← All .science files
pmid:33777260
The Genetic and Epigenetic Mechanisms Involved in Irreversible Pulp Neural Inflammation.
Xiaoxi Xi · Yihong Ma · Yuzhen Xu · Anthony Chukwunonso Ogbuehi · Xiangqiong Liu · Yupei Deng · Junming Xi · Haitong Pan · Qian Lin · Bo Li · Wanchen Ning · Xiao Jiang · Hanluo Li · Simin Li · Xianda Hu
Disease markers · 2021 doi:10.1155/2021/8831948
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
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 · 15 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 · 11 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 12 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 12 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 3 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 4 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 21 items
[0] array · 7 items
[1] array · 7 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[12] array · 7 items
[13] array · 7 items
[14] array · 7 items
[15] array · 7 items
[16] array · 7 items
[17] array · 7 items
[18] array · 7 items
[19] array · 7 items
[20] array · 7 items
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 21 items
[0] array · 8 items
[1] array · 8 items
[2] array · 8 items
[3] array · 8 items
[4] array · 8 items
[5] array · 8 items
[6] array · 8 items
[7] array · 8 items
[8] array · 8 items
[9] array · 8 items
[10] array · 8 items
[11] array · 8 items
[12] array · 8 items
[13] array · 8 items
[14] array · 8 items
[15] array · 8 items
[16] array · 8 items
[17] array · 8 items
[18] array · 8 items
[19] array · 8 items
[20] array · 8 items
[7] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 21 items
[0] array · 7 items
[1] array · 7 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[12] array · 7 items
[13] array · 7 items
[14] array · 7 items
[15] array · 7 items
[16] array · 7 items
[17] array · 7 items
[18] array · 7 items
[19] array · 7 items
[20] array · 7 items
[8] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 26 items
[0] array · 7 items
[1] array · 7 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[12] array · 7 items
[13] array · 7 items
[14] array · 7 items
[15] array · 7 items
[16] array · 7 items
[17] array · 7 items
[18] array · 7 items
[19] array · 7 items
[20] array · 7 items
[21] array · 7 items
[22] array · 7 items
[23] array · 7 items
[24] array · 7 items
[25] array · 7 items
[9] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 26 items
[0] array · 8 items
[1] array · 8 items
[2] array · 8 items
[3] array · 8 items
[4] array · 8 items
[5] array · 8 items
[6] array · 8 items
[7] array · 8 items
[8] array · 8 items
[9] array · 8 items
[10] array · 8 items
[11] array · 8 items
[12] array · 8 items
[13] array · 8 items
[14] array · 8 items
[15] array · 8 items
[16] array · 8 items
[17] array · 8 items
[18] array · 8 items
[19] array · 8 items
[20] array · 8 items
[21] array · 8 items
[22] array · 8 items
[23] array · 8 items
[24] array · 8 items
[25] array · 8 items
[10] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 21 items
[0] array · 6 items
[1] array · 6 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[8] array · 6 items
[9] array · 6 items
[10] array · 6 items
[11] array · 6 items
[12] array · 6 items
[13] array · 6 items
[14] array · 6 items
[15] array · 6 items
[16] array · 6 items
[17] array · 6 items
[18] array · 6 items
[19] array · 6 items
[20] array · 6 items
gaps array · 4 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 · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
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 · 2 items
resolved_accessions array · 2 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 10 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 · 8 items
assays array · 1 item
