RTP4, a Biomarker Associated with Diagnosing Pulmonary Tuberculosis and Pan-Cancer Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37152371", "kind": "science-record", "revision": 3, "content_hash": "sha256:b1ab28cac4a1b38163438087d8cf9aac137b1265dfd7d71b23fc3511e161cdf9", "created_at": "2026-11-01T19:01:49Z", "updated_at": "2026-11-01T22:09:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "RTP4, a Biomarker Associated with Diagnosing Pulmonary Tuberculosis and Pan-Cancer Analysis.", "doi": "10.1155/2023/2318473", "pmid": "37152371", "authors": ["Hao Li", "Qin Zhou", "ZhiXiang Ding", "QingHai Wang"], "journal": "Mediators of inflammation", "year": 2023, "abstract": "Background: Pulmonary tuberculosis (PTB) is a global epidemic of infectious disease; the purpose of our study was to explore new potential biomarkers for the diagnosis of pulmonary tuberculosis and to use the biomarkers for further pan-cancer analysis.\nMethods: Four microarray gene expression sets were downloaded from the GEO public databases and conducted for further analysis. Healthy control (HC) samples and samples of pulmonary tuberculosis (PTB) were calculated with enrichment scores in folate biosynthesis pathways. The scores acted as a new phenotype combined with clinical information (control or PTB) for subsequent analysis. Weight gene coexpression network analysis (WGCNA) was used to seek the modules mostly related to PTB and folate biosynthesis in training sets. Twenty-nine coexistence genes were screened by intersecting the genes in the green-yellow module of GSE28623 and the brown module of GSE83456. We used the protein-protein interaction network analysis to narrow the gene range to search for hub genes. Then, we downloaded the unified and standardized pan-cancer data set from the UCSC database for correlations between biomarkers and prognosis and tumor stage differences.\nResults: Eventually, RTP4 was selected as a biomarker. To verify the reliability of this biomarker, an area under the ROC (AUC) was calculated in gene sets (GSE28623, GSE83456, and GSE34608). Lastly, to explore the difference in RTP4 expression before and after antituberculosis treatment, the GSE31348 gene set was enrolled to compare the expressions in weeks 0 and 26. The results showed significant differences between these two time points (p < 0.001). RTP4 was significantly upregulated in the pulmonary tuberculosis group compared to the healthy control group in three gene sets and downregulated after antituberculosis therapy in one gene set. These results suggest that RTP4 can be used as a potential biomarker in diagnosing tuberculosis. The results of pan-cancer analysis showed that high expression of RTP4 in 4 tumor types was positively correlated with poor prognosis and high expression of RTP4 in 6 tumor types was negatively correlated with poor prognosis. We found significant differences in the expression of the RTP4 gene at different stages in 5 types of tumors.\nConclusion: RTP4 might be a new potential biomarker for diagnosing pulmonary tuberculosis.", "claims": [{"id": "claim-method", "statement": "The receiver operating characteristic (ROC) curve was used to evaluate the reliability of candidate biomarkers.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37152371", "locator": "sections[8] \"2.6. Statistical Analysis\" paragraph 2", "quote": "The receiver operating characteristic (ROC) curve was used to evaluate the reliability of candidate biomarkers."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data can be obtained from GEO (https://www.ncbi.nlm.nih.gov/geo/) and TCGA (https://www.cancer.gov/ccg/research/genome-sequencing/tcga).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37152371", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "Data can be obtained from GEO (https://www.ncbi.nlm.nih.gov/geo/) and TCGA (https://www.cancer.gov/ccg/research/genome-sequencing/tcga)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The results showed significant differences between these two time points (p < 0.001).", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "Lastly, to explore the difference in RTP4 expression before and after antituberculosis treatment, the GSE31348 gene set was enrolled to compare the expressions in weeks 0 and 26. The results showed significant differences between these two time points (p < 0.001)."}, "evidence": [{"asset": "source:pmid:37152371", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Lastly, to explore the difference in RTP4 expression before and after antituberculosis treatment, the GSE31348 gene set was enrolled to compare the expressions in weeks 0 and 26. The results showed significant differences between these two time points (p < 0.001)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The results showed significant differences between these two time points (p < 0.001).", "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:37152371"], "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:GSE28623"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE28623"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37152371", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2023/2318473", "sha256": "sha256:ce2b10115377ab4f31d2b7d4a91759d6af93d587b222acceca0b5b907eaf3ad8", "bytes": 24702, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2023/2318473", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10156460", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE28623", "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=GSE28623", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28623", "version": null, "note": "Data can be obtained from GEO (https://www.ncbi.nlm.nih.gov/geo/) and TCGA (https://www.cancer.gov/ccg/research/genome-sequencing/tcga).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data can be obtained from GEO (https://www.ncbi.nlm.nih.gov/geo/) and TCGA (https://www.cancer.gov/ccg/research/genome-sequencing/tcga).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM709413", "GSM709414", "GSM709415", "GSM709416", "GSM709417", "GSM709418", "GSM709419", "GSM709420", "GSM709421", "GSM709422", "GSM709423", "GSM709424", "GSM709425", "GSM709426", "GSM709427", "GSM709428", "GSM709429", "GSM709430", "GSM709431", "GSM709432", "GSM709433", "GSM709434", "GSM709435", "GSM709436", "GSM709437", "GSM709438", "GSM709439", "GSM709440", "GSM709441", "GSM709442", "GSM709443", "GSM709444", "GSM709445", "GSM709446", "GSM709447", "GSM709448", "GSM709449", "GSM709450", "GSM709451", "GSM709452", "GSM709453", "GSM709454", "GSM709455", "GSM709456", "GSM709457", "GSM709458", "GSM709459", "GSM709460", "GSM709461", "GSM709462", "GSM709463", "GSM709464", "GSM709465", "GSM709466", "GSM709467", "GSM709468", "GSM709469", "GSM709470", "GSM709471", "GSM709472", "GSM709473", "GSM709474", "GSM709475", "GSM709476", "GSM709477", "GSM709478", "GSM709479", "GSM709480", "GSM709481", "GSM709482", "GSM709483", "GSM709484", "GSM709485", "GSM709486", "GSM709487", "GSM709488", "GSM709489", "GSM709490", "GSM709491", "GSM709492", "GSM709493", "GSM709494", "GSM709495", "GSM709496", "GSM709497", "GSM709498", "GSM709499", "GSM709500", "GSM709501", "GSM709502", "GSM709503", "GSM709504", "GSM709505", "GSM709506", "GSM709507", "GSM709508", "GSM709509", "GSM709510", "GSM709511", "GSM709512", "GSM709513", "GSM709514", "GSM709515", "GSM709516", "GSM709517", "GSM709518", "GSM709519", "GSM709520"], "sample_count": 108, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "Pathway and functional association analysis of whole blood gene expression profiles reveal functional networks underlying TB pathogenesis. 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