Screening of Genes Co-Associated with Sudden Infant Death Syndrome and Infectious Sudden Death in Infancy and Bioinformatics Analysis of Their Regulatory Networks / 法医学杂志

OBJECTIVES@#The common differentially expressed mRNAs in brain, heart and liver tissues of deceased sudden infant death syndrome (SIDS) and infectious sudden death in infancy (ISDI) confirmed by autopsy was screened by bioinformatics to explore the common molecular markers and pathogenesis of SIDS and ISDI.@*METHODS@#The datasets of GSE70422 and GSE136992 were downloaded, the limma of R software was used to screen differentially expressed mRNA in different tissue samples of SIDS and ISDI decedents for overlapping analysis. The clusterProfiler of R software was used to conduct gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The protein-protein interaction (PPI) network was constructed by STRING database, while the hub gene was screened by cytoHubba plug-in.@*RESULTS@#Compared with the control group, there were 19 significant differentially expressed genes in the tissue samples of SIDS and ISDI decedents, among which 16 in the heart tissue and 3 in the liver tissue, and the astrotactin 1 (ASTN1) gene expression difference in the heart tissue was most significant. The PPI network identified Ras homolog family member A (RHOA), integrin subunit alpha 1 (ITGA1), and H2B clustered histone 5 (H2BC5) were hub genes. The analysis of GO and KEGG showed that differentially expressed genes were enriched in the molecular pathways of actin cytoskeleton regulation, focal adhesion and response to mycophenolic acid.@*CONCLUSIONS@#ASTN1, RHOA and ITGA1 may participate in the development of SIDS and ISDI. The enrichment of differentially expressed genes in immune and inflammatory pathways suggests a common molecular regulatory mechanism between SIDS and ISDI. These findings are expected to provide new biomarkers for molecular anatomy and forensic identification of SIDS and ISDI.

Identification and validation of novel biomarkers for cold-dampness syndrome of rheumatoid arthritis based on integration of multiple bioinformatics methods / 中国中药杂志

This study aims to identify the novel biomarkers of cold-dampness syndrome(RA-Cold) of rheumatoid arthritis(RA) by gene set enrichment analysis(GSEA), weighted gene correlation network analysis(WGCNA), and clinical validation. Firstly, transcriptome sequencing was carried out for the whole blood samples from RA-Cold patients, RA patients with other traditional Chinese medicine(TCM) syndromes, and healthy volunteers. The differentially expressed gene(DEG) sets of RA-Cold were screened by comparison with the RA patients with other TCM syndromes and healthy volunteers. Then, GSEA and WGCNA were carried out to screen the key DEGs as candidate biomarkers for RA-Cold. Experimentally, the expression levels of the candidate biomarkers were determined by RT-qPCR for an independent clinical cohort(not less than 10 cases/group), and the clinical efficacy of the candidates was assessed using the receiver operating characteristic(ROC) curve. The results showed that 3 601 DEGs associated with RA-Cold were obtained, including 106 up-regulated genes and 3 495 down-regulated genes. The DEGs of RA-Cold were mainly enriched in the pathways associated with inflammation-immunity regulation, hormone regulation, substance and energy metabolism, cell function regulation, and synovial pannus formation. GSEA and WGCNA showed that recombinant proteasome 26S subunit, ATPase 2(PSMC2), which ranked in the top 50% in terms of coefficient of variation, representativeness of pathway, and biological modules, was a candidate biomarker of RA-Cold. Furthermore, the validation results based on the clinical independent sample set showed that the F1 value, specificity, accuracy, and precision of PSMC2 for RA-Cold were 70.3%, 61.9%, 64.5%, and 81.3%, respectively, and the area under the curve(AUC) value was 0.96. In summary, this study employed the "GSEA-WGCNA-validation" integrated strategy to identify novel biomarkers of RA-Cold, which helped to improve the TCM clinical diagnosis and treatment of core syndromes in RA and provided an experimental basis for TCM syndrome differentiation.

