Use of bioinformatic analyses in identifying characteristic genes and mechanisms active in the progression of idiopathic thrombocytopenic purpura in individuals with different phenotypes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33222560", "kind": "science-record", "revision": 8, "content_hash": "sha256:06d84fcedf514aa3592b9af6890acb7540f24fc83c20607927fbfcedf3926427", "created_at": "2026-11-01T15:41:16Z", "updated_at": "2026-11-01T22:02:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Use of bioinformatic analyses in identifying characteristic genes and mechanisms active in the progression of idiopathic thrombocytopenic purpura in individuals with different phenotypes.", "doi": "10.1177/0300060520971437", "pmid": "33222560", "authors": ["Mengyi Zhang", "Binhan Guo"], "journal": "The Journal of international medical research", "year": 2020, "abstract": "OBJECTIVE: To explore the mechanism underlying the progression of newly diagnosed idiopathic thrombocytopenic purpura (ITP) to its chronic or remission state using bioinformatic methods.\nMETHODS: GSE56232 and GSE46922 gene expression profile datasets were downloaded from Gene Expression Omnibus (GEO). Differentially expressed genes were identified and characteristic genes were screened by weighted gene co-expression network analysis. These genes were used for function enrichment analysis and construction of a protein-protein interaction network. Finally, characteristic genes were verified to determine potential molecular mechanisms underlying ITP progression.\nRESULTS: We found that characteristic genes in the chronic ITP group were mainly involved in intracellular processes and ion binding, while characteristic genes in the remission ITP group were involved in intracellular processes and nuclear physiological activities. We identified a sub-network of characteristic genes, LMNA, JUN, PRKACG, SMC3, which may indicate the mechanism by which newly diagnosed ITP progresses to chronic. Although no meaningful signaling pathways were found, the expression of NR3C1, TPR, SMC4, PANBP2, CHD1, and U2SURP may affect ITP progression from newly diagnosed to remission.\nCONCLUSION: Our findings improve the understanding of the pathogenesis and progression of ITP, and may provide new directions for the development of treatment strategies.", "claims": [{"id": "claim-method", "statement": "The Wilcoxon test was used to compare differences among three groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33222560", "locator": "sections[7] \"Verification of hub genes and construction of sub-network\" paragraph 2", "quote": "The Wilcoxon test was used to compare differences among three groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene expression profile datasets GSE56232 and GSE46922 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo). GSE56232 included mRNA expression profiles from six newly diagnosed ITP patients and six remission ITP patients,17 while GSE46922 contained data from seven newly diagnosed ITP patients and six chronic ITP patients.18 All samples were from human peripheral blood T cells.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33222560", "locator": "sections[3] \"Data source\" paragraph 2", "quote": "Gene expression profile datasets GSE56232 and GSE46922 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo). GSE56232 included mRNA expression profiles from six newly diagnosed ITP patients and six remission ITP patients,17 while GSE46922 contained data from seven newly diagnosed ITP patients and six chronic ITP patients.18 All samples were from human peripheral blood T cells."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:33222560"], "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:GSE46922"], "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:group_comparison_wilcoxon", "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:GSE46922"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33222560", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1177/0300060520971437", "sha256": "sha256:3bdae180133eb3ee8d9a09a77097ac86a31fc8916f157ea2036e40722d620b99", "bytes": 37327, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1177/0300060520971437", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7689594", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE46922", "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=GSE46922", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE46922", "version": null, "note": "Gene expression profile datasets GSE56232 and GSE46922 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo). GSE56232 included mRNA expression profiles from six newly diagnosed ITP patients and six remission ITP patients,17 while GSE46922 contained data from seven newly diagnosed ITP patients and six chronic ITP patients.18 All samples were from human peripheral blood T cells.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Gene expression profile datasets GSE56232 and GSE46922 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo). GSE56232 included mRNA expression profiles from six newly diagnosed ITP patients and six remission ITP patients,17 while GSE46922 contained data from seven newly diagnosed ITP patients and six chronic ITP patients.18 All samples were from human peripheral blood T cells.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1141222", "GSM1141223", "GSM1141224", "GSM1141225", "GSM1141226", "GSM1141227", "GSM1141228", "GSM1141229", "GSM1141230", "GSM1141231", "GSM1141232", "GSM1141233", "GSM1141234"], "sample_count": 13, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Differences in gene expression and cytokines levels between newly diagnosed and chronic pediatric immune thrombocytopenia (ITP)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE56232", "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=GSE56232", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE56232", "version": null, "note": "Gene expression profile datasets GSE56232 and GSE46922 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo). GSE56232 included mRNA expression profiles from six newly diagnosed ITP patients and six remission ITP patients,17 while GSE46922 contained data from seven newly diagnosed ITP patients and six chronic ITP patients.18 All samples were from human peripheral blood T cells.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Gene expression profile datasets GSE56232 and GSE46922 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo). GSE56232 included mRNA expression profiles from six newly diagnosed ITP patients and six remission ITP patients,17 while GSE46922 contained data from seven newly diagnosed ITP patients and six chronic ITP patients.18 All samples were from human peripheral blood T cells.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1357434", "GSM1357435", "GSM1357436", "GSM1357437", "GSM1357438", "GSM1357439", "GSM1357440", "GSM1357441", "GSM1357442", "GSM1357443", "GSM1357444", "GSM1357445"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Molecular basis for remission and tolerance induction in pediatric ITP", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE46922 not downloaded", "asset:data:geo:GSE46922 licence not read", "asset:data:geo:GSE56232 not downloaded", "asset:data:geo:GSE56232 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Wilcoxon test was used to compare differences among three groups."}}, {"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"}}], "targets": [], "gaps": ["method.group_comparison_wilcoxon"]}, "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": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE56232", "GSE46922"], "resolved_accessions": ["GSE56232", "GSE46922"], "statements": ["Gene expression profile datasets GSE56232 and GSE46922 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo). GSE56232 included mRNA expression profiles from six newly diagnosed ITP patients and six remission ITP patients,17 while GSE46922 contained data from seven newly diagnosed ITP patients and six chronic ITP patients.18 All samples were from human peripheral blood T cells."], "basis": "The paper names GSE56232, GSE46922 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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