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pmid:30365077
LASSO‑based Cox‑PH model identifies an 11‑lncRNA signature for prognosis prediction in gastric cancer.
Yonghong Zhang · Huamin Li · Wenyong Zhang · Ya Che · Weibing Bai · Guanglin Huang
Molecular medicine reports · 2018 doi:10.3892/mmr.2018.9567
Paper
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Experiment
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Data
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Complete file
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By integrating gene expression data of GC and normal samples from the National Center for Biotechnology Information Gene Expression Omnibus, the EBI ArrayExpress and The Cancer Genome Atlas (TCGA) repositories, the common RNAs in Genomic Spatial Event (GSE) 65801, GSE29998, E‑MTAB‑1338, and TCGA set were screened and used to construct a weighted correlation network analysis (WGCNA) network for mining GC‑related modules. Consensus differentially expressed RNAs (DERs) between GC and normal samples in the four datasets were screened using the MetaDE method. From the overlapped lncRNAs shared by preserved WGCNA modules and the consensus DERs, an lncRNAs signature was obtained using L1‑penalized (lasso) Cox‑proportional hazard (PH) model. LncRNA‑mRNA networks were constructed for these signature lncRNAs, followed by functional annotation. A total of 14,824 common mRNAs and 2,869 common lncRNAs were identified in the 4 sets and 5 GC‑associated WGCNA modules were preserved across all sets. MetaDE method identified 1,121 consensus DERs. A total of 50 lncRNAs were shared by preserved WGCNA modules and the consensus DERs. Subsequently, an 11‑lncRNA signature was identified by LASSO‑based Cox‑PH model. The lncRNAs signature‑based risk score could divide patients into 2 risk groups with significantly different overall survival and recurrence‑free survival times. The predictive capability of this signature was verified in an independent set. These signature lncRNAs were implicated in several biological processes and pathways associated with the immune response, the inflammatory response and cell cycle control. 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false}}, {"id": "asset:table:pmid:30365077:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:771e62b033bf8f609ceb1a2f422af31c01cf69e012bb4d8d108adce502616470", "bytes": 498, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#tI-mmr-18-06-5579", "version": null, "note": "Basic information of gene expression profiles from NCBI GEO, EBI ArrayExpress and TCGA.", "structure": {"pmcid": "PMC6236314", "section_index": 4, "section_title": "Data resource and preprocessing", "row_count": 5, "column_count": 5}, "table": {"label": "Table I.", "caption": "Basic information of gene expression profiles from NCBI GEO, EBI ArrayExpress and TCGA.", "rows": [["Accession ID", "Platform", "Total