CYTL1, FSTL3, ZEB2, GDNF, TGFB1, HSPH1, SLC11A1, FOS, TEF, SOX18, TBX6, CCNH, NR4A1, ISL1, MECOM, PROX2, JUNB, SHOX2, HHEX, ATF3, IRF2BPL, DBP, TRPS1, NELFE, NFIA"], ["GO BP", "GO:0001525~angiogenesis", "4.50E−02", "COL18A1, SERPINE1, TGFBI, APOLD1, SOX18, PLXND1, EPHB3, THY1"], ["GO BP", "GO:0042542~response to hydrogen peroxide", "4.94E−02", "CDK1, PLA2G4A, DUSP1, ERBB4, MB"], ["GO MF", "GO:0042803~protein homodimerization activity", "6.49E−04", "CADM3, ERBB4, HEXB, ZBTB16, GREM2, GDNF, TGFB1, SLC11A1, ADH1, FAP, ALOX5AP, TEF, CIB2, ZFP423, TESC, OLFML2B, ERP29, EPHX2, FZD1, NR4A1, MECOM, HHEX, C1QB, PPP1R9A, ATF3, NTRK2, CTSE, CRYM"], ["", "GO:0005515~protein binding", "2.81E−03", "COBL, ERBB4, KCNAB1, WASF1, KCNA2, CACNB3, ZBTB16, CDH2, RAB3IP, SDC3, FOS, EZR, HSPA2, NR1D1, ARPC2, SCG3, GUCY1A2, DNAJA1, C2, VMP1, HSPA8, SCN10A, NGEF, CDK1, RAB8B, KCNB1, ERP29, FZD1, NR4A1, NID1, ISL1, THY1, SH3BP5, RT1-A2, EPHA4, PPP1R9A, BTG2, NTRK2, FABP1, ALOX5, MAP6, HTR2B, NFIA"], ["", "GO:0005525~GTP binding", "5.84E−03", "TF, RAB8B, GBP5, GIMAP6, GIMAP8, RRAD, NPR2, RRAGD, GNAT2, RND3, RAB19, RAC3, GUCY1A2, RAB15, RAB26"], ["", "GO:0050840~extracellular matrix binding", "1.06E−02", "OLFML2B, TGFBI, NID1, SPP1"], ["", "GO:0046982~protein heterodimerization activity", "1.50E−02", "ZFP423, CD3G, CD3E, KCNB1, HEXB, CRLF1, FZD1, NR4A1, RRAGD, TGFB1, FOS, ATF3, ALOX5AP, TEF, GUCY1A2, ADRA1A, CENPW, SOX18"], ["GO CC", "GO:0005615~extracellular space", "9.32E−06", "TF, DHH, TNF, LTBP2, IGFBP7, HEXB, PLBD1, SERPINB1A, CCL9, FSTL3, ACP5, POSTN, GREM2, GDNF, TGFB1, CHIT1, MTHFD2, TNFRSF11B, PTGIS, EZR, ALB, SERPINA5, FAP, SERPINE1, TGFBI, SEMA3D, C2, CES1C, HSPA8, SPP1, DPT, WNT8B, COL18A1, CPA6, PRG4, IL9, MGP, CLIC1, SOD3, AFP, CBLN2, F5, IRF2BPL, CPXM1, ALOX5, UBB"], ["", "GO:0031012~extracellular matrix", "1.48E−04", "COL18A1, LTBP2, IGFBP7, CKAP4, MGP, NID1, POSTN, TGFB1, SOD3, CFP, TGFBI, SERPINE1, LOXL1, CLEC14A, DPT"], ["", "GO:0070062~extracellular exosome", "1.59E−04", "LTBP2, IGFBP7, HEXB, TSPAN6, TSPAN8, HSPH1, DES, SLC2A5, SERPINA5, SERPINE1, TGFBI, SCN10A, MB, PTPRJ, DBNL, CDK1, PTPRF, ERP29, MGP, PRKCH, CLIC1, THY1, C1QB, RND3, CHMP1B, DHRS4, BTG2, RELT, RAB19, CTSE, RAB15, UBB, TNFAIP3, AKR1D1, TF, ECH1, SERPINB1A, ACP5, CDH2, GIPC2, ITM2C, EZR, HSPA2, ARPC2, ALB, RAC3, DNAJA1, C2, NDRG2, HSPA8, SPP1, ARHGDIB, DPT, COL18A1, RAB8B, CPPED1, CKAP4, EPHX2, NID1, TMBIM1, RACGAP1, ANXA4, SOD3, NKX6-1, LYVE1, TMEM8A, HEBP1, MYH11, FABP1, CRYM, CLEC14A"], ["", "GO:0005604~basement membrane", "2.12E−04", "COL18A1, TF, LAMC3, ALB, TGFBI, NTN4, NID1, LOXL1, COL4A5"], ["", "GO:0030027~lamellipodium", "3.81E−04", "DBNL, TESC, PPP1R9A, MYO10, WASF1, KCNA2, FAP, CDH2, ARAP3, PLXND1, RAB3IP"], ["KEGG", "rno04010:MAPK signaling pathway", "3.86E−03", "TNF, NR4A1, CACNB3, FGF13, MECOM, TGFB1, FOS, PLA2G4A, HSPA2, DUSP1, NTRK2, GADD45A, HSPA8"], ["KEGG", "rno04610:Complement and coagulation