← All .science files
pmid:32594047
Hub genes and key pathways of traumatic brain injury: bioinformatics analysis and in vivo validation.
Yun-Liang Tang · Long-Jun Fang · Ling-Yang Zhong · Jian Jiang · Xiao-Yang Dong · Zhen Feng
Neural regeneration research · 2020 doi:10.4103/1673-5374.284996
Paper
complete
Experiment
complete
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 6 items
claims array · 2 items
[0] object · 6 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 5 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 47 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 23 items
[0] array · 3 items
[1] array · 3 items
[2] array · 3 items
[3] array · 3 items
[4] array · 3 items
[5] array · 3 items
[6] array · 3 items
[7] array · 3 items
[8] array · 3 items
[9] array · 3 items
[10] array · 3 items
[11] array · 3 items
[12] array · 3 items
[13] array · 3 items
[14] array · 3 items
[15] array · 3 items
[16] array · 3 items
[17] array · 3 items
[18] array · 3 items
[19] array · 3 items
[20] array · 3 items
[21] array · 3 items
[22] array · 3 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 43 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
[17] array · 5 items
[18] array · 5 items
[19] array · 5 items
[20] array · 5 items
[21] array · 5 items
[22] array · 5 items
[23] array · 5 items
[24] array · 5 items
[25] array · 5 items
[26] array · 5 items
[27] array · 5 items
[28] array · 5 items
[29] array · 5 items
[30] array · 5 items
[31] array · 5 items
[32] array · 5 items
[33] array · 5 items
[34] array · 5 items
[35] array · 5 items
[36] array · 5 items
[37] array · 5 items
[38] array · 5 items
[39] array · 5 items
[40] array · 5 items
[41] array · 5 items
[42] array · 5 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 20 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
[17] array · 5 items
[18] array · 5 items
[19] array · 5 items
gaps array · 2 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 5 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 7 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[2] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32594047", "kind": "science-record", "revision": 6, "content_hash": "sha256:7bcd7778b11e12883d51e5b6ead0cf95aa394a1f6eb2e6fb29cd8b2abb46f708", "created_at": "2026-11-01T15:41:04Z", "updated_at": "2026-11-01T21:23:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Hub genes and key pathways of traumatic brain injury: bioinformatics analysis and in vivo validation.", "doi": "10.4103/1673-5374.284996", "pmid": "32594047", "authors": ["Yun-Liang Tang", "Long-Jun Fang", "Ling-Yang Zhong", "Jian Jiang", "Xiao-Yang Dong", "Zhen Feng"], "journal": "Neural regeneration research", "year": 2020, "abstract": "The exact mechanisms associated with secondary brain damage following traumatic brain injury (TBI) remain unclear; therefore, identifying the critical molecular mechanisms involved in TBI is essential. The mRNA expression microarray GSE2871 was downloaded from the Gene Expression Omnibus (GEO) repository. GSE2871 comprises a total of 31 cerebral cortex samples, including two post-TBI time points. The microarray features eight control and seven TBI samples, from 4 hours post-TBI, and eight control and eight TBI samples from 24 hours post-TBI. In this bioinformatics-based study, 109 and 66 differentially expressed genes (DEGs) were identified in a Sprague-Dawley (SD) rat TBI model, 4 and 24 hours post-TBI, respectively. Functional enrichment analysis showed that the identified DEGs were significantly enriched in several terms, such as positive regulation of nuclear factor-κB transcription factor activity, mitogen-activated protein kinase signaling pathway, negative regulation of apoptotic process, and tumor necrosis factor signaling