[0] 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:33777260", "kind": "science-record", "revision": 7, "content_hash": "sha256:2668ac8b38e9a1774682153af311f4a12030a55aab7e5e88890b2df500f5cd54", "created_at": "2026-11-01T15:41:30Z", "updated_at": "2026-11-01T22:03:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Genetic and Epigenetic Mechanisms Involved in Irreversible Pulp Neural Inflammation.", "doi": "10.1155/2021/8831948", "pmid": "33777260", "authors": ["Xiaoxi Xi", "Yihong Ma", "Yuzhen Xu", "Anthony Chukwunonso Ogbuehi", "Xiangqiong Liu", "Yupei Deng", "Junming Xi", "Haitong Pan", "Qian Lin", "Bo Li", "Wanchen Ning", "Xiao Jiang", "Hanluo Li", "Simin Li", "Xianda Hu"], "journal": "Disease markers", "year": 2021, "abstract": "AIM: To identify the critical genetic and epigenetic biomarkers by constructing the long noncoding RNA- (lncRNA-) related competing endogenous RNA (ceRNA) network involved in irreversible pulp neural inflammation (pulpitis).\nMATERIALS AND METHODS: The public datasets regarding irreversible pulpitis were downloaded from the gene expression omnibus (GEO) database. The differential expression analysis was performed to identify the differentially expressed genes (DEGs) and DElncRNAs. Functional enrichment analysis was performed to explore the biological processes and signaling pathways enriched by DEGs. By performing a weighted gene coexpression network analysis (WGCNA), the significant gene modules in each dataset were identified. Most importantly, DElncRNA-DEmRNA regulatory network and DElncRNA-associated ceRNA network were constructed. A transcription factor- (TF-) DEmRNA network was built to identify the critical TFs involved in pulpitis.\nRESULT: Two datasets (GSE92681 and GSE77459) were selected for analysis. DEGs involved in pulpitis were significantly enriched in seven signaling pathways (i.e., NOD-like receptor (NLR), Toll-like receptor (TLR), NF-kappa B, tumor necrosis factor (TNF), cell adhesion molecules (CAMs), chemokine, and cytokine-cytokine receptor interaction pathways). The ceRNA regulatory relationships were established consisting of three genes (i.e., LCP1, EZH2, and NR4A1), five miRNAs (i.e., miR-340-5p, miR-4731-5p, miR-27a-3p, miR-34a-5p, and miR-766-5p), and three lncRNAs (i.e., XIST, MIR155HG, and LINC00630). Six transcription factors (i.e., GATA2, ETS1, FOXP3, STAT1, FOS, and JUN) were identified to play pivotal roles in pulpitis.\nCONCLUSION: This paper demonstrates the genetic and epigenetic mechanisms of irreversible pulpitis by revealing the ceRNA network. The biomarkers identified could provide research direction for the application of genetically modified stem cells in endodontic regeneration.", "claims": [{"id": "claim-method", "statement": "Based on the GSE92681 dataset, the coexpression status of DElncRNAs and DEGs was calculated by using a statistical method—Pearson correlation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33777260", "locator": "sections[9] \"2.7. Functional Enrichment Analysis of DElncRNAs\" paragraph 2", "quote": "Based on the GSE92681 dataset, the coexpression status of DElncRNAs and DEGs was calculated by using a statistical method—Pearson correlation."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33777260", "locator": "sections[28] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author upon 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:33777260"], "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:GSE77459"], "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:GSE77459"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33777260", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/8831948", "sha256": "sha256:0afa4b11bae509d613ea0c98ceb8eef89e88cb12630a2c80871c1df156b5402c", "bytes": 