cascades", "1.22E−02", "C1QB, F10, F5, SERPINA5, SERPINE1, C2"], ["KEGG", "rno05142:Chagas disease (American trypanosomiasis)", "1.69E−02", "C1QB, FOS, CD3G, TNF, CD3E, SERPINE1, TGFB1"], ["KEGG", "rno04110:Cell cycle", "3.54E−02", "CDK1, CCNE1, CCNH, PLK1, GADD45A, WEE1, TGFB1"], ["KEGG", "rno04380:Osteoclast differentiation", "3.78E−02", "FOS, TNFRSF11B, TNF, NCF2, ACP5, JUNB, TGFB1"], ["KEGG", "rno04612:Antigen processing and presentation", "3.89E−02", "RT1-A2, TNF, HSPA2, RT1-CE4, RT1-M2, HSPA8"], ["KEGG", "rno04141:Protein processing in endoplasmic reticulum", "4.30E−02", "HSPH1, HSPA2, CKAP4, ERP29, DNAJA1, DDOST, SSR2, HSPA8"], ["KEGG", "rno04115:p53 signaling pathway", "4.53E−02", "CDK1, CCNE1, SERPINE1, CCNG1, GADD45A"], ["KEGG", "rno04514:Cell adhesion molecules (CAMs)", "4.77E−02", "RT1-A2, CADM3, OCLN, PTPRF, RT1-CE4, RT1-M2, CDH2, SDC3"]], "row_count": 36, "column_count": 4, "numeric_cells": 92, "header_rows": 1, "locator": "section[13]/table-wrap[2]#tV-mmr-20-05-4151"}}, {"id": "asset:table:pmid:31545431:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7fcfaf25df57bf4d37122a907b67647663f736e1a877867464e7daab3e91b240", "bytes": 5052, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[3]#tVI-mmr-20-05-4151", "version": null, "note": "Function enrichment for the genes of SHR-SHRSP shared group in the PPI network.", "structure": {"pmcid": "PMC6797943", "section_index": 13, "section_title": "PPI network and function enrichment analyses", "row_count": 37, "column_count": 4}, "table": {"label": "Table VI.", "caption": "Function enrichment for the genes of SHR-SHRSP shared group in the PPI network.", "rows": [["Category", "Term", "P-value", "Genes"], ["GO BP", "GO:0006954~inflammatory response", "9.20E−05", "CXCL1, BMP2, OLR1, AIF1, PTGS1, CHI3L1, EPHX2, CCL19, TLR3, CX3CL1, CYP4F5, CCR5, CYP26B1, CD27"], ["GO BP", "GO:0006955~immune response", "1.33E−04", "CXCL1, RT1-A2, RT1-A1, RT1-CE1, ENPP1, CCR5, IL12A, RT1-CE10, IFI44L, CX3CL1, CTSS, CD27, RT1-BB"], ["GO BP", "GO:0007631~feeding behavior", "8.99E−04", "HCRTR1, HTR1B, NPY4R, NPY1R, APLN"], ["GO BP", "GO:0002474~antigen processing and presentation of peptide antigen via MHC class I", "1.00E−03", "RT1-A2, RT1-A1, RT1-CE1, RT1-CE10, RT1-S3"], ["GO BP", "GO:0055114~oxidation-reduction process", "1.33E−03", "HSD17B11, PTGR1, BMP2, CYP2D5, ALDH5A1, FADS1, HSD17B13, PTGS1, RDH7, P4HA2, CYP4F5, CPOX, CYP26B1, FMO3, OXNAD1, CYP8B1, BDH1, RETSAT, ALOX12"], ["GO BP", "GO:0001916~positive regulation of T cell mediated cytotoxicity", "1.59E−03", "RT1-A2, RT1-A1, IL12A, RT1-S3"], ["GO BP", "GO:0032355~response to estradiol", "3.72E−03", "CXCL1, PENK, FCGR1A, ENDOG, MAP1B, TFPI, BRCA2, NPY1R, BDH1"], ["GO BP", "GO:0045785~positive regulation of cell adhesion", "5.49E−03", "PTPRJ, DUSP26, IL12A, CX3CL1, ALOX12"], ["GO BP", "GO:0007568~aging", "6.20E−03", "CCR5, PENK, FADS1, ENDOG, PTGS1, GFRA1, EPOR, NPY1R, CX3CL1, TIMP1, ALOX12"], ["GO BP", "GO:0006631~fatty acid metabolic