Screening and identification of key candidate genes and pathways in myelodysplastic syndrome by bioinformatic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31803541", "kind": "science-record", "revision": 5, "content_hash": "sha256:6be629dfa72b2e89b1f43c2c0814c2a4a89acca57e53a57268720ce08f1f5640", "created_at": "2026-11-01T15:40:52Z", "updated_at": "2026-11-01T22:01:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening and identification of key candidate genes and pathways in myelodysplastic syndrome by bioinformatic analysis.", "doi": "10.7717/peerj.8162", "pmid": "31803541", "authors": ["Ying Le"], "journal": "PeerJ", "year": 2019, "abstract": "Myelodysplastic syndrome (MDS) is a heterogeneous hematologic malignancy derived from hematopoietic stem cells and the molecular mechanism of MDS remains unclear. This study aimed to elucidate potential markers of diagnosis and prognosis of MDS. The gene expression profiles GSE19429 and GSE58831 were obtained and downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in MDS were screened using GEO2R and overlapped DEGs were obtained with Venn Diagrams. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway functional enrichment analyses, protein-protein interaction network establishment and survival analyses were performed. Functional enrichment analysis indicated that these DEGs were significantly enriched in the interferon signaling pathway, immune response, hematopoietic cell lineage and the FOXO signaling pathway. Four hub genes and four significant modules including 25 module genes were obtained via Cytoscape MCODE. Survival analysis showed that the overall survival of MDS patients having BLNK, IRF4, IFITM1, IFIT1, ISG20, IFI44L alterations were worse than that without alterations. In conclusion, the identification of these genes and pathways helps understand the underlying molecular mechanisms of MDS and provides candidate targets for the diagnosis and prognosis of MDS.", "claims": [{"id": "claim-method", "statement": "The DEGs between MDS patients and healthy controls samples were screened using GEO2R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31803541", "locator": "sections[4] \"Identification of DEGs and data processing\" paragraph 2", "quote": "The DEGs between MDS patients and healthy controls samples were screened using GEO2R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental File. The gene expression profiles are available at NCBI–GEO: GSE19429, GSE58831.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31803541", "locator": "sections[29] \"Data Availability Statement\" paragraphs 1-3", "quote": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental File. The gene expression profiles are available at NCBI–GEO: GSE19429, GSE58831."}], "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:31803541"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31803541", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.8162", "sha256": "sha256:bace416c459b2fb08b7e0a5070b666ca18c03e48cf0362abf8c0995039b76c96", "bytes": 33948, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.8162", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6886488", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:31803541:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d1bdf273df98670f2ebc00c0616bb1c15924f62221f1a03b45720e31755eb31f", "bytes": 1134, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#table-2", "version": null, "note": "Gene Ontology and KEGG pathway enrichment analysis of DEGs in the significant module.", "structure": {"pmcid": "PMC6886488", "section_index": 6, "section_title": "PPI network establishment and module analysis", "row_count": 17, "column_count": 4}, "table": {"label": "Table 2", "caption": "Gene Ontology and