70049, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/8831948", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7968449", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE77459", "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=GSE77459", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE77459", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2052371", "GSM2052372", "GSM2052373", "GSM2052374", "GSM2052375", "GSM2052376", "GSM2052377", "GSM2052378", "GSM2052379", "GSM2052380", "GSM2052381", "GSM2052382"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "17692", "taxon": "Homo sapiens", "title": "Gene Expression Profile of Pulpitis", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE92681", "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=GSE92681", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE92681", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2434473", "GSM2434474", "GSM2434475", "GSM2434476", "GSM2434477", "GSM2434478", "GSM2434479", "GSM2434480", "GSM2434481", "GSM2434482", "GSM2434483", "GSM2434484"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "16956", "taxon": "Homo sapiens", "title": "Differential Expression of LncRNAs and mRNAs in normal and inflamed human pulp", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33777260:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9543c91f1964c55138d19f715f00bfe4ec2fd9831fe79e4656b72025378e8251", "bytes": 394, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#tab1", "version": null, "note": "The pulpitis-related datasets used for the present analysis.", "structure": {"pmcid": "PMC7968449", "section_index": 16, "section_title": "3.2. Identification of DEGs", "row_count": 3, "column_count": 4}, "table": {"label": "Table 1", "caption": "The pulpitis-related datasets used for the present analysis.", "rows": [["Datasets", "Experimental type of datasets", "Sample size of inflamed pulp tissue", "Sample size of healthy pulp tissue"], ["GSE92681", "Noncoding RNA", "7", "5"], ["GSE77459", "mRNA", "6", "6"]], "row_count": 3, "column_count": 4, "numeric_cells": 6, "header_rows": 1, "locator": "section[16]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:33777260:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a1d1906e3355972c5116d9ae86b966fdf914bd376bc6959471c1d2ef1d81444f", "bytes": 462, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#tab2", "version": null, "note": "The number of upregulated and downregulated DEGs or DElncRNAs identified from included datasets.", "structure": {"pmcid": "PMC7968449", "section_index": 16, "section_title": "3.2. Identification of DEGs", "row_count": 4, "column_count": 4}, "table": {"label": "Table 2", "caption": "The number of upregulated and downregulated DEGs or DElncRNAs identified from included datasets.", "rows": [["Datasets", "Number of upregulated factors", "Number of downregulated factors", "Number of total factors"], ["GSE92681_DElncRNA", "138", "136", "274"], ["GSE92681_DEG", "486", "178", "664"], ["GSE77459_DEG", "823", "278", "1101"]], "row_count": 4, "column_count": 4, "numeric_cells": 12, "header_rows": 1, "locator": "section[16]/table-wrap[2]#tab2"}}, {"id": "asset:table:pmid:33777260:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4c008fd39f8235459a9c7efd95be809429cf452ff4ab4f08deb09f699b5c1808", "bytes": 1766, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#tab3", "version": null, "note": "The topological characteristics of the top 20 nodes in the PPI network.", "structure": {"pmcid": "PMC7968449", "section_index": 18, "section_title": "3.4. Identification of Hub Genes by Constructing the PPI Network", "row_count": 21, "column_count": 7}, "table": {"label": "Table 3", "caption": "The topological characteristics of the top 20 nodes in the PPI network.", "rows": [["Gene