Identification of hub genes and small-molecule compounds related to intracerebral hemorrhage with bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31667013", "kind": "science-record", "revision": 8, "content_hash": "sha256:699fa92289778a7dc052f0e5b2c2e6043ebf83bace0ce95342066d32a8a496fa", "created_at": "2026-11-01T15:40:51Z", "updated_at": "2026-11-01T22:44:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes and small-molecule compounds related to intracerebral hemorrhage with bioinformatics analysis.", "doi": "10.7717/peerj.7782", "pmid": "31667013", "authors": ["Zhendong Liu", "Ruotian Zhang", "Xin Chen", "Penglei Yao", "Tao Yan", "Wenwu Liu", "Jiawei Yao", "Andrei Sokhatskii", "Ilgiz Gareev", "Shiguang Zhao"], "journal": "PeerJ", "year": 2019, "abstract": "BACKGROUND: Because of the complex mechanisms of injury, conventional surgical treatment and early blood pressure control does not significantly reduce mortality or improve patient prognosis in cases of intracerebral hemorrhage (ICH). We aimed to identify the hub genes associated with intracerebral hemorrhage, to act as therapeutic targets, and to identify potential small-molecule compounds for treating ICH.\nMETHODS: The GSE24265 dataset, consisting of data from four perihematomal brain tissues and seven contralateral brain tissues, was downloaded from the Gene Expression Omnibus (GEO) database and screened for differentially expressed genes (DEGs) in ICH, with a fold change (FC) value of (|log2FC|) > 2 and a P-value of <0.05 set as cut-offs. The functional annotation of DEGs was performed using Gene Ontology (GO) resources, and the cell signaling pathway analysis of DEGs was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG), with a P-value of <0.05 set as the cut-off. We constructed a protein-protein interaction (PPI) network to clarify the interrelationships between the different DEGs and to select the hub genes with significant interactions. Next, the DEGs were analyzed using the CMap tool to identify small-molecule compounds with potential therapeutic effects. Finally, we verified the expression levels of the hub genes by RT-qPCR on the rat ICH model.\nRESULT: A total of 59 up-regulated genes and eight down-regulated genes associated with ICH were identified. The biological functions of DEGs associated with ICH are mainly involved in the inflammatory response, chemokine activity, and immune response. The KEGG analysis identified several pathways significantly associated with ICH, including but not limited to HIF-1, TNF, toll-like receptor, cytokine-cytokine receptor interaction, and chemokine molecules. A PPI network consisting of 57 nodes and 373 edges was constructed using STRING, and 10 hub genes were identified with Cytoscape software. These hub genes are closely related to secondary brain injury induced by ICH. RT-qPCR results showed that the expression of ten hub genes was significantly increased in the rat model of ICH. In addition, a CMap analysis of three small-molecule compounds revealed their therapeutic potential.\nCONCLUSION: In this study we obtained ten hub genes, such as IL6, TLR2, CXCL1, TIMP1, PLAUR, SERPINE1, SELE, CCL4, CCL20, and CD163, which play an important role in the pathology of ICH. At the same time, the ten hub genes obtained through PPI network analysis were verified in the rat model of ICH. In addition, we obtained three small molecule compounds that will have therapeutic effects on ICH, including Hecogenin, Lidocaine, and NU-1025.", "claims": [{"id": "claim-method", "statement": "Both the normalization of the data and screening of the DEGs were performed using the limma package in the R language (version 3.5.1) (Guo et al., 2017).