KEGG pathway enrichment analysis of DEGs in the significant module.", "rows": [["Term", "Description", "Count", "P-value"], ["GO:0006955", "Immune response", "10", "3.15E−06"], ["GO:0030098", "Immune cell differentiation", "6", "4.93E−05"], ["GO:0098552", "Side of membrane", "5", "5.71E−04"], ["GO:0000982", "Transcription factor", "5", "4.34E−04"], ["GO:0003677", "DNA binding", "9", "5.97E−04"], ["GO:0016337", "Cell adhesion", "6", "1.24E−03"], ["GO:0030097", "Hemopoiesis", "6", "2.09E−03"], ["GO:0001775", "Cell activation", "6", "2.34E−03"], ["GO:0006952", "Defense response", "7", "2.99E−03"], ["GO:0007166", "Cell surface receptor", "8", "1.22E−02"], ["GO:0006259", "DNA metabolic", "5", "1.83E−02"], ["GO:0001822", "Kidney development", "3", "3.90E−02"], ["Hsa05340", "Primary immunodeficiency", "5", "3.02E−07"], ["Hsa04640", "Hematopoietic cell lineage", "5", "1.36E−05"], ["Hsa04662", "B cell receptor signaling pathway", "3", "6.19E−03"], ["Hsa04068", "FOXO signaling pathway", "3", "2.09E−02"]], "row_count": 17, "column_count": 4, "numeric_cells": 48, "header_rows": 1, "locator": "section[12]/table-wrap[1]#table-2"}}, {"id": "asset:table:pmid:31803541:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6893cbd29b602779968090c8a1c26bf34ce0c4c073395443c6442031ed414621", "bytes": 3928, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#table-3", "version": null, "note": "Functional roles of 25 module genes.", "structure": {"pmcid": "PMC6886488", "section_index": 8, "section_title": "Survival analysis", "row_count": 26, "column_count": 4}, "table": {"label": "Table 3", "caption": "Functional roles of 25 module genes.", "rows": [["No.", "Gene symbol", "Full name", "Function"], ["1", "RAG2", "Recombination activating 2", "RAG2 is involved in B and T cell development and the expression of RAG2 is high in most AMLpatients"], ["2", "EBF1", "Transcription factor, early B cell factor 1", "EBF1 promotes of bone marrow CD34+ cell proliferation and migration,but suppresses the apoptosis of cells"], ["3", "BLNK", "B cell linker", "BLNK regulates the development, maturation and function of B cells"], ["4", "CD79B", "CD79b molecule", "CD79B is necessary for expression and function of the B-cell antigen receptor"], ["5", "VPREB1", "V-set pre-B cell surrogate light chain 1", "VPREB1 is involved in early B cell differentiation and VPREB1 deletion is often detected in relapsed leukemia"], ["6", "BLK", "BLK proto-oncogene, Src family tyrosine kinase", "BLK is involved in cell proliferation and differentiation and has a role in B-cell receptor signaling and B-cell development"], ["7", "IRF4", "Interferon regulatory factor 4", "IRF4 has oncogenic implications in a variety of hematological tumors including multiple myeloma, leukemia and lymphoma"], ["8", "IGLL1", "Immunoglobulin lambda like polypeptide 1", "IGLL1 is involved in cell proliferation and IGLL1 mutation can lead to B cell deficiency and agammaglobulinemia"], ["9", "DNTT", "DNA nucleotidy-lexotransferase", "DNTT acts as a catalyst to add nucleotides during the maturation of B cells and T cells"], ["10", "CD19", "CD19 molecule", "CD19 is a surface-specific marker of B lymphocytes and CD19 decreases the threshold of antigen receptor-dependent"], ["11", "PAX5", "Paired box 5", "PAX5 is involved in cell differentiation and neuro developmentand spermatogenesis"], ["12", "RAG1", "Recombination activating 1", "High expression of RAG1 in B-ALL patients promotes leukemic clonal evolution and high expression of RAG1 is associated with high proliferative markers"], ["13", "IFITM1", "Interferon induced transmembrane protein 1", "IFITM1 promotes proliferation, migration, and invasion of lung cancer"], ["14", "IFIT1", "Interferon induced protein with tetratricopeptide repeats 1", "IFIT1 