sample", "Tumor", "Control"], ["GSE65801", "GPL14550 Agilent", "64", "32", "32"], ["GSE29998", "GPL6947 Illumina", "99", "50", "49"], ["E-MTAB-1338", "Illumina HumanHT", "71", "50", "21"], ["TCGA", "Illumina HiSeq", "420", "384", "36"]], "row_count": 5, "column_count": 5, "numeric_cells": 17, "header_rows": 1, "locator": "section[4]/table-wrap[1]#tI-mmr-18-06-5579"}}, {"id": "asset:table:pmid:30365077:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9167452bb782cdbb5f0de86d324fc43c7cef4c1719444b5c962c13016c55b037", "bytes": 653, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#tII-mmr-18-06-5579", "version": null, "note": "Clinical features of TCGA dataset and GSE622254.", "structure": {"pmcid": "PMC6236314", "section_index": 7, "section_title": "Development of a prognostic risk scoring system for GC", "row_count": 7, "column_count": 3}, "table": {"label": "Table II.", "caption": "Clinical features of TCGA dataset and GSE622254.", "rows": [["Clinical characteristics", "TCGA (n=384)", "GSE62254 (n=300)"], ["Age (years, mean ± SD)", "65.15±10.61", "61.94±11.36"], ["Gender (male/female/data unavailable)", "243/133/8", "199/101"], ["Recurrence (yes/no/data unavailable)", "78/260/46", "125/157/18"], ["Vitality (dead/alive/data unavailable)", "122/238/24", "135/148//17"], ["DFS (months) (mean ± SD)", "15.84±17.05", "33.72±29.82"], ["OS (months) (mean ± SD)", "16.17±16.96", "50.59±31.42"]], "row_count": 7, "column_count": 3, "numeric_cells": 14, "header_rows": 1, "locator": "section[7]/table-wrap[1]#tII-mmr-18-06-5579"}}, {"id": "asset:table:pmid:30365077:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fd15e63f51590a99c1ef088b073c333e4e73290ef50df8bbbb8a6f505d4f0cc9", "bytes": 452, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#tIII-mmr-18-06-5579", "version": null, "note": "Numbers of mRNAs and lncRNAs in the datasets.", "structure": {"pmcid": "PMC6236314", "section_index": 11, "section_title": "RNA expression data", "row_count": 6, "column_count": 4}, "table": {"label": "Table III.", "caption": "Numbers of mRNAs and lncRNAs in the datasets.", "rows": [["Accession ID", "Total count", "mRNA", "lncRNA"], ["GSE65801", "23,081", "17,056", "6,025"], ["E-MTAB-1338", "18,730", "15,376", "3,354"], ["GSE29998", "20,586", "15,376", "5,210"], ["TCGA", "24,840", "17,579", "7,261"], ["Common", "17,693", "14,824", "2,869"]], "row_count": 6, "column_count": 4, "numeric_cells": 18, "header_rows": 1, "locator": "section[11]/table-wrap[1]#tIII-mmr-18-06-5579"}}, {"id": "asset:table:pmid:30365077:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:73ac2c4e9cd3aae3ecefeb2702ffc52f526068f48c8ef7c822096159568cb0c7", "bytes": 1039, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tIV-mmr-18-06-5579", "version": null, "note": "Characteristics of WGCNA network modules.", "structure": {"pmcid": "PMC6236314", "section_index": 12, "section_title": "WGCNA network and modules", "row_count": 12, "column_count": 