Expression and prognostic significance of cell division cycle associated protein 5 in pancreatic cancer tissues / 肿瘤研究与临床

Objective:To analyze the expression of cell division cycle associated protein 5 (CDCA5) in pancreatic cancer tissues and its correlation with prognosis based on the bioinformatics.Methods:The RNA sequencing data (HTSeq-FPKM) and corresponding clinical information of 168 pancreatic cancer samples from January to December 2021 were downloaded from the Cancer Genome Atlas (TCGA) database, and the data of 179 pancreatic patients from January to December 2021 were downloaded from the GEPIA2 database, and 171 normal pancreatic tissues from TCGA and GTEx databases were simultaneously integrated. The relative expression level of CDCA5 mRNA in pancreatic cancer patients in GEPIA2 database and its relationship with overall survival (OS) and disease-free survival (DFS) were explored. Combined with the clinical data of the patients, univariate and multivariate Cox regression model analysis was used to analyze the factors influencing the OS of pancreatic cancer patients. Gene set enrichment analysis (GSEA) was performed to investigate the possibly involved signal pathways of CDCA5 in pancreatic cancer.Results:In the GEPIA2 database, the relative expression level of CDCA5 mRNA in pancreatic cancer tissues was higher than that in normal pancreatic tissues, and the difference was statistically significant ( P < 0.05). The pancreatic cancer patients were divided into the high CDCA5 mRNA expression group (89 cases) and the low CDCA5 mRNA expression group (89 cases) according to the median of relative expression level of CDCA5 mRNA (the case equal to the median value was not subgrouped). Survival analysis showed that patients with high CDCA5 mRNA expression had shorter OS ( P = 0.024) and DFS ( P = 0.025) compared with those with low CDCA5 mRNA expression. Multivariate Cox analysis showed that in TCGA database, N staging ( HR = 2.15, 95% CI 1.24-3.72, P = 0.006) and CDCA5 expression ( HR = 1.71, 95% CI 1.23-2.38, P = 0.001) were independent influencing factors of OS for pancreatic cancer patients. The results of GSEA enrichment analysis indicated that high CDCA5 mRNA expression was enriched in 13 biological pathways [all P < 0.05, false discovery rate (FDR) < 0.005] including cell cycle, DNA replication, homologous recombination, pyrimidine metabolism, mismatch repair, pentose phosphate pathway, glycolysis gluconeogenesis and p53. The expression of CDCA5 mRNA was positively correlated with the expressions of HK2, PKM, PGK1, ALDOA, EN01 and LDHA (all P < 0.05). Conclusions:CDCA5 is highly expressed in pancreatic cancer tissues and is associated with poor prognosis of patients, and it can be used as a prognostic marker for pancreatic cancer.

Construction of a Prognostic Model of Multiple Myeloma Based on Metabolism-Related Genes / 中国实验血液学杂志

OBJECTIVE@#To screen the prognostic biomarkers of metabolic genes in patients with multiple myeloma (MM), and construct a prognostic model of metabolic genes.@*METHODS@#The histological database related to MM patients was searched. Data from MM patients and healthy controls with complete clinical information were selected for analysis.The second generation sequencing data and clinical information of bone marrow tissue of MM patients and healthy controls were collected from human protein atlas (HPA) and multiple myeloma research foundation (MMRF) databases. The gene set of metabolism-related pathways was extracted from Molecular Signatures Database (MSigDB) by Perl language. The biomarkers related to MM metabolism were screened by difference analysis, univariate Cox risk regression analysis and LASSO regression analysis, and the risk prognostic model and Nomogram were constructed. Risk curve and survival curve were used to verify the grouping effect of the model. Gene set enrichment analysis (GSEA) was used to study the difference of biological pathway enrichment between high risk group and low risk group. Multivariate Cox risk regression analysis was used to verify the independent prognostic ability of risk score.@*RESULTS@#A total of 8 mRNAs which were significantly related to the survival and prognosis of MM patients were obtained (P<0.01). As molecular markers, MM patients could be divided into high-risk group and low-risk group. Survival curve and risk curve showed that the overall survival time of patients in the low-risk group was significantly better than that in the high risk group (P<0.001). GSEA results showed that signal pathways related to basic metabolism, cell differentiation and cell cycle were significantly enriched in the high-risk group, while ribosome and N polysaccharide biosynthesis signaling pathway were more enriched in the low-risk group. Multivariate Cox regression analysis showed that the risk score composed of the eight metabolism-related genes could be used as an independent risk factor for the prognosis of MM patients, and receiver operating characteristic curve (ROC) showed that the molecular signatures of metabolism-related genes had the best predictive effect.@*CONCLUSION@#Metabolism-related pathways play an important role in the pathogenesis and prognosis of patients with MM. The clinical significance of the risk assessment model for patients with MM constructed based on eight metabolism-related core genes needs to be confirmed by further clinical studies.