and IFIT3 promote oral squamous cell carcinoma metastasis and contribute to theanti-tumor effect of gefitinib"], ["15", "IFIT3", "Interferon induced protein with tetratricopeptide repeats 3", "IFIT1 and IFIT3 promote oral squamous cell carcinoma metastasis and contribute to the anti-tumor effect of gefitinib"], ["16", "ISG20", "Interferon stimulated exonuclease gene 20", "ISG20 promotes local tumor immunity and has poor survival in human glioma"], ["17", "IFI44L", "Interferon induced protein 44 like", "High expression of IFI44L is associated with poor prognosis of osteosarcoma"], ["18", "IFI27", "Interferon alpha inducible protein 27", "IFI27 promotes cell proliferation and invasion in oral squamous cell carcinoma"], ["19", "CD24", "CD24 molecule", "CD24 modulates growth and differentiation signals to mature granulocytes and B cells"], ["20", "CXCR4", "C-X-C motif chemokine receptor 4", "High expression of CXCR4 has shorter OS time and shorter relapse-free survival time"], ["21", "IL7R", "Interleukin 7 receptor", "IL7R is overexpressed in adult acute lymphoblastic leukemia and is associatedwith JAK/STAT pathway mutations"], ["22", "MME", "Membrane metalloendo-peptidase", "MME inhibits tumor metastasis of esophageal squamous cell carcinoma and interrupt tumor cell adhesion"], ["23", "SKIL", "SKI like proto-oncogene", "SKIL has regulatory role in cell division or differentiation"], ["24", "SMAD7", "SMAD family member 7", "High expression of SMAD7 at diagnosis predicts poor prognosis in acute myeloid leukemia"], ["25", "SMAD1", "SMAD family member 1", "SMAD1 is involved in a range of biological activities including cell growth, apoptosis, morphogenesis, development and immune responses"]], "row_count": 26, "column_count": 4, "numeric_cells": 58, "header_rows": 1, "locator": "section[14]/table-wrap[1]#table-3"}}, {"id": "asset:table:pmid:31803541:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c72bb42491cbf2f297b492fe041ebb870df4a94b2243e67e736ee290aee8dc7a", "bytes": 2469, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#table-1", "version": null, "note": "Gene Ontology term enrichment analysis of DEGs in MDS.", "structure": {"pmcid": "PMC6886488", "section_index": 11, "section_title": "GO and KEGG pathway enrichment analyses of DEGs", "row_count": 40, "column_count": 4}, "table": {"label": "Table 1", "caption": "Gene Ontology term enrichment analysis of DEGs in MDS.", "rows": [["Term", "Description", "Count", "P-value"], ["Upregulated", "", "", ""], ["GO:0060337", "Type I interferon signaling pathway", "4", "2.28E−04"], ["GO:0098542", "Defense response", "5", "4.77E−04"], ["GO:0009605", "Response to external stimulus", "10", "4.04E−03"], ["GO:0002252", "Immune effector", "6", "6.19E−03"], ["GO:0007166", "Cell surface receptor signaling pathway", "11", "6.70E−03"], ["GO:0019221", "Cytokine-mediated signaling pathway", "5", "1.16E−02"], ["GO:0098911", "Regulation of cell action potential", "2", "2.25E−02"], ["GO:0050954", "Sensory perception", "3", "2.69E−02"], ["GO:0006955", "Immune response", "7", "3.50E−02"], ["GO:0045746", "Notch signaling pathway", "2", "4.76E−02"], ["Downregulated", "", "", ""], ["GO:0006955", "Immune response", "27", "9.26E−09"], ["GO:0007166", "Cell surface receptor signaling pathway", "33", "3.21E−07"], ["GO:0000982", "Transcription factor activity", "11", "4.51E−06"], ["GO:0001775", "Cell activation", "16", "2.84E−05"], ["GO:0040011", "Locomotion", "20", "1.06E−04"], ["GO:0005102", "Receptor binding", "19", "1.14E−04"], ["GO:0045595", "Cell differentiation", "20", "1.20E−04"], ["GO:0002684", "Regulation of immune system", "15", "1.99E−04"], ["GO:0010605", "Regulation of macromolecule metabolic", "24", "5.27E−04"], ["GO:0022407", "Cell-cell adhesion", "9", "5.71E−04"], ["GO:0009891", "Biosynthetic