8}, "table": {"label": "Table IV.", "caption": "Characteristics of WGCNA network modules.", "rows": [["TCGA", "GSE29998", "GSE65801", "E-MTAB-133", "Color", "Module size", "Module preservation (Z-score)", "Module characterization"], ["D1M1", "D2M1", "D3M1", "D4M1", "Black", "59", "28.06", "Digestion"], ["D1M2", "D2M2", "D3M2", "D4M2", "Blue", "417", "31.59", "Immune response"], ["D1M3", "D2M3", "D3M3", "D4M3", "Brown", "411", "25.26", "Cell cycle"], ["D1M4", "D2M4", "D3M4", "D4M4", "Green", "111", "6.41", "–"], ["D1M5", "D2M5", "D3M5", "D4M5", "Grey", "1,097", "4.90", "–"], ["D1M6", "D2M6", "D3M6", "D4M6", "Nagenta", "38", "10.21", "–"], ["D1M7", "D2M7", "D3M7", "D4M7", "Pink", "56", "22.08", "–"], ["D1M8", "D2M8", "D3M8", "D4M8", "Red", "78", "17.64", "–"], ["D1M9", "D2M9", "D3M9", "D4M9", "Turquoise", "564", "29.46", "Cell adhesion"], ["D1M10", "D2M10", "D3M10", "D4M10", "Yellow", "215", "14.37", "Protein amino acid glycosylation"], ["D1M11", "D2M11", "D3M11", "D4M11", "Purple", "35", "8.30", "–"]], "row_count": 12, "column_count": 8, "numeric_cells": 33, "header_rows": 1, "locator": "section[12]/table-wrap[1]#tIV-mmr-18-06-5579"}}, {"id": "asset:table:pmid:30365077:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f76879925aeebc4554457fc6e1ac5c09f9d60bf9d4d45d8b5c751bb378ccbf65", "bytes": 830, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tV-mmr-18-06-5579", "version": null, "note": "The 11 prognostic lncRNAs identified by LASSO-based Cox-proportion hazard model.", "structure": {"pmcid": "PMC6236314", "section_index": 14, "section_title": "Development and validation of an lncRNAs-based risk scoring system", "row_count": 12, "column_count": 4}, "table": {"label": "Table V.", "caption": "The 11 prognostic lncRNAs identified by LASSO-based Cox-proportion hazard model.", "rows": [["lncRNA", "Coefficient", "HR", "95% CI"], ["ARHGAP5-AS1", "0.0124", "1.1907", "0.8259–1.7166"], ["FLVCR1-AS1", "−0.1191", "0.6610", "0.4916–0.8886"], ["H19", "0.9171", "1.0497", "0.9390–1.1735"], ["HOTAIR", "−0.4973", "0.8970", "0.6584–1.2222"], ["LINC00221", "1.1799", "1.9190", "1.2021–3.0633"], ["MCF2L-AS1", "−0.7009", "0.7785", "0.6053–1.0014"], ["MUC2", "−0.0902", "0.9516", "0.8631–1.0492"], ["PRSS30P", "0.2572", "1.1254", "0.8263–1.5329"], ["SCARNA9", "−0.8615", "0.7383", "0.5449–1.0004"], ["TP53TG1", "0.1493", "1.1386", "0.8808–1.4720"], ["XIST", "−0.9235", "0.5469", "0.1926–1.5527"]], "row_count": 12, "column_count": 4, "numeric_cells": 38, "header_rows": 1, "locator": "section[14]/table-wrap[1]#tV-mmr-18-06-5579"}}, {"id": "asset:table:pmid:30365077:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4b346e8a06cb7d180d3af7bcc1e46e4a779fa2e020bed81038be8b1447b43505", "bytes": 8056, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#tVI-mmr-18-06-5579", "version": null, "note": "Significant GO terms and KEGG pathways for the genes in the constructed lncRNA-mRNA network of nine