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31667013", "locator": "sections[4] \"Screening results of DEGs\" paragraph 2", "quote": "Both the normalization of the data and screening of the DEGs were performed using the limma package in the R language (version 3.5.1) (Guo et al., 2017)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data is available in the Gene Expression Omnibus: GSE24265.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31667013", "locator": "sections[25] \"Data Availability\" paragraph 2", "quote": "The data is available in the Gene Expression Omnibus: GSE24265."}], "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:31667013"], "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:GSE24265"], "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:GSE24265"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31667013", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.7782", "sha256": "sha256:e766602ecaf398934d8b9aa198682022c8e957fa2707ae055e0b27044b5cbf69", "bytes": 43478, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.7782", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6816389", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE24265", "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=GSE24265", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE24265", "version": null, "note": "The data is available in the Gene Expression Omnibus: GSE24265.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data is available in the Gene Expression Omnibus: GSE24265.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM596842", "GSM596843", "GSM596844", "GSM596845", "GSM596846", "GSM596847", "GSM596848", "GSM596849", "GSM596850", "GSM596851", "GSM596852"], "sample_count": 11, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from human brain samples", "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:31667013:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ea9f09ff824b3fd88d6f80c8332c4ccb07458ec2fdb5e909eb49b811698e9390", "bytes": 297, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#table-1", "version": null, "note": "Details for GEO ICH data.", "structure": {"pmcid": "PMC6816389", "section_index": 11, "section_title": "Identification of DEGs in ICH", "row_count": 2, "column_count": 7}, "table": {"label": "Table 1", "caption": "Details for GEO ICH data.", "rows": [["Reference", "Sample", "GEO", "Platform", "PH", "CW", "CG"], ["Rosell et al. (2011)", "Brain", "GSE24265", "GPL570", "4", "4", "3"]], "row_count": 2, "column_count": 7, "numeric_cells": 6, "header_rows": 1, "locator": "section[11]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:31667013:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a643ad17cca87b31499178549ccd55ecdce71f156cffca2efa2e2229794f35ea", "bytes": 733, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#table-2", "version": null, "note": "Screening DEGs in ICH by integrated microarray.", "structure": {"pmcid": "PMC6816389", "section_index": 11, "section_title": "Identification of DEGs in ICH", "row_count": 3, "column_count": 2}, "table": {"label": "Table 2", "caption": "Screening DEGs in