Bioinformatics analysis of gene expression profile of peripheral blood mononuclear cells in female patients with osteoarthritis / 西安交通大学学报(医学版)

【Objective】 Through bioinformatics methods to analyze the differences in the gene expression profiles of peripheral blood mononuclear cells （PBMCs） between middle-aged and elderly women and normal people， so as to explore the diagnosis and treatment targets of OA. 【Methods】 We downloaded the GSE48556 data set from GEO databases. We utilized the R language to screen out the differentially expressed genes （DEGs） between OA and NC. By gene set enrichment analysis （GSEA）， we obtained the target gene subset. The GO and KEGG pathways of the target gene subset were analyzed by DAVID. We applied STRING and Cytoscape software to construct PPI network. The module analysis was performed by the Mcode and centiscape plug-in， and the key genes were screened out by Cytohubba. 【Results】 By GSEA analysis and P.adjust 0.2， a total of 292 target genes were screened， consisting of 81 upregulated genes and 211 downregulated genes. The GO enrichment analysis of all target genes mainly focused on the biological functions， such as “regulation of NIK/NF-κB”， “monocytes”， “proliferation”， “regulation of apoptosis signaling pathway”， “TNF-mediated signaling pathway”， “regulation of Wnt signaling pathway”， “regulation of MAP kinase activity”， and “regulation of autophagy”. KEGG was mainly enriched in four pathways： cytotoxicity of natural killer cell mediation， TNF signaling pathway， MAPK signaling pathway， and apoptosis. We employed PPI network and related plug-ins to screen out eight core genes highly related to OA inflammation and apoptosis， namely， MAPK1， IL10， PTGS2， IL18， GSK3B， NFKBIA， TNFRSF1A， and EGR1. 【Conclusion】 Bioinformatics analysis revealed that the differences in PBMCs gene expressions between OA and NC were concentrated in the biological events of apoptosis and inflammation， making blood expression profile an effective breakthrough for monitoring OA target markers.

Clinical importance of screening differential gene set of monocytes based on single-cell sequencing and digital polymerase chain reaction technology for early diagnosis of sepsis / 中华危重病急救医学