process", "20", "6.39E−04"], ["GO:0004871", "Signal transducer activity", "19", "1.12E−03"], ["GO:0008283", "Cell proliferation", "20", "1.26E−03"], ["GO:0060548", "Cell death", "13", "1.27E−03"], ["GO:0098552", "Side of membrane", "9", "1.54E−03"], ["GO:0043565", "Specific DNA binding", "14", "1.47E−03"], ["GO:0006915", "Apoptotic process", "19", "1.57E−03"], ["GO:0009892", "Regulation of metabolic process", "24", "1.63E−03"], ["GO:0060429", "Epithelium development", "14", "1.72E−03"], ["GO:0048514", "Blood vessel morphogenesis", "9", "2.64E−03"], ["GO:0003707", "Steroid hormone receptor activity", "4", "2.71E−03"], ["GO:0016477", "Cell migration", "14", "4.50E−03"], ["GO:0060537", "Muscle tissue development", "7", "8.93E−03"], ["GO:0005615", "Extracellular space", "14", "2.40E−03"], ["GO:0051427", "Hormone receptor binding", "4", "3.39E−02"], ["GO:0001047", "Core promoter binding", "4", "4.05E−02"], ["GO:0044877", "Macromolecular complex", "12", "4.16E−02"]], "row_count": 40, "column_count": 4, "numeric_cells": 111, "header_rows": 1, "locator": "section[11]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:31803541:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d1bdf273df98670f2ebc00c0616bb1c15924f62221f1a03b45720e31755eb31f", "bytes": 1134, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#table-2", "version": null, "note": "Gene Ontology and KEGG pathway enrichment analysis of DEGs in the significant module.", "structure": {"pmcid": "PMC6886488", "section_index": 12, "section_title": "PPI network establishment and module analysis", "row_count": 17, "column_count": 4}, "table": {"label": "Table 2", "caption": "Gene Ontology and KEGG pathway enrichment analysis of DEGs in the significant module.", "rows": [["Term", "Description", "Count", "P-value"], ["GO:0006955", "Immune response", "10", "3.15E−06"], ["GO:0030098", "Immune cell differentiation", "6", "4.93E−05"], ["GO:0098552", "Side of membrane", "5", "5.71E−04"], ["GO:0000982", "Transcription factor", "5", "4.34E−04"], ["GO:0003677", "DNA binding", "9", "5.97E−04"], ["GO:0016337", "Cell adhesion", "6", "1.24E−03"], ["GO:0030097", "Hemopoiesis", "6", "2.09E−03"], ["GO:0001775", "Cell activation", "6", "2.34E−03"], ["GO:0006952", "Defense response", "7", "2.99E−03"], ["GO:0007166", "Cell surface receptor", "8", "1.22E−02"], ["GO:0006259", "DNA metabolic", "5", "1.83E−02"], ["GO:0001822", "Kidney development", "3", "3.90E−02"], ["Hsa05340", "Primary immunodeficiency", "5", "3.02E−07"], ["Hsa04640", "Hematopoietic cell lineage", "5", "1.36E−05"], ["Hsa04662", "B cell receptor signaling pathway", "3", "6.19E−03"], ["Hsa04068", "FOXO signaling pathway", "3", "2.09E−02"]], "row_count": 17, "column_count": 4, "numeric_cells": 48, "header_rows": 1, "locator": "section[12]/table-wrap[1]#table-2"}}, {"id": "asset:table:pmid:31803541:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6893cbd29b602779968090c8a1c26bf34ce0c4c073395443c6442031ed414621", "bytes": 3928, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#table-3", "version": null, "note": "Functional roles of 25 module genes.", "structure": {"pmcid": "PMC6886488", "section_index": 14, "section_title": "Survival analysis", "row_count": 26, "column_count": 4}, "table": {"label": "Table 3", "caption": "Functional roles of 25 module genes.", "rows": [["No.", "Gene symbol", "Full name", "Function"], ["1", "RAG2", "Recombination activating 2", "RAG2 is involved in B and T cell development and the expression of RAG2 is high in most AMLpatients"], ["2", "EBF1", "Transcription factor, early B cell factor 1", "EBF1 promotes of bone marrow CD34+ cell proliferation and migration,but suppresses the apoptosis of cells"], ["3", "BLNK", "B cell linker", "BLNK regulates the development, maturation