ICH by integrated microarray.", "rows": [["DEGs", "Gene terms"], ["Upregulated", "CXCL8, CCL20, C15orf48, CXCL1, VMP1, AGPAT9, G0S2, CXCL3, PTX3, TFPI2, CYTIP, TNFAIP3, PPBP, HSPA6, BCL2A1, TREM1, CCL4, IL18RAP, PMAIP1, SERPINE1, HBD, TGFBI, PNP, SELE, TIMP1, IL6, NCF2, PLAUR, LAPTM5, TCIRG1, OLR1, HBB, DUSP5, ISG20,S100P, PROK2, METRNL, CTGF, CD93,HCAR3, ANXA2P2, C5AR1, TLR2, FGR,MARCO, HMOX1, TUBB6, CYB5R2 ADM, UPP1, SLC2A3, CD163, BCAT1,CLEC5A, CCL8, HLA-DRA, TNFRSF12A,ANXA2, S100A11."], ["Downregulated", "NXPH1, PRRT2, SLITRK5, SOWAHA, CNTN3, CACNA2D3, MUM1L1, ZNRF3."]], "row_count": 3, "column_count": 2, "numeric_cells": 1, "header_rows": 1, "locator": "section[11]/table-wrap[2]#table-2"}}, {"id": "asset:table:pmid:31667013:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f6e45cb3bc72bc77ed1ac87e5d8fc2314fd2ec4feb80585312e93cb2f2308d7e", "bytes": 2085, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#table-3", "version": null, "note": "Top 10 of the most significantly enriched GO terms.", "structure": {"pmcid": "PMC6816389", "section_index": 12, "section_title": "Functional annotation analysis of DEGs using GO", "row_count": 34, "column_count": 4}, "table": {"label": "Table 3", "caption": "Top 10 of the most significantly enriched GO terms.", "rows": [["Pathway ID", "Terms", "Gene count", "P-value"], ["BP", "", "", ""], ["GO:0006954", "Inflammatory response", "16", "5.41E−12"], ["GO:0030593", "Neutrophil chemotaxis", "8", "4.33E−09"], ["GO:0006955", "Immune response", "13", "3.67E−08"], ["GO:0070098", "Chemokine-mediated signaling pathway", "7", "2.35E−07"], ["GO:0006935", "Chemotaxis", "7", "5.73E−06"], ["GO:0001525", "Angiogenesis", "8", "1.75E−05"], ["GO:0032496", "Response to lipopolysaccharide", "7", "3.10E−05"], ["GO:0090023", "Positive regulation of neutrophil chemotaxis", "4", "7.02E−05"], ["GO:0071347", "Cellular response to interleukin-1", "5", "1.36E−04"], ["GO:0045765", "Regulation of angiogenesis", "4", "2.00E−04"], ["CC", "", "", ""], ["GO:0005615", "Extracellular space", "19", "5.27E−07"], ["GO:0005576", "Extracellular region", "19", "6.79E−06"], ["GO:0005886", "Plasma membrane", "27", "9.38E−04"], ["GO:0005604", "Basement membrane", "4", "2.70E−03"], ["GO:0005887", "Integral component of plasma membrane", "13", "3.43E−03"], ["GO:0070062", "Extracellular exosome", "19", "6.75E−03"], ["GO:0009986", "Cell surface", "7", "1.18E−02"], ["GO:0031093", "Platelet alpha granule lumen", "3", "1.60E−02"], ["GO:0031012", "Extracellular matrix", "5", "2.02E−02"], ["GO:0030666", "Endocytic vesicle membrane", "3", "2.25E−02"], ["MF", "", "", ""], ["GO:0008009", "Chemokine activity", "7", "2.25E−02"], ["GO:0045236", "CXCR chemokine receptor binding", "3", "2.25E−02"], ["GO:0008083", "Growth factor activity", "5", "2.25E−02"], ["GO:0002020", "Protease binding", "4", "2.25E−02"], ["GO:0004872", "Receptor activity", "5", "2.25E−02"], ["GO:0048306", "Calcpium-dependent protein binding", "3", "2.25E−02"], ["GO:0008329", "Signaling pattern recognition receptor activity", "2", "2.25E−02"], ["GO:0001849", "Complement component C1q binding", "2", "2.25E−02"], ["GO:0005102", "Receptor binding", "5", "2.25E−02"], ["GO:0004859", "Phospholipase inhibitor activity", "2", "2.25E−02"]], "row_count": 34, "column_count": 4, "numeric_cells": 91, "header_rows": 1, "locator": "section[12]/table-wrap[1]#table-3"}}, {"id": "asset:table:pmid:31667013:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8b97292bc0269a4b9613006c39a753185ab84ce77cbf759ba40370a5956f3b9a", "bytes": 