Objective:To verify the specific differentiated subsets of monocytes in sepsis, and to screen and construct the differential gene set of monocytes used for early diagnosis of sepsis.Methods:Patients with sepsis admitted to Guangdong Provincial People's Hospital from June 2020 to March 2021 were enrolled, and peripheral blood mononuclear cells (PBMC) were extracted. Single-cell sequencing technology and pseudo-time analysis were used to verify the differential subsets of monocytes. Bioinformatics methods were used to analyze the expression of genes in differential subsets of monocytes and screen out differential genes for the preliminary construction of a candidate differential gene set. The digital polymerase chain reaction (PCR) technology was used to verify the candidate differential genes in PBMC of sepsis patients and sepsis human myeloid leukemia mononuclear cells (THP-1) models, and the Venn diagram was used to construct the final differential gene set of monocytes. Gene Expression Omnibus (GEO) database was used to validate the differential gene set of monocytes.Results:① The results of cell annotation and pseudo-time analysis showed that the differentiation of NEAT1 +CD163 + monocyte occurred in the early stage of sepsis was significantly different from other subsets, which validated that NEAT1 +CD163 + monocyte was the characteristic subset in the pathological process of sepsis. ② Twenty-two differential genes related to sepsis were screened out from the gene expression of NEAT1 +CD163 + monocyte. After further verification by digital PCR, basic leucine zipper ATF-like transcription factor (BATF), JUNB proto-oncogene, carcinoembryonic antigen-related cell adhesion molecule 4 (CEACAM4), chromosome 9 open reading frame 95 (C9orf95), G protein subunit alpha 15 (GNA15), complement C3a receptor 1 (C3AR1), transforming growth factor beta 1 (TGFB1) and mitochondrial carrier homolog 1 (MTCH1) were screened out to construct the final differential gene set of monocytes. ③ The external validation results showed that C9orf95 gene had no data in GSE154918 and GSE133822 from GEO, it was excluded during validation. In GSE154918, the expressions of BATF, JUNB, CEACAM4, GNA15, C3AR1, TGFB1, and MTCH1 in the sepsis group were significantly higher than those in the healthy control group (log 2expression level: BATF was 12.78±0.08 vs. 11.39±0.35, JUNB was 16.88±0.07 vs. 16.04±0.03, CEACAM4 was 14.73±0.08 vs. 13.77±0.05, GNA15 was 13.16±0.06 vs. 12.30±0.04, C3AR1 was 14.62±0.13 vs. 12.87±0.05, TGFB1 was 16.95±0.05 vs. 16.57±0.36, MTCH1 was 14.80±0.02 vs. 14.61±0.15, all P < 0.05). In GSE133822, the expressions of BATF, CEACAM4, GNA15, and C3AR1 in the sepsis group were significantly higher than those in the health control group (log 2expression level: BATF was 8.66±0.16 vs. 7.92±0.14, CEACAM4 was 9.20±0.16 vs. 8.36±0.20, GNA15 was 10.66±0.18 vs. 10.13±0.16, C3AR1 was 11.49±0.27 vs. 10.48±0.16, all P < 0.05), while the expressions of JUNB, TGFB1, and MTCH1 were not statistically different between two groups. The results of gene set variation analysis (GSVA) showed that the enrichment scores of monocytes differential gene set of sepsis group were significantly higher than those of the healthy control group in both GSE154918 (0.38±0.04 vs. -0.44±0.02) and GSE133822 (0.56±0.02 vs. 0.20±0.05, both P < 0.01). Receiver operator characteristic curve (ROC curve) analysis showed that the differential gene set of monocytes had a reliable diagnostic value for early sepsis with the area under ROC curve (AUC) of 0.993 [95% confidence interval (95% CI) was 0.980-1.000] in GSE154918 and 0.944 (95% CI was 0.873-1.000) in GSE133822. Conclusion:A differential gene set of monocytes (BATF, JUNB, CEACAM4, GNA15, C3AR1, TGFB1, and MTCH1) screened out by single-cell sequencing and digital PCR technology has a reliable diagnostic value for the early sepsis, and may provide a new idea for the early diagnosis of sepsis.

Analysis on Gene Set Enrichment of Related Signaling Pathways and Immune Infiltration in Intracranial Aneurysm / 中国实验方剂学杂志