name", "Degree", "Average shortest path length", "Betweenness centrality", "Closeness centrality", "Clustering coefficient", "Topological coefficient"], ["UBD", "656", "2.700089", "0.092136", "0.370358", "0.001564", "0.003702"], ["UBC", "460", "2.20363", "0.309699", "0.453797", "0.004092", "0.005551"], ["IFI16", "436", "2.853032", "0.052658", "0.350504", "0.001381", "0.005531"], ["ARRB2", "369", "2.872067", "0.040035", "0.348181", "0.001915", "0.007365"], ["HLA-B", "338", "2.825255", "0.037735", "0.35395", "0.002915", "0.00551"], ["EZH2", "301", "2.891545", "0.030774", "0.345836", "0.00206", "0.008083"], ["SFN", "296", "2.903608", "0.032059", "0.344399", "0.00213", "0.00725"], ["ADRB2", "294", "2.855246", "0.033685", "0.350233", "0.003088", "0.006755"], ["LYN", "243", "2.795595", "0.03365", "0.357706", "0.013332", "0.008931"], ["MAP3K1", "229", "2.901173", "0.021399", "0.344688", "0.00406", "0.009621"], ["FOS", "226", "2.943448", "0.02579", "0.339738", "0.00468", "0.010265"], ["RPS9", "208", "2.82127", "0.017896", "0.35445", "0.009337", "0.00958"], ["KPNA2", "205", "2.867641", "0.022731", "0.348719", "0.00263", "0.009771"], ["IL7R", "199", "2.931496", "0.015151", "0.341123", "0.002944", "0.011601"], ["LGR4", "198", "3.039287", "0.020276", "0.329025", "3.59E-04", "0.010662"], ["CASP8", "196", "2.906707", "0.020462", "0.344032", "0.008791", "0.010607"], ["CD247", "196", "2.964697", "0.024808", "0.337303", "0.00539", "0.010402"], ["HIF1A", "174", "2.950089", "0.016343", "0.338973", "0.003123", "0.013813"], ["MYO19", "173", "2.93548", "0.0148", "0.34066", "0.010687", "0.00917"], ["MNDA", "168", "3.236498", "0.007305", "0.308976", "7.84E − 04", "0.012766"]], "row_count": 21, "column_count": 7, "numeric_cells": 123, "header_rows": 1, "locator": "section[18]/table-wrap[1]#tab3"}}, {"id": "asset:table:pmid:33777260:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1a8cf64588172a8d97eff01713ed1181e13c6e3b739d606e17cd5aef60223a56", "bytes": 2264, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[1]#tab4", "version": null, "note": "The topological characteristics of the top 20 nodes in the DElncRNA-DEG regulatory network.", "structure": {"pmcid": "PMC7968449", "section_index": 21, "section_title": "3.7. The DElncRNA-DEG Regulatory Network", "row_count": 21, "column_count": 8}, "table": {"label": "Table 4", "caption": "The topological characteristics of the top 20 nodes in the DElncRNA-DEG regulatory network.", "rows": [["Name", "Degree", "Average shortest path length", "Betweenness centrality", "Closeness centrality", "Clustering coefficient", "Topological coefficient", "Regulate"], ["RP11-702F3.3", "32", "2.26666667", "0.09257337", "0.44117647", "0.36363636", "0.2867215", "lncRNAup"], ["RP5-963E22.4", "32", "2.05", "0.14685811", "0.48780488", "0.3982684", "0.27954545", "lncRNAup"], ["RP11-555G19.1", "25", "2.21666667", "0.08384754", "0.45112782", "0.37908497", "0.30401235", "lncRNAup"], ["CTD-2568A17.1", "21", "2.56666667", "0.17922917", "0.38961039", "0.37179487", "0.26627219", "lncRNAup"], ["PRSS29P", "21", "2.28333333", "0.18869008", "0.4379562", "0.20588235", "0.26916221", "lncRNAup"], ["RP11-686F15.2", "20", "2.53333333", "0.01950748", "0.39473684", "0.44761905", "0.35757576", "lncRNAup"], ["RP11-783L4.1", "19", "2.58333333", "0.01555518", "0.38709677", "0.47252747", "0.37327189", "lncRNAup"], ["RP11-1M18.1", "18", "2.06666667", "0.32645541", "0.48387097", "0.3030303", "0.22644928", "lncRNAup"], ["LINC01043", "17", "2.61666667", "0.01053104", "0.38216561", "0.43589744", "0.36923077", "lncRNAup"], ["RP1-15D23.2", "17", "2.48333333", "0.00914061", "0.40268456", "0.59090909", "0.38333333", "lncRNAup"], ["RP11-442O18.1", "17", "2.66666667", "0.03491119", "0.375", "0.3974359", "0.33846154", "lncRNAup"], ["AC017002.1", "16", "2.35", "0.51050061", "0.42553191", "0.05714286", "0.17333333", "lncRNAup"], ["CTD-2275D24.1", "14", "3.23333333", "0.02043004", "0.30927835", "0.44444444", "0.41176471", "lncRNAup"], ["PDE7A", "13", "2.15", "0.08844751", "0.46511628", "0.35897436", "0.33208255", "mRNA