2816, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#table-4", "version": null, "note": "Significantly enriched KEGG pathway.", "structure": {"pmcid": "PMC6816389", "section_index": 13, "section_title": "KEGG pathway analysis of DEGs", "row_count": 30, "column_count": 5}, "table": {"label": "Table 4", "caption": "Significantly enriched KEGG pathway.", "rows": [["Pathway ID", "Terms", "Gene count", "P-Value", "Genes"], ["hsa04060", "Cytokine-cytokine receptor interaction", "10", "1.59E−09", "CCL4, CCL8, CXCL8, CCL20, TNFRSF12A, IL18RAP, CXCL3, PPBP, CXCL1, IL6"], ["hsa05323", "Rheumatoid arthritis", "7", "3.50E−09", "TCIRG1, CXCL8, CCL20, TLR2, CXCL1, HLA-DRA, IL6"], ["hsa05134", "Legionellosis", "6", "9.62E−09", "CXCL8, TLR2, CXCL3, CXCL1, IL6, HSPA6"], ["hsa04062", "Chemokine signaling pathway", "8", "3.28E−08", "CCL4, CCL8, CXCL8, CCL20, FGR, CXCL3, PPBP, CXCL1"], ["hsa04145", "Phagosome", "7", "1.45E−07", "TCIRG1, OLR1, NCF2, TLR2, TUBB6, HLA-DRA, MARCO"], ["hsa05144", "Malaria", "5", "2.19E−07", "IL6, CXCL8, HBB, SELE, TLR2"], ["hsa04668", "TNF signaling pathway", "6", "5.37E−07", "TNFAIP3, CCL20, CXCL3, SELE, CXCL1, IL6"], ["hsa05132", "Salmonella infection", "5", "3.30E−06", "CXCL1, CCL4, IL6, CXCL3, CXCL8"], ["hsa04621", "NOD-like receptor signaling pathway", "4", "1.78E−05", "CXCL1, IL6, TNFAIP3, UPP1"], ["hsa05321", "Inflammatory bowel disease (IBD)", "4", "2.43E−05", "HLA-DRA, IL6, IL18RAP, TLR2,"], ["hsa04064", "NF-kappa B signaling pathway", "4", "1.04E−04", "CCL4, TNFAIP3, BCL2A1, CXCL8"], ["hsa05143", "African trypanosomiasis", "3", "1.09E−04", "IL6, HBB, SELE"], ["hsa05146", "Amoebiasis", "4", "1.36E−04", "CXCL1, IL6, CXCL8, TLR2"], ["hsa04933", "AGE-RAGE signaling pathway in diabetic complications", "4", "1.52E−04", "IL6, SERPINE1, SELE, CXCL8"], ["hsa04066", "HIF-1 signaling pathway", "4", "1.63E−04", "IL6, SERPINE1, TIMP1, HMOX1"], ["hsa05142", "Chagas disease (American trypanosomiasis)", "4", "1.69E−04", "IL6, CXCL8, SERPINE1, TLR2"], ["hsa04620", "Toll-like receptor signaling pathway", "4", "1.81E−04", "CCL4, IL6, CXCL8, TLR2"], ["hsa05162", "Measles", "4", "4.47E−04", "IL6, TNFAIP3, HSPA6, TLR2"], ["hsa05120", "Epithelial cell signaling in Helicobacter pylori infection", "3", "7.57E−04", "CXCL1, TCIRG1, CXCL8"], ["hsa05140", "Leishmaniasis", "3", "8.21E−04", "HLA-DRA, NCF2, TLR2"], ["hsa05152", "Tuberculosis", "4", "1.04E−03", "TCIRG1, IL6, HLA-DRA, TLR2"], ["hsa05164", "Influenza A", "4", "1.06E−03", "HLA-DRA, IL6, HSPA6, CXCL8"], ["hsa04610", "Complement and coagulation cascades", "3", "1.15E−03", "C5AR1, PLAUR, SERPINE1"], ["hsa05169", "Epstein-Barr virus infection", "4", "1.85E−03", "HLA-DRA, FGR, TNFAIP3, HSPA6"], ["hsa05145", "Toxoplasmosis", "3", "3.57E−03", "HLA-DRA, HSPA6, TLR2"], ["hsa05332", "Graft-versus-host disease", "2", "4.53E−03", "HLA-DRA, IL6"], ["hsa04672", "Intestinal immune network for IgA production", "2", "6.46E−03", "HLA-DRA, IL6"], ["hsa05161", "Hepatitis B", "3", "6.47E−03", "IL6, CXCL8, TLR2"], ["hsa05150", "Staphylococcus aureus infection", "2", "8.12E−03", "HLA-DRA, C5AR1"]], "row_count": 30, "column_count": 5, "numeric_cells": 93, "header_rows": 1, "locator": "section[13]/table-wrap[1]#table-4"}}, {"id": "asset:table:pmid:31667013:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ec3f73777e8807c510ac4a9076c43b9d42a29a0a4e9682db72a479b9c1a0e95e", "bytes": 