pathway. Moreover, the hub genes with high connectivity degrees were primarily related to inflammatory mediators. To validate the top five hub genes, a rat model of TBI was established using the weight-drop method, and real-time quantitative polymerase chain reaction analysis of the cerebral cortex was performed. The results showed that compared with control rats, Tnf-α, c-Myc, Spp1, Cxcl10, Ptprc, Egf, Mmp9, and Lcn2 were upregulated, and Fn1 was downregulated in TBI rats. Among these hub genes, Fn1, c-Myc, and Ptprc may represent novel biomarkers or therapeutic targets for TBI. These identified pathways and key genes may provide insights into the molecular mechanisms of TBI and provide potential treatment targets for patients with TBI. This study was approved by the Experimental Animal Ethics Committee of the First Affiliated Hospital of Nanchang University, China (approval No. 003) in January 2016.", "claims": [{"id": "claim-method", "statement": "We used GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r) to identify DEGs between control and TBI cortical samples at both time points.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32594047", "locator": "sections[5] \"Data processing\" paragraph 2", "quote": "We used GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r) to identify DEGs between control and TBI cortical samples at both time points."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Datasets analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32594047", "locator": "sections[18] \"Footnotes\" paragraph 2", "quote": "Datasets analyzed during the current study are available from the corresponding author on reasonable 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:32594047"], "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:GSE2871"], "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:GSE2871"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32594047", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.4103/1673-5374.284996", "sha256": "sha256:6c52a32aae66466a61db6749a5bbdccc5bb13bb14caa80d0b6b850f836309d05", "bytes": 35216, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.4103/1673-5374.284996", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7749465", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE2871", "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=GSE2871", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE2871", "version": null, "note": "Datasets analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Datasets analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM53252", "GSM53253", "GSM53254", "GSM53255", "GSM53256", "GSM53257", "GSM53258", "GSM53259", "GSM53260", "GSM53261", "GSM53262", "GSM53263", "GSM53264", "GSM53265", "GSM53266", "GSM53267", "GSM53268", "GSM53269", "GSM53270", "GSM53271", "GSM53272", "GSM53273", "GSM53274", "GSM53275", "GSM53276", "GSM53277", "GSM53278", "GSM53279", "GSM53280", "GSM53281", "GSM53282", "GSM53283", "GSM53284", "GSM53285", "GSM53286", "GSM53287", "GSM53288", "GSM53289", "GSM53290", "GSM53291", "GSM53292", "GSM53293", "GSM53294", "GSM53295", "GSM53296", "GSM53297", "GSM53298"], "sample_count": 47, "group_sizes": null, "group_sizes_basis": null, "platform": "85", "taxon": "Rattus norvegicus", "title": "giza-affy-rat-84719", "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:32594047:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c6c7537f9f6e4fdb368c9a278f68ed19d3eb9e0b6772bbfe5e262e96257b883f", "bytes": 1531, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T1", "version": null, "note": "Primer sequences for polymerase chain reaction amplification", "structure": {"pmcid": "PMC7749465", "section_index": 9, "section_title": "Real-time quantitative PCR", "row_count": 23, "column_count": 