up"], ["RP11-145G20.1", "13", "3.33333333", "0.01660117", "0.3", "0.36111111", "0.39869281", "lncRNAup"], ["RP11-521D12.1", "13", "3.35", "0.00459174", "0.29850746", "0.5", "0.43382353", "lncRNAup"], ["RP5-991O23.1", "13", "3.03333333", "0.01404135", "0.32967033", "0.33333333", "0.31481481", "lncRNAup"], ["CTD-2296D1.1", "12", "3.36666667", "0.00429011", "0.2970297", "0.5", "0.453125", "lncRNAup"], ["RP3-340N1.6", "12", "3.35", "0.0054601", "0.29850746", "0.57142857", "0.44852941", "lncRNAup"], ["MIR155HG", "11", "2.55", "0.41865079", "0.39215686", "0", "0.12121212", "lncRNAup"]], "row_count": 21, "column_count": 8, "numeric_cells": 139, "header_rows": 1, "locator": "section[21]/table-wrap[1]#tab4"}}, {"id": "asset:table:pmid:33777260:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fb5350f95fcf420118a8e113d9cf5b3526b64219cb00c054243ac056279c539b", "bytes": 1980, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[1]#tab5", "version": null, "note": "The topological characteristics of the top 20 nodes in the TF-DEG regulatory network.", "structure": {"pmcid": "PMC7968449", "section_index": 22, "section_title": "3.8. Identification of Hub Transcription Factor", "row_count": 21, "column_count": 7}, "table": {"label": "Table 5", "caption": "The topological characteristics of the top 20 nodes in the TF-DEG regulatory network.", "rows": [["Name", "Degree", "Average shortest path length", "Betweenness centrality", "Closeness centrality", "Clustering coefficient", "Topological coefficient"], ["GATA2", "518", "2.03887936", "0.11659147", "0.49046551", "0.00308432", "0.02016302"], ["ETS1", "508", "2.05603202", "0.11527216", "0.48637375", "0.0028654", "0.02038007"], ["YBX1", "425", "2.22012579", "0.09284757", "0.45042493", "0.00137625", "0.02440558"], ["AR", "414", "2.18753573", "0.08279112", "0.45713539", "0.0032635", "0.02330064"], ["FOXP3", "407", "2.24013722", "0.09211348", "0.44640123", "0.00128297", "0.02202286"], ["GATA1", "322", "2.30360206", "0.03470622", "0.43410276", "0.00336681", "0.02811219"], ["SP1", "214", "2.3619211", "0.02271018", "0.42338417", "0.00842438", "0.03168479"], ["E2F4", "203", "2.50714694", "0.02510997", "0.39885975", "0.00248744", "0.03155395"], ["PRDM14", "194", "2.47970269", "0.01761185", "0.40327415", "0.00459377", "0.03274385"], ["ARNT", "190", "2.47970269", "0.00990145", "0.40327415", "0.00668338", "0.04482786"], ["MIA3", "182", "2.51172098", "0.00828163", "0.39813339", "0.00558557", "0.04629319"], ["JUN", "179", "2.45740423", "0.0132459", "0.40693346", "0.01726194", "0.03584432"], ["CREB1", "178", "2.43853631", "0.0134572", "0.41008206", "0.01314035", "0.03899076"], ["FOS", "178", "2.04116638", "0.03258878", "0.48991597", "0.05986161", "0.0352397"], ["STAT1", "176", "2.51229274", "0.01672367", "0.39804279", "0.00525974", "0.03983636"], ["CEBPA", "168", "2.58604917", "0.01187163", "0.38669025", "0.00377816", "0.04812159"], ["AHR", "168", "2.53459119", "0.00776619", "0.39454094", "0.00620188", "0.04722287"], ["E2F1", "165", "2.50085763", "0.01123109", "0.39986283", "0.00657797", "0.04104892"], ["PAX5", "164", "2.51172098", "0.00771197", "0.39813339", "0.00890319", "0.0434212"], ["Pax-5", "161", "2.56089194", "0.0066902", "0.39048895", "0.00535714", "0.04834386"]], "row_count": 21, "column_count": 7, "numeric_cells": 122, "header_rows": 1, "locator": "section[22]/table-wrap[1]#tab5"}}, {"id": "asset:table:pmid:33777260:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:656908f5b07b7f754b76691f1100a6b249c0238399910197741f9b290a8b473b", "bytes": 