prognostic lncRNAs involved in the blue module.", "structure": {"pmcid": "PMC6236314", "section_index": 15, "section_title": "Function analysis of the 11-lncRNA signature", "row_count": 32, "column_count": 5}, "table": {"label": "Table VI.", "caption": "Significant GO terms and KEGG pathways for the genes in the constructed lncRNA-mRNA network of nine prognostic lncRNAs involved in the blue module.", "rows": [["GO category", "Term", "Count", "Genes", "FDR"], ["Biology process", "Immune response", "80", "MICB, CD8A, LY86, HLA-DMB, HLA-DMA, C1QC, PDCD1, CD96, SH2D1A, CLEC4E, MS4A1, LTF, FAS, FCGR3A, SPN, CIITA, LAIR1, POU2AF1, SIT1, NCF2, GZMA, NCF1, LY96, CMKLR1, TNFRSF17, WAS, HLA-DQA1, PDCD1LG2, TRAT1, CTSW, IGSF6, C1QB, LILRB2, IL18BP, CCR5, TNFSF13B, CCR4, LAX1, LILRB4, HLA-DPA1, MADCAM1, GBP4, LCP1, GBP1, LCP2, HLA-DQB1, PSMB10, ITGAL, CCR1, GPSM3, CXCL9, CX3CL1, IL7R, CCL5, CCL4, POU2F2, ZAP70, HLA-DRB5, IL2RG, CD4, HLA-DPB1, HLA-DOA, PTPRC, IL2RA, TNFRSF13C, CCL19, SLAMF7, CD180, AIM2, CORO1A, TNFSF10, CYBB, APOL1, CD300A, CXCL13, CD209, IRF8, CD274, CD79B, CD79A", "5.39×10−49"], ["", "Regulation of cell activation", "30", "KLRK1, IL7R, HLA-DMA, CD2, ZAP70, CD4, IL2RG, FAS, HLA-DOA, LAG3, SPN, PTPRC, SIT1, IL2RA, IKZF1, PLEK, CD3E, TNFRSF13C, CD40, PDCD1LG2, CD38, PRKCQ, CORO1A, SIRPG, TNFSF13B, LAX1, CD274, JAK2, IRF4, SASH3", "6.22×10−20"], ["", "Regulation of lymphocyte activation", "28", "KLRK1, IL7R, HLA-DMA, CD2, ZAP70, CD4, IL2RG, FAS, HLA-DOA, LAG3, SPN, PTPRC, SIT1, IL2RA, IKZF1, CD3E, TNFRSF13C, CD40, PDCD1LG2, CD38, PRKCQ, CORO1A, SIRPG, TNFSF13B, LAX1, CD274, IRF4, SASH3", "1.53×10−19"], ["", "Lymphocyte activation", "31", "ITGAL, MICB, CD8A, IL21R, KLRK1, PTPN22, IL7R, HLA-DMA, DOCK2, CXCR5, ZAP70, MS4A1, CD2, CD4, FAS, SPN, RHOH, PTPRC, CD3G, CD3D, IKZF1, CD3E, SLAMF7, ITGA4, CD40, WAS, LAX1, CD79A, IRF4, BANK1, LCP1", "1.83×10−19"], ["", "Positive regulation of immune system process", "33", "C3AR1, MICB, CD247, KLRK1, PTPN22, IL7R, C1QC, HLA-DMA, SH2D1A, CD2, ZAP70, CD4, IL2RG, LAG3, SPN, PTPRC, IL2RA, IKZF1, CD3E, TNFRSF13C, CD40, PDCD1LG2, TRAT1, CD38, PRKCQ, C1QB, CORO1A, CD37, SIRPG, TNFSF13B, LAX1, CD79A, SASH3", "2.32×10−19"], ["", "Leukocyte activation", "33", "ITGAL, MICB, CD8A, IL21R, KLRK1, PTPN22, CX3CL1, IL7R, HLA-DMA, DOCK2, CXCR5, ZAP70, MS4A1, CD2, CD4, FAS, SPN, RHOH, PTPRC, CD3G, CD3D, IKZF1, CD3E, SLAMF7, ITGA4, CD40, WAS, LAX1, CD79A, IRF4, BANK1, LCP1, LCP2", "3.92×10−19"], ["", "Regulation of T cell activation", "25", "PTPRC, SIT1, IL2RA, IKZF1, CD3E, TNFRSF13C, KLRK1, IL7R, HLA-DMA, PDCD1LG2, PRKCQ, CORO1A, SIRPG, TNFSF13B, LAX1, CD274, ZAP70, CD2, CD4, IL2RG, IRF4, HLA-DOA, SPN, LAG3, SASH3", "2.21×10−18"], ["", "Defense response", "47", "C3AR1, ITGAL, PRF1, AIF1, CCR1, LY86, CXCL9, ITGB2, CX3CL1, CCL5, PTPRCAP, CCL4, C1QC, SH2D1A, AOAH, LTF, SPN, CIITA, ITK, PTPRC, IL2RA, NCF2, NCF1, LY96, HCK, CCL19, CD40, SLAMF7, WAS, CD180, SP140, TRAT1, CD163, LSP1, CD84, APOL3, SIGLEC1, C1QB, LILRB2, CORO1A, CYBB, APOL1, CCR5, CCR4, CXCL13, MNDA, PLA2G7", "3.44×10−18"], ["", "Regulation