3185, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#table-5", "version": null, "note": "Significantly enriched GO of hub genes.", "structure": {"pmcid": "PMC6816389", "section_index": 14, "section_title": "PPI network construction and hub gene identification", "row_count": 38, "column_count": 5}, "table": {"label": "Table 5", "caption": "Significantly enriched GO of hub genes.", "rows": [["ID", "Description", "P-value", "Count", "Gene names"], ["BP", "", "", "", ""], ["GO:0009611", "Response to wounding", "4.58E−11", "9", "CXCL1/ IL6/ CCL20/ SERPINE1/ TLR2/ SELE/ CCL4/ PLAUR/ CD163."], ["GO:0006954", "Inflammatory response", "1.45E−08", "7", "CXCL1/ IL6/ CCL20/ TLR2/ SELE/ CCL4/ CD163."], ["GO:0006952", "Defense response", "6.44E−07", "7", "CXCL1/ IL6/ CCL20/ TLR2/ SELE/ CCL4/ CD163."], ["GO:0042330", "Taxis", "2.27E−06", "5", "CXCL1/ IL6/ CCL20/ CCL4/ PLAUR."], ["GO:0006935", "Chemotaxis", "2.27E−06", "5", "CXCL1/ IL6/ CCL20/ CCL4/ PLAUR."], ["GO:0006955", "Immune response", "2.25E−04", "4", "CXCL1/ IL6/ CCL20/ TLR2/ CCL4."], ["GO:0007596", "Blood coagulation", "6.88E−04", "5", "IL6/ SERPINE1/ PLAUR."], ["GO:0050817", "Coagulation", "0.001396979", "3", "IL6/ SERPINE1/ PLAUR."], ["GO:0007599", "Hemostasis", "0.001957914", "3", "IL6/ SERPINE1/ PLAUR."], ["GO:0042742", "Defense response to bacterium", "0.001957914", "3", "IL6/ CCL20/ TLR2."], ["GO:0006928", "Cell motion", "0.002191691", "3", "IL6/ SELE/ CCL4/ PLAUR."], ["GO:0050878", "Regulation of body fluid levels", "0.002354575", "3", "IL6/ SERPINE1/ PLAUR."], ["GO:0032101", "Regulation of response to external stimulus", "0.003084628", "4", "IL6/ SERPINE1/ SELE."], ["GO:0042060", "Wound healing", "0.003701403", "3", "IL6/ SERPINE1/ PLAUR."], ["GO:0032755", "Positive regulation of interleukin-6 production", "0.004681351", "3", "IL6/ TLR2."], ["GO:0042127", "Regulation of cell proliferation", "0.006688038", "3", "CXCL1/ IL6/ SERPINE1/ TIMP1."], ["GO:0042246", "Tissue regeneration", "0.012573365", "2", "SERPINE1/ PLAUR."], ["GO:0032675", "Regulation of interleukin-6 production", "0.012647695", "4", "IL6/ TLR2."], ["GO:0006953", "Acute-phase response", "0.02109503", "2", "IL6/ CD163."], ["GO:0030162", "Regulation of proteolysis", "0.023703896", "2", "PLAUR/ TIMP1."], ["GO:0050900", "Leukocyte migration", "0.02630658", "2", "IL6/ SELE."], ["GO:0051091", "Positive regulation of transcription factor activity", "0.034722761", "2", "IL6/ TLR2."], ["GO:0045765", "Regulation of angiogenesis", "0.037299313", "2", "IL6/ SERPINE1."], ["GO:0031099", "Regeneration", "0.039227714", "2", "SERPINE1/ PLAUR."], ["GO:0043388", "Positive regulation of DNA binding", "0.04115268", "2", "IL6/ TLR2."], ["GO:0031349", "Positive regulation of defense response", "0.044992331", "2", "IL6/ TLR2."], ["GO:0050727", "Regulation of inflammatory response", "0.049454644", "2", "IL6/ SELE."], ["CC", "", "", "", ""], ["GO:0009611", "Extracellular region", "2.86E−06", "9", "CXCL1/ IL6/ CCL20/ SERPINE1/ SELE/ CCL4/ PLAUR/ CD163/ TIMP1."], ["GO:0006954", "Extracellular region part", "2.31E−04", "6", "CXCL1/ IL6/ CCL20/ SELE/ CCL4/ TIMP1."], ["GO:0006952", "Extracellular space", "8.30E−04", "5", "CXCL1/ IL6/ CCL20/ SELE/ CCL4."], ["MF", "", "", "", ""], ["GO:0005125", "Cytokine activity", "2.62E−04", "4", "CXCL1/ IL6/ CCL20/ CCL4."], ["GO:0008009", "Chemokine activity", "4.35E−04", "3", "CXCL1/ CCL20/ CCL4."], ["GO:0042379", "Chemokine receptor binding", "4.94E−04", "3", "CXCL1/ CCL20/ CCL4."], ["GO:0019899", "Enzyme binding", "0.048323907", "3", "SERPINE1/ SELE/ PLAUR."]], "row_count": 38, "column_count": 5, "numeric_cells": 118, "header_rows": 1, "locator": "section[14]/table-wrap[1]#table-5"}}, {"id": "asset:table:pmid:31667013:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ac1f5f61fc235fdde9c5ec43bc16f030b19564d2ada5c0132f740e7bb46fcb86", "bytes": 1269, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#table-6", "version": null, "note": "Significantly enriched KEGG pathway of hub genes.", "structure": {"pmcid": "PMC6816389", "section_index": 14, "section_title": "PPI network construction and hub gene identification", "row_count": 14, "column_count": 5}, "table": {"label": "Table 6", "caption": "Significantly enriched KEGG pathway of hub genes.", "rows": [["Pathway ID", "Terms", "Gene count", "P-Value", "Genes"], ["hsa04668", "TNF signaling pathway", "4", "5.54E−08", "CXCL1, CCL20, IL6, SELE."], ["hsa04066", "HIF-1 signaling pathway", "3", "6.38E−06", "IL6, SERPINE1, TIMP1."], ["hsa04060", "Cytokine-cytokine receptor interaction", "3", "9.63E−05", "CXCL1, CCL20, IL6."], ["hsa04621", "NOD-like receptor signaling pathway", "2", "0.000199993", "CXCL1,IL6."], ["hsa04610", "Complement and coagulation cascades", "2", "0.000364662", "SERPINE1,PLAUR."], ["hsa04620", "Toll-like receptor signaling pathway", "2", "0.000671108", "IL6,TLR2."], ["hsa04062", "Chemokine signaling pathway", "2", "0.00200085", "CXCL1,CCL20."], ["hsa04151", "PI3K-Akt signaling pathway", "2", "0.006358451", "IL6,TLR2."], ["hsa04672", "Intestinal immune network for IgA production", "1", "0.016724268", "IL6"], ["hsa04623", "Cytosolic DNA-sensing pathway", "1", "0.022711959", "IL6"], ["hsa04115", "p53 signaling pathway", "1", "0.02481751", "SERPINE1"], ["hsa01521", "EGFR tyrosine kinase inhibitor resistance", "1", "0.029714789", "IL6"], ["hsa04068", "FoxO signaling pathway", "1", "0.047713858", "IL6"]], "row_count": 14, "column_count": 5, "numeric_cells": 44, "header_rows": 1, "locator": "section[14]/table-wrap[2]#table-6"}}, {"id": "asset:table:pmid:31667013:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:69545480f490ec046c51ab20d70513b0ba45a5bb6fb9920df82c00dbe7bbea63", "bytes": 731, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#table-7", "version": null, "note": "Results of CMap analysis.", "structure": {"pmcid": "PMC6816389", "section_index": 15, "section_title": "CMap analysis", "row_count": 10, "column_count": 6}, "table": {"label": "Table 7", "caption": "Results of CMap analysis.", "rows": [["Rank", "CMap name", "Mean", "N", "Enrichment", "P-value"], ["1", "Hecogenin", "−0.613", "4", "−0.931", "0.00002"], ["2", "Pralidoxime", "−0.529", "4", "−0.872", "0.00056"], ["3", "Metolazone", "−0.282", "5", "−0.779", "0.00096"], ["4", "Lidocaine", "−0.258", "5", "−0.766", "0.0013"], ["5", "NU-1025", "−0.579", "2", "−0.956", "0.00414"], ["6", "Ambroxol", "−0.269", "4", "−0.774", "0.00527"], ["7", "Pipemidic acid", "−0.336", "3", "−0.846", "0.00735"], ["8", "Yohimbic acid", "−0.345", "3", "−0.845", "0.00747"], ["9", "Chlorphenesin", "−0.354", "4", "−0.74", "0.00899"]], "row_count": 10, "column_count": 6, "numeric_cells": 46, "header_rows": 1, "locator": "section[15]/table-wrap[1]#table-7"}}], "gaps": ["asset:data:geo:GSE24265 not downloaded", "asset:data:geo:GSE24265 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": "Both the normalization of the data and screening of the DEGs were performed using the limma package in the R language (version 3.5.1) (Guo et al., 2017)."