Objective::Based on gene array technology, gene set enrichment analysis (GSEA) and immune infiltration analysis were performed on chip data of intracranial aneurysm (IA) mRNA expression profile, in order to provide theoretical basis for understanding the formation mechanism of IA. Method::The GSE75436 raw data were obtained from the gene expression omnibus (GEO). GSEA of biological process (BP) in gene ontology (GO) and Kyoto gene and genome encyclopedia (KEGG) signaling pathways were analyzed for gene expression profile by R software. The CIBERSORT deconvolution method was used to analyze the infiltration ratio of 22 types of immune cells in the expression profile. And COREMINE database was used to predict traditional Chinese medicines (TCMs), which were significant correlation with the enrichment result. Result::The GSEA results showed that the changes in gene expression of IA samples mainly involved in the regulation of cytokines, activation and differentiation of leukocyte, inflammatory immune response and other processes. The infiltration matrix analysis of immune cells showed that mast cells resting and neutrophils were significantly reduced in IA samples. The comparison of paired samples showed that mast cells and natural killer cells (NK cells) were significantly activated in the IA samples of the same individual, while neutrophils and T cells CD4 naive were significantly reduced. Through COREMINE prediction, it was found that Stephaniae Tetrandrae Radix was correlated with the activation of granulocytes, Sapindi Mukorossi Semen and Pistaciae Chinensis Cortex were correlated with the activation of neutrophils, Trichosanthis Semen, Paeoniae Radix Alba and Ligustri Lucidi Fructus were correlated with the cytotoxicity mediated by NK cells. Conclusion::Activation of mast cells and NK cells are closely associated with the occurrence and development of IA. The inflammatory immune processes and pathways such as nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) signaling pathway and cytotoxicity mediated by NK cells may be important factors in the pathogenesis of IA, and TCMs such as Stephaniae Tetrandrae Radix may be the potential molecular drug sources.

Bioinformatics analysis of ulcerative colitis and its malignant complications and screening of potential therapeutic drugs / 上海交通大学学报（医学版）

Objective: To explore the pathogenic genes and potential drug therapeutic targets of ulcerative colitis and its malignant complications by a variety of bioinformatics analysis. Methods: Four expression profiling datasets (GSE13367, GSE9452 and GSE36807 as UC group, and GSE37283 as UCN group) downloaded from the Gene Expression Omnibus (GEO) database were jointly analyzed to identify the differential genes. Key genes related to ulcerative colitis and its malignant complications were obtained by subsequent immunoassay and gene correlation analysis, and a number of small molecule drugs with potential therapeutic effects were screened by LINCS L1000 database. Results: Eighty-six and 253 significant differentially expressed genes were identified respectively in the differential gene analysis of UC group and UCN group. The scoring analysis of the node genes in protein-protein interaction (PPI) network of UC group showed that the core gene of the network was CXCL8. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis indicated that CXCL8 mainly participated in the recruitment of neutrophils in IL-17 signaling pathway, and three small molecule drugs (butein, levocetirizine, pseudoephedrine) for CXCL8 were found based on the screening results of LINCS L1000 database. Conclusion: The core differentially expressed gene CXCL8 may be a new drug target for the treatment of ulcerative colitis and its malignant complications. The three screened small molecule drugs may have potential treatment effect on ulcerative colitis and its malignant complications.

Gene set enrichment analysis of alpha-glucosidase inhibitors from Ficus benghalensis

Objective: To identify alpha-glucosidase inhibitors from Ficus benghalensis and analyze gene set enrichment of regulated protein molecules. Methods: The phytoconstituents of Ficus benghalensis were queried for inhibitors of alpha-glucosidase, also identified as aldose reductase inhibitors. Druglikeness score, absorption, distribution, metabolism, excretion and toxicity profile, biological spectrum, and gene expression were predicated for each compound. Docking study was performed to predict the binding affinity with alpha-glucosidase and aldose reductase and compared with clinically proven molecules. Kyoto Encyclopedia of Genes and Genomes pathway analysis was performed for the regulated genes to identify the modulated pathways. Results: Apigenin, 3,4',5,7-tetrahydroxy-3'-methoxyflavone, and kaempferol were identified as inhibitors of alpha-glucosidase and aldose reductase. Kaempferol was predicted to possess the highest binding affinity with both targets. The p53 signaling pathway was predicted to modulate the majority of protein molecules in diabetes mellitus. All the alpha-glucosidase inhibitors were also predicted as membrane integrity agonist and anti-mutagenic compounds. Conclusions: The current study indicates alpha-glucosidase inhibitors from Ficus benghalensis can act as aldose reductase inhibitors after absorption from the intestinal tract. Furthermore, these phytoconstituents are involved in the regulation of numerous protein molecules and pathways. Hence, the anti-diabetic efficacies of these compounds are due to their action on multiple protein molecules and synergistic effects which should be confirmed by future investigations.