process", "6.58E−03", "ACOX2, PER2, ACSF2, ACSM5, CROT"], ["GO BP", "GO:0007417~central nervous system development", "8.57E−03", "NOG, ALDH5A1, DNER, VCAN, LIG4, ZBTB16"], ["GO BP", "GO:0001666~response to hypoxia", "2.00E−02", "AJUBA, VEGFB, PLAT, BMP2, PENK, EPOR, CX3CL1, CBFA2T3, AGTRAP"], ["GO BP", "GO:0009612~response to mechanical stimulus", "4.08E−02", "ACTB, BMP2, ENDOG, MAP1B, CHI3L1"], ["GO MF", "GO:0042605~peptide antigen binding", "1.09E−03", "RT1-A1, RT1-CE1, RT1-CE10, RT1-S3, RT1-BB"], ["", "GO:0005102~receptor binding", "1.83E−03", "ACOX2, PLAT, BMP2, RT1-CE1, HFE2, EPHX2, RT1-S3, HCST, TRDN, RT1-A1, RT1-CE10, CROT, TEC"], ["", "GO:0008083~growth factor activity", "8.50E−03", "VEGFB, CXCL1, BMP2, IL12A, GDNF, TIMP1, THBS4"], ["", "GO:0004829~threonine-tRNA ligase activity", "3.67E−02", "TARS2, TARSL2"], ["", "GO:0001602~pancreatic polypeptide receptor activity", "3.67E−02", "NPY4R, NPY1R"], ["GO CC", "GO:0005615~extracellular space", "2.96E−06", "CXCL1, NAMPT, NOG, HFE2, ENPP1, GLDN, MST1, CX3CL1, C1QC, GDNF, TIMP1, GPC2, APOA1, SERPINA5, PTX3, APLN, SRGN, SPON1, THBS4, ACTB, PLAT, BMP2, UCMA, IL1F10, CHI3L1, CILP, CCL19, CTSS, VEGFB, PROM1, AFP, SERPINA3M, CD59, TFPI, IL12A, SEMA4B, GFRA1, VCAN"], ["", "GO:0009986~cell surface", "9.64E−06", "PLAT, PTPRJ, ITGAL, BMP2, HFE2, ENPP1, TNMD, TLR3, RT1-S3, CX3CL1, CTSS, RT1-BB, HCST, PROM1, APOA1, CCR5, FOLR2, CD59, TFPI, VCAN, ROS1, CLEC5A, CD27"], ["", "GO:0009897~external side of plasma membrane", "3.39E−05", "LY75, ITGAL, TRPM8, ANO1, CCL19, RT1-BB, RT1-A2, CCR5, SERPINA5, FCGR1A, GFRA1, EPOR, CD27, ICOSLG"], ["", "GO:0042612~MHC class I protein complex", "1.76E−04", "RT1-A2, RT1-A1, RT1-CE1, RT1-CE10, RT1-S3"], ["", "GO:0005576~extracellular region", "1.70E−03", "HSD17B11, COL4A2, OLR1, ENPP1, HSD17B13, CTSS, CX3CL1, GDNF, C1QC, TIMP1, DNASE2B, VEGFB, APOA1, PENK, TFPI, VCAN, APOL11A, PLA2G2D, NMU, THBS4"], ["KEGG", "rno04145:Phagosome", "1.97E−06", "ACTB, MSR1, RT1-CE1, OLR1, CTSS, ATP6V1G1, RT1-S3, RT1-BB, RT1-A2, RT1-A1, FCGR1A, ATP6V1E2, RT1-CE10, RT1-N1, THBS4"], ["KEGG", "rno05416:Viral myocarditis", "8.38E−05", "ACTB, RT1-A2, ITGAL, RT1-A1, RT1-CE1, RT1-CE10, RT1-S3, RT1-N1, RT1-BB"], ["KEGG", "rno05330:Allograft rejection", "1.12E−04", "RT1-A2, RT1-A1, RT1-CE1, IL12A, RT1-CE10, RT1-S3, RT1-N1, RT1-BB"], ["KEGG", "rno04940:Type I diabetes mellitus", "1.89E−04", "RT1-A2, RT1-A1, RT1-CE1, IL12A, RT1-CE10, RT1-S3, RT1-N1, RT1-BB"], ["KEGG", "rno04514:Cell adhesion molecules (CAMs)", "3.86E−04", "RT1-A2, SIGLEC1, ITGAL, RT1-A1, RT1-CE1, RT1-CE10, VCAN, RT1-S3, RT1-N1, ICOSLG, RT1-BB"], ["KEGG", "rno05332:Graft-versus-host disease", "5.91E−04", "RT1-A2, RT1-A1, RT1-CE1, RT1-CE10, RT1-S3, RT1-N1, RT1-BB"], ["KEGG", "rno04612:Antigen processing and presentation", "8.43E−04", "RT1-A2, RT1-A1, RT1-CE1, RT1-CE10, RT1-S3, CTSS, RT1-N1, RT1-BB"], ["KEGG", "rno05320:Autoimmune thyroid disease", "1.34E−03", "RT1-A2, RT1-A1, RT1-CE1, RT1-CE10, RT1-S3, RT1-N1, RT1-BB"], ["KEGG", "rno05168:Herpes