of leukocyte activation", "28", "KLRK1, IL7R, HLA-DMA, CD2, ZAP70, CD4, IL2RG, FAS, HLA-DOA, LAG3, SPN, PTPRC, SIT1, IL2RA, IKZF1, CD3E, TNFRSF13C, CD40, PDCD1LG2, CD38, PRKCQ, CORO1A, SIRPG, TNFSF13B, LAX1, CD274, IRF4, SASH3", "3.64×10−18"], ["", "Cell activation", "34", "ITGAL, MICB, CD8A, IL21R, KLRK1, PTPN22, CX3CL1, IL7R, HLA-DMA, DOCK2, CXCR5, ZAP70, MS4A1, CD2, CD4, FAS, SPN, RHOH, PTPRC, CD3G, CD3D, PLEK, IKZF1, CD3E, SLAMF7, ITGA4, CD40, WAS, LAX1, CD79A, IRF4, BANK1, LCP1, LCP2", "7.10×10−18"], ["", "Positive regulation of cell activation", "23", "PTPRC, IL2RA, IKZF1, PLEK, CD3E, KLRK1, TNFRSF13C, CD40, IL7R, HLA-DMA, PDCD1LG2, CD38, PRKCQ, CORO1A, SIRPG, TNFSF13B, CD2, ZAP70, JAK2, CD4, IL2RG, SASH3, SPN", "2.55×10−16"], ["", "Positive regulation of leukocyte activation", "21", "PTPRC, IL2RA, IKZF1, CD3E, KLRK1, TNFRSF13C, CD40, IL7R, HLA-DMA, PDCD1LG2, CD38, PRKCQ, CORO1A, SIRPG, TNFSF13B, CD2, ZAP70, CD4, IL2RG, SASH3, SPN", "3.41×10−14"], ["", "Positive regulation of lymphocyte activation", "20", "PTPRC, IL2RA, IKZF1, CD3E, KLRK1, TNFRSF13C, CD40, IL7R, HLA-DMA, PDCD1LG2, CD38, PRKCQ, CORO1A, SIRPG, TNFSF13B, ZAP70, CD4, IL2RG, SASH3, SPN", "1.78×10−13"], ["", "T cell activation", "21", "ITGAL, PTPRC, MICB, CD3G, CD3D, IKZF1, CD8A, CD3E, PTPN22, IL7R, HLA-DMA, WAS, DOCK2, ZAP70, CD2, CD4, FAS, IRF4, LCP1, SPN, RHOH", "1.09×10−12"], ["", "Hemopoietic or lymphoid organ development", "24", "PTPRC, CD3D, PLEK, IKZF1, CD8A, CD3E, HCLS1, PTPN22, ITGA4, IFI16, IL7R, HLA-DMA, DOCK2, CXCR5, CXCL13, IRF8, ZAP70, JAK2, CD4, FAS, CD79A, IRF4, SPN, RHOH", "2.97×10−09"], ["", "Inflammatory response", "26", "ITGAL, C3AR1, AIF1, LY86, CCR1, CXCL9, ITGB2, CCL5, C1QC, CCL4, AOAH, CIITA, IL2RA, LY96, CCL19, CD40, CD180, CD163, C1QB, SIGLEC1, APOL3, CYBB, CCR5, CXCL13, CCR4, PLA2G7", "6.83×10−09"], ["", "Immune system development", "24", "PTPRC, CD3D, PLEK, IKZF1, CD8A, CD3E, HCLS1, PTPN22, ITGA4, IFI16, IL7R, HLA-DMA, DOCK2, CXCR5, CXCL13, IRF8, ZAP70, JAK2, CD4, FAS, CD79A, IRF4, SPN, RHOH", "1.02×10−08"], ["", "Hemopoiesis", "22", "PTPRC, CD3D, PLEK, IKZF1, CD8A, CD3E, HCLS1, PTPN22, ITGA4, IFI16, IL7R, HLA-DMA, DOCK2, IRF8, ZAP70, JAK2, CD4, FAS, CD79A, IRF4, SPN, RHOH", "2.60×10−08"], ["", "Positive regulation of response to stimulus", "22", "C3AR1, PTPRC, MICB, CD3E, CD247, KLRK1, TNFRSF13C, PTPN22, CX3CL1, CCL5, HLA-DMA, C1QC, C1QB, SH2D1A, TNFSF13B, LAX1, CCR4, ZAP70, JAK2, CD79A, SASH3, LAG3", "2.60×10−08"], ["", "Response to wounding", "30", "C3AR1, ITGAL, AIF1, LY86, CCR1, CXCL9, ITGB2, CCL5, C1QC, CCL4, AOAH, CIITA, IL2RA, PLEK, LY96, CCL19, CD40, WAS, CD180, CD163, APOL3, PRKCQ, C1QB, SIGLEC1, CYBB, CCR5, CCR4, CXCL13, PLA2G7, JAK2", "4.82×10−07"], ["", "Cell surface receptor linked signal