Gene set enrichment analysis of alpha-glucosidase inhibitors from Ficus benghalensis

Objective: To identify alpha-glucosidase inhibitors from Ficus benghalensis and analyze gene set enrichment of regulated protein molecules. Methods: The phytoconstituents of Ficus benghalensis were queried for inhibitors of alpha-glucosidase, also identified as aldose reductase inhibitors. Druglikeness score, absorption, distribution, metabolism, excretion and toxicity profile, biological spectrum, and gene expression were predicated for each compound. Docking study was performed to predict the binding affinity with alpha-glucosidase and aldose reductase and compared with clinically proven molecules. Kyoto Encyclopedia of Genes and Genomes pathway analysis was performed for the regulated genes to identify the modulated pathways. Results: Apigenin, 3,4',5,7-tetrahydroxy-3'-methoxyflavone, and kaempferol were identified as inhibitors of alpha-glucosidase and aldose reductase. Kaempferol was predicted to possess the highest binding affinity with both targets. The p53 signaling pathway was predicted to modulate the majority of protein molecules in diabetes mellitus. All the alpha-glucosidase inhibitors were also predicted as membrane integrity agonist and anti-mutagenic compounds. Conclusions: The current study indicates alpha-glucosidase inhibitors from Ficus benghalensis can act as aldose reductase inhibitors after absorption from the intestinal tract. Furthermore, these phytoconstituents are involved in the regulation of numerous protein molecules and pathways. Hence, the anti-diabetic efficacies of these compounds are due to their action on multiple protein molecules and synergistic effects which should be confirmed by future investigations.

Expression of FN1 in gastric cancer and its clinical significance / 医学研究生学报

Objective Fibronectin 1 (FN1) is a glycoprotein involved in cellular adhesion and migration processes. The aim of this study was to investigate the expression and clinicopathological significance of FN1 in gastric cancer and to predict the possible mechanism of FN1. Methods GEO data and TCGA data were downloaded. FN1 expression in gastric cancer and adjacent tissues was analyzed by GSE54129 data, and then verified by GSE29272 and TCGA data. According to the expression profile data and FN1 expression, mRNA expression value was divided into low expression(<-0.475), and medium expression(-0.475~1.036), high expression (>1.036). FN1 expression in gastric cancer and clinicopathological relationship were analyzed. TCGA data and Kaplan Meier were used to analyze the relationship between the expression level of FN1 and the prognosis of gastric cancer patients; while gene concentration analysis (GSEA) was used to predict the related path of FN1. Results TCGA data showed the medium survival time of low, medium, high FN1 expression was respectively 63.5, 55.7, 39.4 months, and the difference between low expression and high expression in survival time was of statistical significance. Kaplan Meier Plotter online data analysis showed the medium survival time of FN1 high expression was shorter than that of low expression(P<0.01), which meant the higher the FN1 expression was, the worse the prognosis was. FN1 expression is an independent prognostic factor (HR=0.480,95% CI:0.336~0.686). High expression of FN1 samples enriched gene sets such as KRAS (FDR=0.052), P53(FDR=0.052), TGF-β(FDR=0.052), cell adhesion(FDR=0.0), extracellular matrix (FDR=0.043)and cytoskeletal protein regulation (FDR=0.052). Conclusion The high expression of FN1 is a poor prognostic factor for gastric cancer and can be used as an effective biomarker for predicting the metastasis and prognosis of gastric cancer. High expression of FN1 leads to abnormalities in KRAS, P53, TGF-β, ECM, cell adhesion and cytoskeletal protein regulatory pathways.