3}, "table": {"label": "Table 1", "caption": "Primer sequences for polymerase chain reaction amplification", "rows": [["Gene", "Sequence", "Product size (bp)"], ["Fn1", "Forward: 5′-TAC ACG GTT TCC CAT TAC GC-3′", "224"], ["", "Reverse: 5′-CCT TTC CAT TCC CGA GAC AT-3′", ""], ["Tnf-α", "Forward: 5′-AGA TGT GGA ACT GGC AGA GG-3′", "178"], ["", "Reverse: 5′-CCC ATT TGG GAA CTT CTC CT-3′", ""], ["c-Myc", "Forward: 5′-GGT CAT CCC CAT CAA GAG-3′", "187"], ["", "Reverse: 5′-GAG GAG AAG GCG CAT TAC AG-3′", ""], ["Spp1", "Forward: 5′-GAG GAG AAG GCG CAT TAC AG-3′", "165"], ["", "Reverse:5′-ATG GCT TTC ATT GGA GTT GC-3′", ""], ["Cxcl10", "Forward: 5′-CAC ACC CTC CTT CTC CCT-3′", "88"], ["", "Reverse: 5′-TGC CAT CTC ACC TGG ACT-3′", ""], ["Ptprc", "Forward: 5′-CGA ACA AAT CCT CAG CCT A-3′", "108"], ["", "Reverse: 5′-CCT CCC CTT TCC ATG TG-3′", ""], ["Egf", "Forward: 5′-ACA GGC TTT GTT CTG CTT CCT-3′", "195"], ["", "Reverse: 5′-GCT GCA TCC ACC ATT ATC GGA G-3′", ""], ["Mmp9", "Forward: 5′-GCC GGG AAC GTA TCT GGA AA-3′", "177"], ["", "Reverse: 5′-GGT TGT GGA AAC TCA CAC GC-3′", ""], ["Nox4", "Forward: 5′-GGG CCT AGG ATT GTG TTT GA-3′", "245"], ["", "Reverse: 5′-CTG AGA AGT TCA GGG CGT TC-3′", ""], ["Lcn2", "Forward: 5′-GGC CTC AAG GAT AAC A-3′", "150"], ["", "Reverse: 5′-GGC AAC AGG AAA GAT GGA-3′", ""], ["GAPDH", "Forward: 5′-CCT TCC GTG TCC CCA CT-3′", "100"], ["", "Reverse: 5′-GCC TGC TTC ACC TTC-3′", ""]], "row_count": 23, "column_count": 3, "numeric_cells": 34, "header_rows": 1, "locator": "section[9]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32594047:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c00cedb6ff5c90264ea8b29b9cbd851273a440f2eed63a2cd7b824b821cb20da", "bytes": 3971, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T2", "version": null, "note": "Functional and pathway enrichment analysis of differentially expressed genes", "structure": {"pmcid": "PMC7749465", "section_index": 13, "section_title": "Functional enrichment analysis of identified DEGs in TBI", "row_count": 43, "column_count": 5}, "table": {"label": "Table 2", "caption": "Functional and pathway enrichment analysis of differentially expressed genes", "rows": [["Category", "Term", "Count", "Gene ratio (%)", "P-value"], ["4 h post-traumatic brain injury", "", "", "", ""], ["GOTERM_BP_DIRECT", "GO:0051092~positive regulation of NF-kappaB transcription factor activity", "8", "0.058642428", "3.89E-06"], ["GOTERM_BP_DIRECT", "GO:0009612~response to mechanical stimulus", "7", "0.051312124", "2.55E-05"], ["GOTERM_BP_DIRECT", "GO:0031663~lipopolysaccharide-mediated signaling pathway", "5", "0.036651517", "2.57E-05"], ["GOTERM_BP_DIRECT", "GO:0032496~response to lipopolysaccharide", "10", "0.073303035", "2.70E-05"], ["GOTERM_BP_DIRECT", "GO:0033280~response to vitamin D", "5", "0.036651517", "2.93E-05"], ["GOTERM_CC_DIRECT", "GO:0005615~extracellular space", "26", "0.19058789", "2.12E-08"], ["GOTERM_CC_DIRECT", "GO:0005576~extracellular region", "16", "0.117284856", "6.43E-06"], ["GOTERM_CC_DIRECT", "GO:0072562~blood microparticle", "7", "0.051312124", "4.31E-05"], ["GOTERM_CC_DIRECT", "GO:0005829~cytosol", "19", "0.139275766", "0.001995362"], ["GOTERM_CC_DIRECT", "GO:0048471~perinuclear region of cytoplasm", "11", "0.080633338", "0.002452866"], ["GOTERM_MF_DIRECT", "GO:0005125~cytokine activity", "9", "0.065972731", "2.93E-06"], ["GOTERM_MF_DIRECT", "GO:0002020~protease binding", "7", "0.051312124", "6.58E-05"], ["GOTERM_MF_DIRECT", "GO:0008201~heparin binding", "7", "0.051312124", "1.77E-04"], ["GOTERM_MF_DIRECT", "GO:0008083~growth factor activity", "6", "0.043981821", "0.00125609"], ["GOTERM_MF_DIRECT", "GO:0044183~protein binding involved in protein folding", "3", "0.02199091", "0.00236215"], ["KEGG_PATHWAY", "rno04010:MAPK signaling