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pmid:30723390
Bladder cancer stage-associated hub genes revealed by WGCNA co-expression network analysis.
Yu Di · Dongshan Chen · Wei Yu · Lei Yan
Hereditas · 2019 doi:10.1186/s41065-019-0083-y
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Experiment
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Complete file
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Molecular complex detection(MCODE) was used to identify hub genes. The most significant cluster including 16 genes: CDH11, COL3A1, COL6A3, COL5A1, AEBP1, COL1A2, NTM, COL11A1, THBS2, COL8A1, COL1A1, BGN, MMP2, PXDN, THY1, and TGFB1I1 was identified. After annotated by BiNGO, they were suggested associated with collagen fibril organization and blood vessel development. In addition, the Kaplan Meier curves were obtained by UALCAN. The high expression of THY1, AEBP1, CDH11, COL1A1, COL1A2, COL11A1, MMP2, PXDN, BGN, COL5A1, COL8A1, and TGFB1I1 indicated poor prognosis of the patients(P < 0.05). Finally, we examined genes' expression between low and high tumor stage by the Wilcoxon test(P < 0.05), TGFB1I1 was excluded.\nCONCLUSION: THY1, AEBP1, CDH11, COL1A1, COL1A2, COL11A1, MMP2, PXDN, BGN, COL5A1, COL8A1 associated with the tumor stage as well as tumor patients' prognosis. COL5A1, COL8A1(P < 0.01) may serve as therapeutic targets for the disease.", "claims": [{"id": "claim-method", "statement": "The “WGCNA” R package was used to construct a co-expression network for the filtered genes [21]. 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"extracellular matrix organization", "COL1A1,COL3A1,COL1A2,COL5A1,COL11A1,PXDN"], ["32,964", "1.94E-08", "collagen biosynthetic process", "COL1A1,COL3A1,COL5A1"], ["32,963", "2.59E-08", "collagen metabolic process", "COL1A1,COL3A1,COL5A1,MMP2"], ["43,588", "4.26E-08", "skin development", "COL1A1,COL3A1,COL1A2,COL5A1"], ["44,236", "7.36E-08", "multicellular organismal metabolic process", "COL1A1,COL3A1,COL5A1,MMP2"], ["48,513", "9.99E-08", "organ development", "COL1A1,COL3A1,COL1A2,COL5A1,MMP2,TGFB1I1,BGN,COL6A3,COL8A1,AEBP1,THY1"], ["48,731", "1.52E-07", "system development", "COL1A1,COL3A1,COL1A2,COL5A1,MMP2,TGFB1I1,CDH11,BGN,COL6A3,COL8A1,AEBP1,THY1"], ["1501", "6.53E-07", "skeletal system development", "COL1A1,COL3A1,COL1A2,MMP2,CDH11,AEBP1"], ["60,346", "2.05E-06", "bone trabecula formation", "COL1A1,MMP2"], ["9653", "1.03E-05", "anatomical structure morphogenesis", "COL1A1,COL1A2,COL5A1,MMP2,TGFB1I1,BGN,COL8A1,THY1"], ["32,501", "1.11E-05", "multicellular organismal process", 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(ranked by degree)", "rows": [["Gene Name", "Degree", "Neighborhood Connectivity", "Average Shortest Path Length", "Closeness Centrality", "Clustering Coefficient", "Stress", "Topological Coefficient"], ["CDH11", "49", "6.244898", "1.27941176", "0.7816092", "0.089286", "4554", "0.115646"], ["COL3A1", "35", "8.971429", "1.5", "0.66666667", "0.191597", "2022", "0.133902"], ["COL6A3", "31", "9.16129", "1.55882353", "0.64150943", "0.197849", "1944", "0.141633"], ["COL5A1", "25", "10.72", "1.66176471", "0.60176991", "0.266667", "1420", "0.16625"], ["AEBP1", "21", "12.61905", "1.70588235", "0.5862069", "0.347619", "852", "0.190476"], ["COL1A2", "19", "14", "1.75", "0.57142857", "0.432749", "464", "0.212121"], ["NTM", "11", "19.81818", "1.85294118", "0.53968254", "0.418182", "544", "0.295794"], ["COL11A1", "10", "20.7", "1.86764706", "0.53543307", "0.511111", "388", "0.312121"], ["THBS2", "10", "21.6", "1.86764706", "0.53543307", "0.488889", "432", "0.322388"], ["COL8A1", "10", "21.6", "1.86764706", "0.53543307", "0.488889", "432", "0.322388"], ["COL1A1", "9", "21.55556", "1.91176471", "0.52307692", "0.694444", "194", "0.331624"], ["BGN", "8", "24.5", "1.92647059", "0.51908397", "0.964286", "2", "0.376923"], ["MMP2", "7", "26.85714", "1.94117647", "0.51515152", "1", "0", "0.413187"], ["PXDN", "6", "30", "1.95588235", "0.5112782", "1", "0", "0.461538"], ["THY1", "6", "30", "1.95588235", "0.5112782", "1", "0", "0.461538"], ["TGFB1I1", "6", "30", "1.95588235", "0.5112782", "1", "0", "0.461538"]], "row_count": 