and function of B cells"], ["4", "CD79B", "CD79b molecule", "CD79B is necessary for expression and function of the B-cell antigen receptor"], ["5", "VPREB1", "V-set pre-B cell surrogate light chain 1", "VPREB1 is involved in early B cell differentiation and VPREB1 deletion is often detected in relapsed leukemia"], ["6", "BLK", "BLK proto-oncogene, Src family tyrosine kinase", "BLK is involved in cell proliferation and differentiation and has a role in B-cell receptor signaling and B-cell development"], ["7", "IRF4", "Interferon regulatory factor 4", "IRF4 has oncogenic implications in a variety of hematological tumors including multiple myeloma, leukemia and lymphoma"], ["8", "IGLL1", "Immunoglobulin lambda like polypeptide 1", "IGLL1 is involved in cell proliferation and IGLL1 mutation can lead to B cell deficiency and agammaglobulinemia"], ["9", "DNTT", "DNA nucleotidy-lexotransferase", "DNTT acts as a catalyst to add nucleotides during the maturation of B cells and T cells"], ["10", "CD19", "CD19 molecule", "CD19 is a surface-specific marker of B lymphocytes and CD19 decreases the threshold of antigen receptor-dependent"], ["11", "PAX5", "Paired box 5", "PAX5 is involved in cell differentiation and neuro developmentand spermatogenesis"], ["12", "RAG1", "Recombination activating 1", "High expression of RAG1 in B-ALL patients promotes leukemic clonal evolution and high expression of RAG1 is associated with high proliferative markers"], ["13", "IFITM1", "Interferon induced transmembrane protein 1", "IFITM1 promotes proliferation, migration, and invasion of lung cancer"], ["14", "IFIT1", "Interferon induced protein with tetratricopeptide repeats 1", "IFIT1 and IFIT3 promote oral squamous cell carcinoma metastasis and contribute to theanti-tumor effect of gefitinib"], ["15", "IFIT3", "Interferon induced protein with tetratricopeptide repeats 3", "IFIT1 and IFIT3 promote oral squamous cell carcinoma metastasis and contribute to the anti-tumor effect of gefitinib"], ["16", "ISG20", "Interferon stimulated exonuclease gene 20", "ISG20 promotes local tumor immunity and has poor survival in human glioma"], ["17", "IFI44L", "Interferon induced protein 44 like", "High expression of IFI44L is associated with poor prognosis of osteosarcoma"], ["18", "IFI27", "Interferon alpha inducible protein 27", "IFI27 promotes cell proliferation and invasion in oral squamous cell carcinoma"], ["19", "CD24", "CD24 molecule", "CD24 modulates growth and differentiation signals to mature granulocytes and B cells"], ["20", "CXCR4", "C-X-C motif chemokine receptor 4", "High expression of CXCR4 has shorter OS time and shorter relapse-free survival time"], ["21", "IL7R", "Interleukin 7 receptor", "IL7R is overexpressed in adult acute lymphoblastic leukemia and is associatedwith JAK/STAT pathway mutations"], ["22", "MME", "Membrane metalloendo-peptidase", "MME inhibits tumor metastasis of esophageal squamous cell carcinoma and interrupt tumor cell adhesion"], ["23", "SKIL", "SKI like proto-oncogene", "SKIL has regulatory role in cell division or differentiation"], ["24", "SMAD7", "SMAD family member 7", "High expression of SMAD7 at diagnosis predicts poor prognosis in acute myeloid leukemia"], ["25", "SMAD1", "SMAD family member 1", "SMAD1 is involved in a range of biological activities including cell growth, apoptosis, morphogenesis, development and immune responses"]], "row_count": 26, "column_count": 4, "numeric_cells": 58, "header_rows": 1, "locator": "section[14]/table-wrap[1]#table-3"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The DEGs between MDS patients and healthy controls samples were screened using GEO2R."}}], "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", 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