pathway", "10", "0.073303035", "2.08E-04"], ["KEGG_PATHWAY", "rno04668:TNF signaling pathway", "7", "0.051312124", "2.39E-04"], ["KEGG_PATHWAY", "rno05323:Rheumatoid arthritis", "6", "0.043981821", "7.82E-04"], ["KEGG_PATHWAY", "rno04623:Cytosolic DNA-sensing pathway", "5", "0.036651517", "0.001061882"], ["KEGG_PATHWAY", "rno04620:Toll-like receptor signaling pathway", "6", "0.043981821", "0.001097316"], ["24 h post-traumatic brain injury", "", "", "", ""], ["GOTERM_BP_DIRECT", "GO:0043066~negative regulation of apoptotic process", "11", "0.152417902", "9.12E-06"], ["GOTERM_BP_DIRECT", "GO:0071222~cellular response to lipopolysaccharide", "7", "0.09699321", "2.23E-05"], ["GOTERM_BP_DIRECT", "GO:0045087~innate immune response", "8", "0.110849383", "2.94E-05"], ["GOTERM_BP_DIRECT", "GO:0030593~neutrophil chemotaxis", "5", "0.069280865", "4.58E-05"], ["GOTERM_BP_DIRECT", "GO:0032496~response to lipopolysaccharide", "8", "0.110849383", "4.60E-05"], ["GOTERM_CC_DIRECT", "GO:0005615~extracellular space", "20", "0.277123459", "1.64E-08"], ["GOTERM_CC_DIRECT", "GO:0070062~extracellular exosome", "22", "0.304835804", "4.77E-05"], ["GOTERM_CC_DIRECT", "GO:0005576~extracellular region", "11", "0.152417902", "8.97E-05"], ["GOTERM_CC_DIRECT", "GO:0048471~perinuclear region of cytoplasm", "9", "0.124705556", "0.001041127"], ["GOTERM_CC_DIRECT", "GO:0005737~cytoplasm", "27", "0.374116669", "0.008608494"], ["GOTERM_MF_DIRECT", "GO:0008083~growth factor activity", "5", "0.069280865", "0.001505624"], ["GOTERM_MF_DIRECT", "GO:0016301~kinase activity", "4", "0.055424692", "0.016521332"], ["GOTERM_MF_DIRECT", "GO:0005125~cytokine activity", "4", "0.055424692", "0.01738503"], ["GOTERM_MF_DIRECT", "GO:0016175~superoxide-generating NADPH oxidase activity", "2", "0.027712346", "0.027536173"], ["GOTERM_MF_DIRECT", "GO:0050786~RAGE receptor binding", "2", "0.027712346", "0.034302944"], ["KEGG_PATHWAY", "rno04668:TNF signaling pathway", "4", "0.055050922", "0.013802516"], ["KEGG_PATHWAY", "rno05168:Herpes simplex infection", "5", "0.068813653", "0.017207178"], ["KEGG_PATHWAY", "rno04010:MAPK signaling pathway", "5", "0.068813653", "0.030289942"], ["KEGG_PATHWAY", "rno04925:Aldosterone synthesis and secretion", "3", "0.041288192", "0.057689656"], ["KEGG_PATHWAY", "rno04612:Antigen processing and presentation", "3", "0.041288192", "0.074243304"]], "row_count": 43, "column_count": 5, "numeric_cells": 162, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:32594047:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:246d3168ccb9fbce8c7b68a7f1d6c35045a591c1f9e9ed48427c85cc100ddd0e", "bytes": 1630, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T3", "version": null, "note": "Functional and pathway enrichment analysis of hub genes", "structure": {"pmcid": "PMC7749465", "section_index": 14, "section_title": "PPI network construction and hub genes analysis", "row_count": 20, "column_count": 5}, "table": {"label": "Table 3", "caption": "Functional and pathway enrichment analysis of hub genes", "rows": [["Category", "Term", "Count", "Gene ratio (%)", "P-value"], ["4 h post-traumatic brain injury", "", "", "", ""], ["GOTERM_BP_DIRECT", "GO:0033280~response to vitamin D", "5", "25", "3.47E-08"], ["GOTERM_BP_DIRECT", "GO:0071222~cellular response to lipopolysaccharide", "6", "30", "7.70E-07"], ["GOTERM_BP_DIRECT", "GO:0042493~response to drug", "8", "40", "7.94E-07"], ["GOTERM_BP_DIRECT", "GO:0000165~MAPK cascade", "5", "25", "3.20E-06"], ["GOTERM_BP_DIRECT", "GO:0031663~lipopolysaccharide-mediated signaling pathway", "4", "20", "4.76E-06"], ["KEGG_PATHWAY", "rno04668:TNF signaling pathway", "5", "25", "7.66E-05"], ["KEGG_PATHWAY", "rno05146:Amoebiasis", "5", "25", "8.51E-05"], ["KEGG_PATHWAY", "rno04010:MAPK signaling