The association between axon guidance pathway single nucleotide polymorphisms and susceptibility to schizophrenia / 中华行为医学与脑科学杂志

Objective To investigate the susceptibility related sites to schizophrenia through whole genome analysis combined with bioinformatics analysis method.Methods The research was carried out by two stages.In the first stage,300 cases of schizophrenia and 300 healthy controls were enrolled,and 5ml pe-ripheral venous blood was drawn to extract genome DNA.After quality control and concentration adjustment by ultraviolet spectrophotometer,equal mass of DNA was mixed into DNA pooling for case group and control group respectively.Genome-Wide Human SNP Array 6.0 chips were used to detect the polymorphism of the SNP.Plink software was used to locate the differential SNP to genes.GSEA was used to analyze the gene to pathway.Ten loci with the smallest P value of screened pathway were chosen as investigated subjects.In the second stage,240 schizophrenias and 200 healthy controls were collected to gain the genome DNA to verity the genotype of the 10 loci.Results Many single nucleotide polymorphism loci which P<9.2×10-8were found in GWAS.The GSEA pathway analysis showed that the axon guidance pathway was significantly related to the incidence of schizophrenia.The distribution of rs4632195 genotypes involved the distribution of among 10 loci(χ2=11.484,P=0.003)and alleles(χ2=8.824,P=0.009)were statistically significant,and T al-lele was susceptibility genes of schizophrenia(OR=1.537,95%CI:1.157-2.203).Conclusion rs4632195 of DCC gene in the axon guidance pathway is associated with schizophrenia,and the T allele is associated with susceptibility to schizophrenia.

Differential analysis of gene expression profiles for lymphonode metastasis of colon cancer / 临床检验杂志

Objective To investigate the differences in the gene expression profiles between SW480 and SW620 cell lines.Methods A dataset of GDS756 containing the gene expression profiles of SW480 and SW620 was downloaded from the GEO database in NCBI.The differential expression genes between SW480 and SW620 were analyzed with gene set enrichment analysis (GSEA) and leading edge subset analysis.The genes in leading edge subset were re-annotated by FunRich software.The core genes of leading edge subset closely relating to SW480 or SW620 were analyzed with the STRING on-line analytical system.The functional core genes closely relating to SW480 or SW620 were obtained by the combined analysis of the core genes and high frequency genes from leading edge subset.Results GSEA identified 12 significantly enriched gene sets,491 leading edge genes and 7 highly overlapping genes from SW480 and 80 significantly enriched gene sets,870 leading edge genes and 6 highly overlapping genes from SW620.The STRING system identified 5 core genes from SW480 and 8 from SW620.The combined analysis of GSEA and bionetwork obtained 2 functional core genes,TOP2A and CDK1,from SW620.Conclusion The SW480 and SW620 cells with identical genetic background have different functional gene expression profiles,and the functional core genes TOP2A and CDK1 in SW620 cells may be related to the signal pathways of colon cancer metastasis.

Analysis of Gene Expression in Human Dermal Fibroblasts Treated with Senescence-Modulating COX Inhibitors

We have previously reported that NS-398, a cyclooxygenase-2 (COX-2)–selective inhibitor, inhibited replicative cellular senescence in human dermal fibroblasts and skin aging in hairless mice. In contrast, celecoxib, another COX-2–selective inhibitor, and aspirin, a non-selective COX inhibitor, accelerated the senescence and aging. To figure out causal factors for the senescence-modulating effect of the inhibitors, we here performed cDNA microarray experiment and subsequent Gene Set Enrichment Analysis. The data showed that several senescence-related gene sets were regulated by the inhibitor treatment. NS-398 up-regulated gene sets involved in the tumor necrosis factor β receptor pathway and the fructose and mannose metabolism, whereas it down-regulated a gene set involved in protein secretion. Celecoxib up-regulated gene sets involved in G2M checkpoint and E2F targets. Aspirin up-regulated the gene set involved in protein secretion, and down-regulated gene sets involved in RNA transcription. These results suggest that COX inhibitors modulate cellular senescence by different mechanisms and will provide useful information to understand senescence-modulating mechanisms of COX inhibitors.

Gene Set Analyses of Genome-Wide Association Studies on 49 Quantitative Traits Measured in a Single Genetic Epidemiology Dataset

Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP) genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO) terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait (pcorr < 0.05). Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.