17, "column_count": 8, "numeric_cells": 114, "header_rows": 1, "locator": "section[10]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:30723390:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:404878eb87b4179a94e9806faa803ab29b5a45b0ce364557a934ab90c5848cf6", "bytes": 1683, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab3", "version": null, "note": "The top 15 GO items of the 16 hub genes provided by BINGO", "structure": {"pmcid": "PMC6350372", "section_index": 11, "section_title": "Function annotation of the module of interest and the hub genes", "row_count": 16, "column_count": 4}, "table": {"label": "Table 3", "caption": "The top 15 GO items of the 16 hub genes provided by BINGO", "rows": [["GO-ID", "P-value", "Description", "Genes in the test set"], ["30,199", "7.08-E-11", "collagen fibril organization", "COL1A1,COL3A1,COL1A2,COL5A1,COL11A1"], ["1568", "7.94E-11", "blood vessel development", "COL1A1,COL3A1,COL1A2,COL5A1,MMP2,BGN,COL8A1,THY1"], ["7155", "2.19E-10", "cell adhesion", "COL3A1,COL5A1,COL11A1,TGFB1I1,CDH11,COL6A3,COL8A1,AEBP1,THY1,THBS2"], ["30,198", "6.59E-10", "extracellular matrix organization", "COL1A1,COL3A1,COL1A2,COL5A1,COL11A1,PXDN"], ["32,964", "1.94E-08", "collagen biosynthetic process", "COL1A1,COL3A1,COL5A1"], ["32,963", "2.59E-08", "collagen metabolic process", "COL1A1,COL3A1,COL5A1,MMP2"], ["43,588", "4.26E-08", "skin development", "COL1A1,COL3A1,COL1A2,COL5A1"], ["44,236", "7.36E-08", "multicellular organismal metabolic process", "COL1A1,COL3A1,COL5A1,MMP2"], ["48,513", "9.99E-08", "organ development", "COL1A1,COL3A1,COL1A2,COL5A1,MMP2,TGFB1I1,BGN,COL6A3,COL8A1,AEBP1,THY1"], ["48,731", "1.52E-07", "system development", "COL1A1,COL3A1,COL1A2,COL5A1,MMP2,TGFB1I1,CDH11,BGN,COL6A3,COL8A1,AEBP1,THY1"], ["1501", "6.53E-07", "skeletal system development", "COL1A1,COL3A1,COL1A2,MMP2,CDH11,AEBP1"], ["60,346", "2.05E-06", "bone trabecula formation", "COL1A1,MMP2"], ["9653", "1.03E-05", "anatomical structure morphogenesis", "COL1A1,COL1A2,COL5A1,MMP2,TGFB1I1,BGN,COL8A1,THY1"], ["32,501", "1.11E-05", "multicellular organismal process", "COL11A1,MMP2,TGFB1I1,BGN,AEBP1,THY1,COL1A1,COL3A1,COL1A2,COL5A1,CDH11,COL6A3,COL8A1"], ["43,589", "1.28E-05", "skin morphogenesis", "COL1A1,COL1A2"]], "row_count": 16, "column_count": 4, "numeric_cells": 36, "header_rows": 1, "locator": "section[11]/table-wrap[1]#Tab3"}}], "gaps": ["asset:data:geo:GSE31684 not downloaded", "asset:data:geo:GSE31684 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": 0.7, "band": "medium", "quote": "Wilcoxon"}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan Meier"}}, {"id": "method-3", "family": "clustering", "specific": "hierarchical", "label": "Clustering", 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The gene chip GSE31684 [19] of bladder cancer with its clinical manifestation data was downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/)."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "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. 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