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pmid:28627654
Bioinformatics analysis of transcription profiling of solid pseudopapillary neoplasm of the pancreas.
Yongping Zhang · Xu Han · Hao Wu · Yifeng Zhou
Molecular medicine reports · 2017 doi:10.3892/mmr.2017.6800
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Complete file
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The transcription profiling data (GSE43795) of 14 SPN and 6 control samples were downloaded from the Gene Expression Omnibus (GEO) database. Using the Limma package, Student's t‑tests were performed to identify differentially expressed genes (DEGs) between SPN and control samples [with the following criterion: False discovery rate (FDR)<0.01 and log2 fold‑change (FC)≥3]. Pathway and functional enrichment analyses were performed to investigate the biological processes that the DEGs were involved in. Protein‑protein interaction (PPI) network and sub‑network analyses were conducted to comprehensively understand the interactions between DEGs. The screened DEGs were further annotated according to information relating to transcription factors and tumor associated genes (TAGs). A total of 710 upregulated and 710 downregulated DEGs were observed, including 74 transcriptional factors and 124 TAGs. Membrane metallo‑endopeptidase (MME), matrix metalloproteinase (MMP)-2 and MMP‑9 were also identified as key TAGs. Following PPI network analysis, hub nodes of epidermal growth factor receptor (EGFR), proto‑oncogene tyrosine protein kinase Fyn (FYN), c‑JUN (JUN), glucagon (GCG), c‑Myc (MYC) and CD44 were identified, the majority of which participate in the epidermal growth factor receptor (ErbB) and gonadotropin-releasing hormone (GnRH) signaling pathways. A sub‑network involving 70 gene nodes was also identified, with EGFR as the central gene. MME, MMP‑2 and MMP‑9 contribute to proliferative diabetic retinopathy and also involved in SPN. The genes EGFR, FYN, JUN, GCG, MYC and CD44 may therefore be key genes in SPN, and the ErbB and GnRH signaling pathways may be an important contributor to SPN progression.", "claims": [{"id": "claim-method", "statement": "Bayesian analysis was performed using the Limma package (15), to identify DEGs between SPN and control samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28627654", "locator": "sections[5] \"DEGs screening\" paragraph 2", "quote": "Bayesian analysis was performed using the Limma package (15), to identify DEGs between SPN and control samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mRNA expression profiles of SPN and non-neoplastic pancreatic tissues were obtained from the National Center of Biotechnology Information Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) database. 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"section_index": 7, "section_title": "Gene functional annotation analysis", "row_count": 6, "column_count": 5}, "table": {"label": "Table III.", "caption": "Functional statistics of differentially expressed genes between solid pseudopapillary neoplasm and control samples.", "rows": [["Pattern", "TF counts", "TF genes", "TAG counts", "TAG genes"], ["Down", "31", "CDX2, EHF, ELF3, FOSB, FOXA2, FOXA3, FOXC1, FOXQ1, GATA4, HEYL, HHEX, HNF4G", "73", "Oncogene: CD24, CXCL1, EGFR, ELF3, ERBB3, FGFR1, FGFR3, GATA4, GFI1, GPX2, JUN, LCN2, MEIS1, MYC, SPHK1"], ["", "", "INSM1, ISL1, KCNIP3, KLF5, LMO3, MEIS1, NKX2.2, NKX2.5, NR4A2, NR5A2, ONECUT1, PAX6, PBX3, PDX1, PKNOX2, PLAGL1, SOX9, TEAD4, XBP1", "", "Tumor suppressor: WNK2, VIL1, UCHL1, TPM1, TFPI2, SYT13, STEAP3, SRPX, SIK1, SFRP5, SERPINI2, RAP1GAP, RAB25, PTPRK, PRKCDBP, PLK2, PLAGL1, PDX1, PDGFRL, PAX6, ONECUT1, NRCAM, MUC1, MTUS1, MT1G, MEG3, LPL, KLF5, KLF10, ID4, GNMT, GAS1, FOXC1, FOXA2, ERRFI1, EPHA1, ENC1, EHF, DEFB1, DAPK1, CLDN23, CEBPA, CDH1, C2orf40, BTG2, BMP2, BIN1, ADAMTS9 Other: TACC2, SLC43A1, RRAS2, PBX3, NR4A2, MAP3K5, GRB7, CHRM3, CDX2, CD44"], ["Up", "43", "TWIST2, TFAP2C, TCF7, TBX3, T, SOX11, SIM2, SHOX2, RUVBL1", "51", "Oncogene: RUNX2, NRAS, NOV, NET1, MME, MLLT11, MAP3K8, MAFG, LAMC2, GNA12, FYN, FGF20"], ["", "", "RUNX2, REST, PRDM1, PITX2, PGR, NR0B1, NFAT5, MAFG, MAF, LEF1, KLF12, HOXC9, HOXC8, HOXC6, HOXC5, HOXC4, HOXB8, HOXB7, HOXB3, HEY2, HEY1, HAND2, HAND1, GTF2H2, GLI2", "", "Tumor Suppressor: ZBTB7C, WNT5A, WIF1, TWIST2, TMEM127, TMEFF2, THSD1, SOX11, RASL10B, PTPRG, PRDM1, PPP1R1B, MIR185, MCPH1, LSAMP, ISG15, HPGD, GLIPR1, FANCD2, DKK3, CSMD1, CNTNAP2, CDKN2D, CDH11, CABLES2, C10orf90, BIK, AXIN2, ARHGAP29, ARHGAP20"], ["", "", "GATA1, FUBP1, ETV5, ESRRG, EMX2, DR1, DBP, BARX2, AR", "", "Other: WNT2B, TPH1, TPD52L1, TFAP2C, PITPNA, OGG1, MCC, MAF, HOXC6"]], "row_count": 6, "column_count": 5, "numeric_cells": 12, "header_rows": 1, "locator": 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"section_index": 13, "section_title": "Gene functional annotation analysis", "row_count": 6, "column_count": 5}, "table": {"label": "Table III.", "caption": "Functional statistics of differentially expressed genes between solid pseudopapillary neoplasm and control samples.", "rows": [["Pattern", "TF counts", "TF genes", "TAG counts", "TAG genes"], ["Down", "31", "CDX2, EHF, ELF3, FOSB, FOXA2, FOXA3, FOXC1, FOXQ1, GATA4, HEYL, HHEX, HNF4G", "73", "Oncogene: CD24, CXCL1, EGFR, ELF3, ERBB3, FGFR1, FGFR3, GATA4, GFI1, GPX2, JUN, LCN2, MEIS1, MYC, SPHK1"], ["", "", "INSM1, ISL1, KCNIP3, KLF5, LMO3, MEIS1, NKX2.2, NKX2.5, NR4A2, NR5A2, ONECUT1, PAX6, PBX3, PDX1, PKNOX2, PLAGL1, SOX9, TEAD4, XBP1", "", "Tumor suppressor: WNK2, VIL1, UCHL1, TPM1, TFPI2, SYT13, STEAP3, SRPX, SIK1, SFRP5, SERPINI2, RAP1GAP, RAB25, PTPRK, PRKCDBP, PLK2, PLAGL1, PDX1, PDGFRL, PAX6, ONECUT1, NRCAM, MUC1, MTUS1, MT1G, MEG3, LPL, KLF5, KLF10, ID4, GNMT, GAS1, FOXC1, FOXA2, ERRFI1, EPHA1, ENC1, EHF, DEFB1, DAPK1, 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