transduction", "56", "MICB, CD8A, PTPN22, CXCR5, CXCR6, SPN, LAG3, KLRB1, PIK3CG, CD3G, CD3D, LY96, CMKLR1, CD3E, GPR171, CD40, IGSF6, LILRB2, DOK2, CCR5, CCR4, LAX1, LCP2, C3AR1, ITGAL, CCR1, CD247, KLRK1, CXCL9, FPR3, ITGB2, IL7R, CCL5, P2RY6, ITGAX, ITGB7, GPR25, ZAP70, CD2, CD4, PTPRC, IL2RA, PLEK, DTX1, CCL19, RGS19, EVL, ITGA4, BIRC3, P2RY10, CD274, CD79B, JAK2, JAK3, CD79A, ADAMDEC1", "4.54×10−05"], ["", "Cell adhesion", "29", "ITGAL, CCR1, FERMT3, ITGB2, CX3CL1, CCL5, CCL4, CD96, ITGAX, ITGB7, CD2, CD22, CD4, CD6, SELPLG, PARVG, PTPRC, PLEK, SIGLEC10, ITGA4, SLAMF7, EMILIN2, CD84, SIGLEC1, CORO1A, SIRPG, CD300A, CD209, MADCAM1", "8.34×10−04"], ["", "Biological adhesion", "29", "ITGAL, CCR1, FERMT3, ITGB2, CX3CL1, CCL5, CCL4, CD96, ITGAX, ITGB7, CD2, CD22, CD4, CD6, SELPLG, PARVG, PTPRC, PLEK, SIGLEC10, ITGA4, SLAMF7, EMILIN2, CD84, SIGLEC1, CORO1A, SIRPG, CD300A, CD209, MADCAM1", "8.58×10−04"], ["KEGG pathway", "Cell adhesion molecules (CAMs)", "26", "HLA-DQB1, ITGAL, PTPRC, CD8A, ITGB2, CD40, ITGA4, HLA-DMB, HLA-DMA, PDCD1, HLA-DQA1, PDCD1LG2, SIGLEC1, ITGB7, CD274, CD2, CD22, HLA-DRB5, CD4, HLA-DPA1, MADCAM1, HLA-DPB1, HLA-DOA, CD6, SELPLG, SPN", "6.37×10−15"], ["", "Allograft rejection", "12", "HLA-DQB1, PRF1, HLA-DRB5, GZMB, HLA-DPA1, HLA-DPB1, FAS, CD40, HLA-DMB, HLA-DOA, HLA-DMA, HLA-DQA1", "8.68×10−08"], ["", "Cytokine-cytokine receptor interaction", "24", "IL2RB, IL2RA, CCR1, IL21R, TNFRSF13C, CXCL9, TNFRSF17, CCL19, CD40, CX3CL1, IL7R, CCL5, CCL4, TNFSF10, TNFSF13B, CXCR5, CCR5, CCR4, CXCL13, IL10RA, CXCR6, CSF2RB, IL2RG, FAS", "2.80×10−06"], ["", "Graft vs.host disease", "11", "HLA-DQB1, PRF1, HLA-DRB5, GZMB, HLA-DPA1, HLA-DPB1, FAS, HLA-DMB, HLA-DOA, HLA-DMA, HLA-DQA1", "4.48×10−06"], ["", "Chemokine signaling pathway", "19", "PIK3CG, ITK, NCF1, HCK, CCR1, CXCL9, CCL19, CX3CL1, CCL5, CCL4, WAS, DOCK2, CXCR5, CCR5, CCR4, CXCL13, CXCR6, JAK2, JAK3", "4.64×10−05"], ["", "Natural killer cell mediated cytotoxicity", "15", "PIK3CG, PRF1, ITGAL, MICB, CD247, KLRK1, GZMB, ITGB2, HCST, SH2D1A, TNFSF10, ZAP70, FAS, FCGR3A, LCP2", "5.69×10−04"], ["", "T cell receptor signaling pathway", "13", "PIK3CG, ITK, PRKCQ, PTPRC, CD3G, CD8A, CD3D, CD3E, CD247, ZAP70, CD4, PDCD1, LCP2", "2.20×10−03"], ["", "Antigen processing and presentation", "11", "HLA-DQB1, CIITA, CD8A, HLA-DRB5, CD4, HLA-DPA1, HLA-DPB1, HLA-DMB, HLA-DOA, HLA-DMA, HLA-DQA1", "7.92×10−03"]], "row_count": 32, "column_count": 5, "numeric_cells": 91, "header_rows": 1, "locator": "section[15]/table-wrap[1]#tVI-mmr-18-06-5579"}}, {"id": "asset:table:pmid:30365077:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ce21f75d762a32eff6eb90a4316b1cd200e918801cbfb2c9555d68a734692f79", "bytes": 4234, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[2]#tVII-mmr-18-06-5579", "version": null, "note": "Significant GO terms and KEGG pathways for the genes in the constructed lncRNA-mRNA network of two prognostic lncRNAs in the brown module.", "structure": {"pmcid": "PMC6236314", "section_index": 