2124, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[24]/table-wrap[1]#tab6", "version": null, "note": "The topological characteristics of the top 25 gene nodes in the PPI network of the blue module within the GSE77549 dataset.", "structure": {"pmcid": "PMC7968449", "section_index": 24, "section_title": "3.10. Construction of PPI Network for Selected Significant Gene Modules", "row_count": 26, "column_count": 7}, "table": {"label": "Table 6", "caption": "The topological characteristics of the top 25 gene nodes in the PPI network of the blue module within the GSE77549 dataset.", "rows": [["Name", "Degree", "Betweenness centrality", "Closeness centrality", "Clustering coefficient", "Topological coefficient", "Regulate"], ["NTRK1", "1981", "0.797678", "0.550769", "8.10E − 05", "0.00147", "Other_gene"], ["TUBA4A", "182", "0.057422", "0.34576", "2.46E − 04", "0.012097", "Other_gene"], ["PTPRK", "110", "0.048111", "0.334924", "5.10E − 04", "0.017763", "Other_gene"], ["ACTN2", "101", "0.04028", "0.340466", "8.08E − 04", "0.012519", "Other_gene"], ["MSH6", "98", "0.029296", "0.414544", "0.009211", "0.011399", "Other_gene"], ["COPS7A", "87", "0.027065", "0.331267", "0", "0.024951", "Other_gene"], ["BIRC3", "79", "0.030191", "0.33259", "0", "0.022419", "mRNA up"], ["SH3GL1", "79", "0.025169", "0.330228", "0", "0.023044", "Other_gene"], ["EPS8", "78", "0.030772", "0.33259", "0", "0.022436", "Other_gene"], ["PTPRJ", "76", "0.02319", "0.408163", "0.008288", "0.014223", "Other_gene"], ["UBC", "75", "0.16533", "0.47619", "0.005405", "0.017173", "Other_gene"], ["RPRD1B", "71", "0.019601", "0.329863", "0", "0.026232", "Other_gene"], ["TJP2", "68", "0.019477", "0.328079", "0", "0.027715", "Other_gene"], ["BID", "65", "0.018865", "0.33035", "0", "0.030769", "Other_gene"], ["TBL1XR1", "62", "0.023597", "0.409283", "0.010929", "0.017196", "Other_gene"], ["GRAP2", "59", "0.019032", "0.330838", "6.05E − 04", "0.027809", "Other_gene"], ["MAP2", "57", "0.016676", "0.406541", "0.014935", "0.018914", "Other_gene"], ["TIMMDC1", "53", "0.022335", "0.327539", "7.54E − 04", "0.025227", "Other_gene"], ["BACH1", "48", "0.013952", "0.327929", "0", "0.036859", "Other_gene"], ["DTL", "48", "0.009929", "0.332961", "0.006475", "0.032282", "Other_gene"], ["CORO1A", "46", "0.016515", "0.327929", "0", "0.029927", "mRNA up"], ["MX1", "43", "0.013576", "0.329347", "0", "0.037265", "Other_gene"], ["TWIST1", "41", "0.011401", "0.290915", "0", "0.053215", "Other_gene"], ["ITPR3", "39", "0.011085", "0.327419", "0", "0.039683", "mRNA up"], ["PTPRB", "36", "0.007233", "0.37609", "0.018487", "0.029667", "mRNA up"]], "row_count": 26, "column_count": 7, "numeric_cells": 125, "header_rows": 1, "locator": "section[24]/table-wrap[1]#tab6"}}, {"id": "asset:table:pmid:33777260:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8d3f7bb9b5c16e8b4e57df092662be8bbd20ef772c93a8800f4ee4ba1352e21d", "bytes": 2507, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[24]/table-wrap[2]#tab7", "version": null, "note": "The topological characteristics of the top 25 gene nodes in the PPI network of the green module within the GSE92681 dataset.", "structure": {"pmcid": "PMC7968449", "section_index": 24, "section_title": "3.10. Construction of PPI Network for Selected Significant Gene Modules", "row_count": 26, "column_count": 8}, "table": {"label": "Table 7", "caption": "The topological characteristics of the top 25 gene nodes in the PPI network of the green module within the GSE92681 dataset.", "rows": [["Name", "Degree", "Average shortest path length", "Betweenness centrality", "Closeness centrality", "Clustering coefficient", "Topological coefficient", "Regulate"], ["PSMA2", "145", "2.84572072", "0.30956005", "0.35140483", "0", "0.01436782", "Other