pathway", "6", "30", "1.72E-04"], ["KEGG_PATHWAY", "rno05144:Malaria", "4", "20", "2.64E-04"], ["KEGG_PATHWAY", "rno05164:Influenza A", "5", "25", "4.35E-04"], ["24 h post-traumatic brain injury", "", "", "", ""], ["GOTERM_BP_DIRECT", "GO:0001666~response to hypoxia", "6", "30", "8.13E-06"], ["GOTERM_BP_DIRECT", "GO:0043066~negative regulation of apoptotic process", "7", "35", "1.25E-05"], ["GOTERM_BP_DIRECT", "GO:0042493~response to drug", "7", "35", "1.41E-05"], ["GOTERM_BP_DIRECT", "GO:0030593~neutrophil chemotaxis", "4", "20", "3.20E-05"], ["GOTERM_BP_DIRECT", "GO:0000187~activation of MAPK activity", "4", "20", "7.79E-05"], ["KEGG_PATHWAY", "rno04668:TNF signaling pathway", "3", "15", "0.015978393"], ["KEGG_PATHWAY", "rno04062:Chemokine signaling pathway", "3", "15", "0.039429064"]], "row_count": 20, "column_count": 5, "numeric_cells": 70, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:GSE2871 not downloaded", "asset:data:geo:GSE2871 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We used GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r) to identify DEGs between control and TBI cortical samples at both time points."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pathway_enrichment."}, "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": ["GSE2871"], "resolved_accessions": ["GSE2871"], "statements": ["Datasets analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE2871 in Gene Expression Omnibus (GEO) repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pathway_enrich"], "assets": ["source:pmid:32594047", "data:geo:GSE2871", "asset:table:pmid:32594047:1", "asset:table:pmid:32594047:2", "asset:table:pmid:32594047:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE2871"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:20:41Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28499, "completion_tokens": 1127, "cached_tokens": 779}}, "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:32594047", "type": "paper", "label": "pmid:32594047"}, {"id": "source:pmid:32594047", "type": "manuscript", "label": "PMID 32594047 full text"}, {"id": "data:geo:GSE2871", "type": "dataset", "label": "GEO GSE2871"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32594047", "type": "paper", "label": "pmid:32594047"}, {"id": "source:pmid:32594047", "type": "manuscript", "label": "PMID 32594047 full text"}, {"id": "data:geo:GSE2871", "type": "dataset", "label": "GEO GSE2871"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32594047", "type": "extraction", "used": ["source:pmid:32594047"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE2871", "type": "accession_resolution", "used": ["data:geo:GSE2871"], "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:32594047", "parent_hash": "sha256:04a3c410ea4be404e021837c55251ac41881ccccac5aab1bb855ecbc56b88ca4", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE2871 licence not read", "asset:data:geo:GSE2871 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": ["ic brain injury: bioinformatics analysis and in vivo validation.", "Gs) were identified in a Sprague-Dawley (SD) rat TBI model, 4 and 24 hours post-TBI, respecti", "ators. To validate the top five hub genes, a rat model of TBI was established using the weigh", "he results showed that compared with control rats, Tnf-α, c-Myc, Spp1, Cxcl10, Ptprc, Egf, Mmp"], "order_basis": "paper_text_order:37", "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": 0.99, "evidence": ["ved in TBI is essential. The mRNA expression microarray GSE2871 was downloaded from the Gene Express", "les, including two post-TBI time points. The microarray features eight control and seven TBI samples"], "order_basis": "paper_text_order:279", "id": "assay:2"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["GO enrichment"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}