}}, {"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": "protein-protein interaction"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}], "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": ["GSE24265"], "resolved_accessions": ["GSE24265"], "statements": ["The data is available in the Gene Expression Omnibus: GSE24265."], "basis": "The paper names GSE24265 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:31667013", "data:geo:GSE24265", "asset:table:pmid:31667013:1", "asset:table:pmid:31667013:2", "asset:table:pmid:31667013:3", "asset:table:pmid:31667013:4", "asset:table:pmid:31667013:5", "asset:table:pmid:31667013:6", "asset:table:pmid:31667013:7"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE24265"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:16:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 34604, "completion_tokens": 1253, "cached_tokens": 792}}, "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:31667013", "type": "paper", "label": "pmid:31667013"}, {"id": "source:pmid:31667013", "type": "manuscript", "label": "PMID 31667013 full text"}, {"id": "data:geo:GSE24265", "type": "dataset", "label": "GEO GSE24265"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31667013", "type": "paper", "label": "pmid:31667013"}, {"id": "source:pmid:31667013", "type": "manuscript", "label": "PMID 31667013 full text"}, {"id": "data:geo:GSE24265", "type": "dataset", "label": "GEO GSE24265"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31667013", "type": "extraction", "used": ["source:pmid:31667013"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE24265", "type": "accession_resolution", "used": ["data:geo:GSE24265"], "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:31667013", "parent_hash": "sha256:cdf9852fd58bbe7dd5ca883f3f6bc57aa291a20ea7b3beb1f14f49da2a2e678a", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE24265 licence not read", "asset:data:geo:GSE24265 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ed the expression levels of the hub genes by RT-qPCR on the rat ICH model. RESULT: A total of 59", "ed to secondary brain injury induced by ICH. RT-qPCR results showed that the expression of ten hu", "the expression levels of the hub genes by RT-qPCR on the rat ICH model. RESULT: A total of 59", "to secondary brain injury induced by ICH. RT-qPCR results showed that the expression of ten hu"], "order_basis": "paper_text_order:1443", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["of ten hub genes was significantly increased in the rat model of ICH. In addition, a CMap analysis o", "d through PPI network analysis were verified in the rat model of ICH. In addition, we obtained three", "on levels of the hub genes by RT-qPCR on the rat ICH model. RESULT: A total of 59 up-regulate", "hub genes was significantly increased in the rat model of ICH. In addition, a CMap analysis o"], "order_basis": "paper_text_order:1458", "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": 1.0, "evidence": ["Both the normalization of the data and screening of the DEGs were performed using the limma package in the R language (version 3.5.1) (Guo et al., 2017)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}