gene"], ["IK", "83", "3.14752252", "0.16898579", "0.3177102", "0", "0.02628697", "mRNA down"], ["BCAR1", "82", "3.0731982", "0.18704239", "0.32539392", "0", "0.02264808", "Other gene"], ["TCF12", "77", "2.88400901", "0.27221312", "0.34673955", "0", "0.01974026", "Other gene"], ["SAV1", "74", "3.6768018", "0.14809265", "0.2719755", "0", "0.02402402", "Other gene"], ["NDN", "61", "3.29391892", "0.12878792", "0.30358974", "0", "0.02157032", "Other gene"], ["ERGIC3", "55", "3.31644144", "0.11672478", "0.30152801", "0", "0.02121212", "Other gene"], ["ASB3", "38", "3.51914414", "0.07839935", "0.28416", "0", "0.03827751", "Other gene"], ["MMP7", "37", "4.70157658", "0.08120061", "0.21269461", "0", "0.04054054", "mRNA up"], ["WT1", "35", "3.74887387", "0.08035061", "0.26674677", "0", "0.04642857", "Other gene"], ["DGCR14", "32", "3.37274775", "0.05414526", "0.29649416", "0", "0.05208333", "Other gene"], ["RIOK3", "28", "3.19256757", "0.06657298", "0.31322751", "0", "0.05844156", "Other gene"], ["DUS3L", "26", "3.3704955", "0.04976931", "0.29669228", "0", "0.05668016", "Other gene"], ["FAM74A4", "26", "4.65202703", "0.02931155", "0.21496006", "0", "0.19230769", "Other gene"], ["FAM74A6", "25", "4.65427928", "0.0262998", "0.21485604", "0", "0.19333333", "Other gene"], ["LRRC1", "23", "3.20157658", "0.05583233", "0.31234611", "0", "0.06126482", "Other gene"], ["PCYT2", "21", "3.31869369", "0.04192798", "0.30132338", "0", "0.05555556", "Other gene"], ["UBC", "18", "2.51351351", "0.42421401", "0.39784946", "0", "0.06050955", "Other gene"], ["BCORL1", "16", "3.4786036", "0.02550435", "0.28747167", "0", "0.08455882", "Other gene"], ["NCOA7", "13", "4.68581081", "0.02298401", "0.21341024", "0", "0.07692308", "Other gene"], ["STX10", "13", "3.48536036", "0.02685944", "0.28691438", "0", "0.07692308", "Other gene"], ["SGK3", "12", "3.35472973", "0.03075664", "0.29808661", "0", "0.11507937", "Other gene"], ["PRKX", "11", "4.67004505", "0.01823525", "0.2141307", "0", "0.18181818", "Other gene"], ["RNF135", "10", "4.73536036", "0.01245585", "0.21117717", "0", "0.2", "Other gene"], ["DFNA5", "9", "3.49436937", "0.01078561", "0.28617467", "0", "0.16339869", "Other gene"]], "row_count": 26, "column_count": 8, "numeric_cells": 156, "header_rows": 1, "locator": "section[24]/table-wrap[2]#tab7"}}, {"id": "asset:table:pmid:33777260:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6cbf384f0c00e50ca5a1a669716338108bb092b6801dfff62c384919bd441507", "bytes": 1818, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[25]/table-wrap[1]#tab8", "version": null, "note": "The topological characteristics of the top 20 nodes in the ceRNA network.", "structure": {"pmcid": "PMC7968449", "section_index": 25, "section_title": "3.11. The ceRNA Network", "row_count": 21, "column_count": 6}, "table": {"label": "Table 8", "caption": "The topological characteristics of the top 20 nodes in the ceRNA network.", "rows": [["Name", "Degree", "Average shortest path length", "Betweenness centrality", "Closeness centrality", "Topological coefficient"], ["XIST", "95", "1.85534591", "0.78103311", "0.53898305", "0.03168803"], ["hsa-miR-340-5p", "21", "2.58490566", "0.07287356", "0.38686131", "0.06802721"], ["MIR155HG", "17", "3.73899371", "0.06134578", "0.26745164", "0.09207161"], ["hsa-miR-4731-5p", "15", "2.7327044", "0.05609297", "0.36593786", "0.07777778"], ["hsa-miR-5590-3p", "15", "2.71069182", "0.03529256", "0.36890951", "0.09122807"], ["hsa-miR-27a-3p", "14", "2.75157233", "0.02751162", "0.36342857", "0.0924812"], ["hsa-miR-27b-3p", "14", "2.75157233", "0.02751162", "0.36342857", "0.0924812"], ["hsa-miR-329-3p", "14", "2.71698113", "0.03095743", "0.36805556", "0.09323308"], ["hsa-miR-362-3p", "13", "2.72327044", "0.02835696", "0.36720554", "0.09797571"], ["LCP1", "13", "3.71069182", "0.0012642", "0.