simplex infection", "2.21E−03", "RT1-A2, RT1-A1, RT1-CE1, CSNK2A1, PER2, IL12A, RT1-CE10, TLR3, RT1-S3, RT1-N1, RT1-BB"], ["KEGG", "rno04610:Complement and coagulation cascades", "5.57E−03", "PLAT, C1QA, CD59, SERPINA5, TFPI, C1QC"], ["KEGG", "rno00650:Butanoate metabolism", "9.57E−03", "HMGCS2, ALDH5A1, BDH1, ACSM5"], ["KEGG", "rno05150:Staphylococcus aureus infection", "1.04E−02", "C1QA, ITGAL, FCGR1A, C1QC, RT1-BB"], ["KEGG", "rno05169:Epstein-Barr virus infection", "3.01E−02", "RT1-A2, ITGAL, RT1-A1, RT1-CE1, RT1-CE10, RT1-S3, RT1-N1"]], "row_count": 37, "column_count": 4, "numeric_cells": 99, "header_rows": 1, "locator": "section[13]/table-wrap[3]#tVI-mmr-20-05-4151"}}, {"id": "asset:table:pmid:31545431:9", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3916b5ad2baf3cc4d147d5bd61d3e5ff6581a9175d5e3e750fe87ac5118927e1", "bytes": 671, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#tVII-mmr-20-05-4151", "version": null, "note": "Candidate small-molecule drugs.", "structure": {"pmcid": "PMC6797943", "section_index": 15, "section_title": "Prediction of potential therapeutic agents", "row_count": 12, "column_count": 3}, "table": {"label": "Table VII.", "caption": "Candidate small-molecule drugs.", "rows": [["CMAP name", "Enrichment", "P-value"], ["Betulin", "−0.96", "2.20E−04"], ["Gly-His-Lys", "−0.93", "5.40E−04"], ["Benzathine Benzylpenicillin", "−0.90", "1.60E−04"], ["Prestwick-1103", "−0.89", "4.00E−04"], ["PF-00539745-00", "−0.88", "3.43E−03"], ["Quinostatin", "−0.88", "2.99E−02"], ["5279552", "−0.86", "3.77E−02"], ["Podophyllotoxin", "−0.86", "7.00E−04"], ["Cefuroxime", "0.80", "3.00E−03"], ["STOCK1N-35215", "0.81", "1.37E−02"], ["NS-398", "0.91", "1.38E−02"]], "row_count": 12, "column_count": 3, "numeric_cells": 27, "header_rows": 1, "locator": "section[15]/table-wrap[1]#tVII-mmr-20-05-4151"}}], "gaps": ["asset:data:geo:GSE31457 not downloaded", "asset:data:geo:GSE31457 licence not read", "asset:data:geo:GSE41452 not downloaded", "asset:data:geo:GSE41452 licence not read", "asset:data:geo:GSE41453 not downloaded", "asset:data:geo:GSE41453 licence not read", "asset:data:geo:GSE53361 not downloaded", "asset:data:geo:GSE53361 licence not read", "asset:data:geo:GSE53363 not downloaded", "asset:data:geo:GSE53363 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": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-2", "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": "PPI"}}], "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": ["GSE41452", "GSE31457", "GSE41453", "GSE53363", "GSE53361"], "resolved_accessions": ["GSE41452", "GSE31457", "GSE41453", "GSE53363", "GSE53361"], "statements": ["The sequencing data GSE41452, GSE31457, GSE41453, GSE53363 and GSE53361 were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/)."], "basis": "The paper names GSE41452, GSE31457, GSE41453, GSE53363, GSE53361 in Gene Expression Omnibus (GEO) database in NCBI 