15, "section_title": "Function analysis of the 11-lncRNA signature", "row_count": 19, "column_count": 5}, "table": {"label": "Table VII.", "caption": "Significant GO terms and KEGG pathways for the genes in the constructed lncRNA-mRNA network of two prognostic lncRNAs in the brown module.", "rows": [["GO category", "Term", "Count", "Genes", "FDR"], ["Biology process", "Cell cycle phase", "40", "E2F1, KIF23, PRC1, NEK3, NEK2, DBF4, TTK, PKMYT1, ANLN, AURKA, PTTG1, CEP55, AURKB, CCNE1, CDCA2, CDCA5, TRIP13, CDCA3, CDC6, MKI67, MSH5, TPX2, SKP2, NUF2, CENPF, CDC20, BIRC5, CENPE, NDC80, ESPL1, PBK, CDKN3, UBE2C, TACC3, CDC25B, CCNB1, MAD2L1, PLK1, POLD1, DSCC1", "2.14×10−22"], ["", "Cell cycle", "50", "E2F1, KIF23, CEP72, PRC1, DBF4, E2F7, TTK, PKMYT1, AURKA, PTTG1, AURKB, CDT1, CCNE2, CCNE1, CDCA2, CDCA5, CDCA3, CDC6, SKP2, TPX2, ESPL1, MCM2, PBK, TACC3, UBE2C, UHRF1, MAD2L1, DSCC1, NEK3, NEK2, FOXM1, ANLN, CEP55, CENPA, TRIP13, CKAP2, MKI67, MSH5, PSRC1, NUF2, CENPF, BIRC5, NDC80, CENPE, CDC20, CDKN3, CDC25B, CCNB1, PLK1, POLD1", "2.83×10−21"], ["", "Mitotic cell cycle", "37", "KIF23, E2F1, PRC1, NEK3, NEK2, DBF4, TTK, PKMYT1, ANLN, AURKA, PTTG1, CEP55, AURKB, CCNE1, CENPA, CDCA2, CDCA5, CDCA3, CDC6, TPX2, SKP2, NUF2, CENPF, CDC20, BIRC5, CENPE, NDC80, ESPL1, PBK, CDKN3, UBE2C, CDC25B, CCNB1, MAD2L1, PLK1, POLD1, DSCC1", "6.89×10−21"], ["", "Cell cycle process", "42", "E2F1, KIF23, CEP72, PRC1, NEK3, NEK2, DBF4, TTK, PKMYT1, ANLN, AURKA, PTTG1, AURKB, CEP55, CCNE1, CENPA, CDCA2, CDCA5, CDCA3, TRIP13, CDC6, MKI67, MSH5, TPX2, SKP2, NUF2, CENPF, CDC20, BIRC5, CENPE, NDC80, ESPL1, PBK, CDKN3, UBE2C, TACC3, CDC25B, CCNB1, MAD2L1, PLK1, POLD1, DSCC1", "2.26×10−19"], ["", "M phase", "34", "KIF23, PRC1, NEK3, NEK2, TTK, PKMYT1, ANLN, AURKA, PTTG1, CEP55, AURKB, CDCA2, CDCA5, TRIP13, CDCA3, CDC6, MKI67, MSH5, TPX2, NUF2, CENPF, CDC20, BIRC5, CENPE, NDC80, ESPL1, PBK, UBE2C, TACC3, CDC25B, CCNB1, MAD2L1, PLK1, DSCC1", "2.68×10−19"], ["", "Mitosis", "28", "KIF23, NEK3, NEK2, PKMYT1, AURKA, ANLN, CEP55, AURKB, PTTG1, CDCA2, CDCA5, CDCA3, CDC6, TPX2, NUF2, CENPF, BIRC5, CENPE, NDC80, ESPL1, CDC20, PBK, UBE2C, CDC25B, CCNB1, MAD2L1, PLK1, DSCC1", "1.39×10−17"], ["", "Nuclear division", "28", "KIF23, NEK3, NEK2, PKMYT1, AURKA, ANLN, CEP55, AURKB, PTTG1, CDCA2, CDCA5, CDCA3, CDC6, TPX2, NUF2, CENPF, BIRC5, CENPE, NDC80, ESPL1, CDC20, PBK, UBE2C, CDC25B, CCNB1, MAD2L1, PLK1, DSCC1", "1.39×10−17"], ["", "M phase of mitotic cell cycle", "28", "KIF23, NEK3, NEK2, PKMYT1, AURKA, ANLN, CEP55, AURKB, PTTG1, CDCA2, CDCA5, CDCA3, CDC6, TPX2, NUF2, CENPF, BIRC5, CENPE, NDC80, ESPL1, CDC20, PBK, UBE2C, CDC25B, CCNB1, MAD2L1, PLK1, DSCC1", "2.25×10−17"], ["", "Organelle fission", "28", "KIF23, NEK3, NEK2, PKMYT1, AURKA, ANLN, CEP55, AURKB, PTTG1, CDCA2, CDCA5, CDCA3, CDC6, TPX2, NUF2, CENPF, BIRC5, CENPE, NDC80, ESPL1, CDC20, PBK, UBE2C, CDC25B, CCNB1, MAD2L1, PLK1, DSCC1", "4.04×10−17"], ["", "Cell