26949153", "0.36153846"], ["hsa-miR-494-3p", "13", "2.72955975", "0.03199119", "0.36635945", "0.10576923"], ["hsa-miR-424-5p", "12", "2.71698113", "0.02811", "0.36805556", "0.12152778"], ["hsa-miR-2682-5p", "12", "2.72327044", "0.02462859", "0.36720554", "0.12457045"], ["hsa-miR-515-5p", "12", "2.78301887", "0.02610732", "0.35932203", "0.10283688"], ["hsa-miR-766-5p", "12", "2.70440252", "0.04407579", "0.36976744", "0.11139456"], ["hsa-miR-449c-5p", "12", "2.72327044", "0.01602592", "0.36720554", "0.13058419"], ["EZH2", "11", "3.40880503", "0.01905647", "0.29335793", "0.27548209"], ["NR4A1", "11", "3.46226415", "0.01590906", "0.28882834", "0.30976431"], ["hsa-miR-34a-5p", "11", "2.77044025", "0.01309547", "0.36095346", "0.13492823"], ["hsa-miR-449a", "11", "2.77044025", "0.01309547", "0.36095346", "0.13492823"]], "row_count": 21, "column_count": 6, "numeric_cells": 116, "header_rows": 1, "locator": "section[25]/table-wrap[1]#tab8"}}], "gaps": ["asset:data:geo:GSE77459 not downloaded", "asset:data:geo:GSE77459 licence not read", "asset:data:geo:GSE92681 not downloaded", "asset:data:geo:GSE92681 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Based on the GSE92681 dataset, the coexpression status of DElncRNAs and DEGs was calculated by using a statistical method—Pearson correlation."}}, {"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": 0.8, "band": "high", "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": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "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": ["GSE92681", "GSE77459"], "resolved_accessions": ["GSE92681", "GSE77459"], "statements": ["The data used to support the findings of this study are available from the corresponding author upon reasonable request."], "basis": "The paper names GSE92681, GSE77459 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": ["pearson_r"], "assets": ["source:pmid:33777260", "data:geo:GSE77459", "asset:table:pmid:33777260:1", "asset:table:pmid:33777260:2", "asset:table:pmid:33777260:3", "asset:table:pmid:33777260:4", "asset:table:pmid:33777260:5", "asset:table:pmid:33777260:6", "asset:table:pmid:33777260:7", "asset:table:pmid:33777260:8"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE77459"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:31Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 57309, "completion_tokens": 1468, "cached_tokens": 19208}}, "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:33777260", "type": "paper", "label": "pmid:33777260"}, {"id": "source:pmid:33777260", "type": "manuscript", "label": "PMID 33777260 full text"}, {"id": "data:geo:GSE77459", "type": "dataset", "label": "GEO GSE77459"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33777260", "type": "paper", "label": "pmid:33777260"}, {"id": "source:pmid:33777260", "type": "manuscript", "label": "PMID 33777260 full text"}, {"id": "data:geo:GSE77459", "type": "dataset", "label": "GEO GSE77459"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33777260", "type": "extraction", "used": ["source:pmid:33777260"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE77459", "type": "accession_resolution", "used": ["data:geo:GSE77459"], "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:33777260", "parent_hash": "sha256:c994fceab4542fb2d8980aac3c3a737479fb56ff1e967b908b95ae15ae9e8e43", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE77459 licence not read", "asset:data:geo:GSE77459 not downloaded", "asset:data:geo:GSE92681 licence not read", "asset:data:geo:GSE92681 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Based on the GSE92681 dataset, the coexpression status of DElncRNAs and DEGs was calculated by using a statistical method—Pearson correlation."], "order_basis": "analysis_only", "id": "assay:1"}]}