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:31545431", "data:geo:GSE31457", "asset:table:pmid:31545431:1", "asset:table:pmid:31545431:2", "asset:table:pmid:31545431:3", "asset:table:pmid:31545431:4", "asset:table:pmid:31545431:5", "asset:table:pmid:31545431:6", "asset:table:pmid:31545431:7", "asset:table:pmid:31545431:8", "asset:table:pmid:31545431:9"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE31457"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:50:10Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 38592, "completion_tokens": 1814, "cached_tokens": 785}}, "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:31545431", "type": "paper", "label": "pmid:31545431"}, {"id": "source:pmid:31545431", "type": "manuscript", "label": "PMID 31545431 full text"}, {"id": "data:geo:GSE31457", "type": "dataset", "label": "GEO GSE31457"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31545431", "type": "paper", "label": "pmid:31545431"}, {"id": "source:pmid:31545431", "type": "manuscript", "label": "PMID 31545431 full text"}, {"id": "data:geo:GSE31457", "type": "dataset", "label": "GEO GSE31457"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31545431", "type": "extraction", "used": ["source:pmid:31545431"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE31457", "type": "accession_resolution", "used": ["data:geo:GSE31457"], "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:31545431", "parent_hash": "sha256:2a97d409214d93d23dc0ce64321bdd69d1ce863c65c72fe376983e6468704baa", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE31457 licence not read", "asset:data:geo:GSE31457 not downloaded", "asset:data:geo:GSE41452 licence not read", "asset:data:geo:GSE41452 not downloaded", "asset:data:geo:GSE41453 licence not read", "asset:data:geo:GSE41453 not downloaded", "asset:data:geo:GSE53361 licence not read", "asset:data:geo:GSE53361 not downloaded", "asset:data:geo:GSE53363 licence not read", "asset:data:geo:GSE53363 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": 0.99, "evidence": ["ssion profiles of spontaneously hypertensive rats (SHR rats) and stroke‑prone spontaneously hy", "iles of spontaneously hypertensive rats (SHR rats) and stroke‑prone spontaneously hypertensive", "and stroke‑prone spontaneously hypertensive rats (SHRSP rats) to screen for potential therape", "prone spontaneously hypertensive rats (SHRSP rats) to screen for potential therapeutic targets"], "order_basis": "paper_text_order:185", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["Kyoto (WKY) rats using the Linear Models for Microarray (limma) data method. Venn diagrams were used"], "order_basis": "paper_text_order:719", "id": "assay:2"}, {"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": 0.7, "evidence": ["limma"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"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":"2026-11-04T01:49:54+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}}}