division", "26", "KIF23, PRC1, NEK3, NEK2, ANLN, CEP55, PTTG1, AURKB, CCNE2, CCNE1, CDCA2, CDCA5, CDCA3, CDC6, NUF2, CENPF, BIRC5, CDC20, CENPE, NDC80, ESPL1, UBE2C, CDC25B, CCNB1, MAD2L1, PLK1", "3.42×10−12"], ["", "Regulation of cell cycle", "19", "E2F1, CDC6, HOXA13, NEK2, SKP2, CENPF, TTK, PKMYT1, ESPL1, CENPE, ANLN, BIRC5, TACC3, UBE2C, CDKN3, CDT1, CCNE2, CCNB1, MAD2L1", "4.79×10−05"], ["", "Microtubule-based process", "16", "KIFC2, KIF23, CEP72, PRC1, NEK2, PSRC1, TTK, ESPL1, AURKA, NDC80, CENPE, TACC3, UBE2C, HOOK1, CENPA, KIF20A", "2.40×10−04"], ["", "Pattern specification process", "15", "SATB2, FOXA2, FOXJ1, OTX1, HOXA11, HOXC6, FOXH1, HOXC10, HOXC9, HOXC11, HOXB7, VEGFA, HOXA10, HOXA9, HOXB9", "2.78×10−03"], ["", "DNA metabolic process", "20", "RECQL4, GINS1, CDC6, RAD51AP1, DBF4, MSH5, CENPF, MCM2, PTTG1, MCM4, CDT1, CCNE2, TYMS, UHRF1, RFC3, POLD1, DNMT3B, TOP2A, TRIP13, DSCC1", "5.77×10−03"], ["KEGG pathway", "Cell cycle", "18", "E2F1, CDC6, E2F5, DBF4, SKP2, PKMYT1, TTK, CDC20, ESPL1, MCM2, PTTG1, MCM4, CDC25B, CCNE2, CCNB1, CCNE1, MAD2L1, PLK1", "1.01×10−12"], ["", "DNA replication", "4", "RFC3, POLD1, MCM2, MCM4", "5.38×10−03"], ["", "Progesterone-mediated oocyte maturation", "5", "CCNB1, MAD2L1, PLK1, PKMYT1, CDC25B", "1.04×10−02"], ["", "Steroid biosynthesis", "3", "CYP51A1, SQLE, DHCR7", "1.22×10−02"]], "row_count": 19, "column_count": 5, "numeric_cells": 53, "header_rows": 1, "locator": "section[15]/table-wrap[2]#tVII-mmr-18-06-5579"}}], "gaps": ["asset:data:geo:E-MTAB-1338 not downloaded", "asset:data:geo:E-MTAB-1338 licence not read", "asset:data:geo:GSE29998 not downloaded", "asset:data:geo:GSE29998 licence not read", "asset:data:geo:GSE62254 not downloaded", "asset:data:geo:GSE62254 licence not read", "asset:data:geo:GSE6580 not downloaded", "asset:data:geo:GSE6580 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-2", "family": null, "specific": null, "label": "MetaDE meta-analysis method", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Consensus differentially expressed RNAs (DERs) between GC specimens and normal control specimens across the 4 datasets (GSE6580, GSE29998, E-MTAB-1338 and TCGA) were identified with metaDE package (22,23) (https://cran.r-project.org/web/packages/MetaDE/) in R language version 3.4.1."}}], "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", "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": ["pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pathway_enrichment."}, "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": ["GSE6580", "GSE29998", "E-MTAB-1338", "GSE62254"], "resolved_accessions": ["GSE6580", "GSE29998", "E-MTAB-1338", "GSE62254"], "statements": ["The datasets analyzed during the present study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE6580, GSE29998, E-MTAB-1338, GSE62254 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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