Analysis of gene expression during odontogenic differentiation of cultured human dental pulp cells

OBJECTIVES: We analyzed gene-expression profiles after 14 day odontogenic induction of human dental pulp cells (DPCs) using a DNA microarray and sought candidate genes possibly associated with mineralization. MATERIALS AND METHODS: Induced human dental pulp cells were obtained by culturing DPCs in odontogenic induction medium (OM) for 14 day. Cells exposed to normal culture medium were used as controls. Total RNA was extracted from cells and analyzed by microarray analysis and the key results were confirmed selectively by reverse-transcriptase polymerase chain reaction (RT-PCR). We also performed a gene set enrichment analysis (GSEA) of the microarray data. RESULTS: Six hundred and five genes among the 47,320 probes on the BeadChip differed by a factor of more than two-fold in the induced cells. Of these, 217 genes were upregulated, and 388 were down-regulated. GSEA revealed that in the induced cells, genes implicated in Apoptosis and Signaling by wingless MMTV integration (Wnt) were significantly upregulated. CONCLUSIONS: Genes implicated in Apoptosis and Signaling by Wnt are highly connected to the differentiation of dental pulp cells into odontoblast.

Performance Comparison of Two Gene Set Analysis Methods for Genome-wide Association Study Results: GSA-SNP vs i-GSEA4GWAS

Gene set analysis (GSA) is useful in interpreting a genome-wide association study (GWAS) result in terms of biological mechanism. We compared the performance of two different GSA implementations that accept GWAS p-values of single nucleotide polymorphisms (SNPs) or gene-by-gene summaries thereof, GSA-SNP and i-GSEA4GWAS, under the same settings of inputs and parameters. GSA runs were made with two sets of p-values from a Korean type 2 diabetes mellitus GWAS study: 259,188 and 1,152,947 SNPs of the original and imputed genotype datasets, respectively. When Gene Ontology terms were used as gene sets, i-GSEA4GWAS produced 283 and 1,070 hits for the unimputed and imputed datasets, respectively. On the other hand, GSA-SNP reported 94 and 38 hits, respectively, for both datasets. Similar, but to a lesser degree, trends were observed with Kyoto Encyclopedia of Genes and Genomes (KEGG) gene sets as well. The huge number of hits by i-GSEA4GWAS for the imputed dataset was probably an artifact due to the scaling step in the algorithm. The decrease in hits by GSA-SNP for the imputed dataset may be due to the fact that it relies on Z-statistics, which is sensitive to variations in the background level of associations. Judicious evaluation of the GSA outcomes, perhaps based on multiple programs, is recommended.

Comparative Evaluation of Gene-set Analysis Methods / 中国卫生统计

Objective To compare the efficiency of χ~2-Fisher's exact test which is one of the competitive null hypothesis approaches with SAM-GS which belongs toself-contained null hypothesis approaches. Methods The two methods were used to analyze a simulation experiment which contained five different scenarios. The results were compared with the simulated initialization,and assessing indexes were calculated to compare the efficiency. Results Under the same conditions,SAM-GS always have higher power than that of χ~2-fisher's exact test. However, the final inference is equivalent, namely if the difference between the two groups are smaller than 0.30,the two methods can not be better to identify differences between them. By contrary, when the differences between the two phenotypes are larger than 0.30, the two ways can both identify differences. Conclusion SAM-GS tends to have slightly higher power thanχ~2-Fisher' s exact test. The two methods can be used for screening enrichment gene sets of gene expression profile.χ~2-Fisher's exact test has the important advantage of being able to analyze multi-class phenotype.

GSnet: An Integrated Tool for Gene Set Analysis and Visualization

The Gene Set network viewer (GSnet) visualizes the functional enrichment of a given gene set with a protein interaction network and is implemented as a plug-in for the Cytoscape platform. The functional enrichment of a given gene set is calculated using a hypergeometric test based on the Gene Ontology annotation. The protein interaction network is estimated using public data. Set operations allow a complex protein interaction network to be decomposed into a functionally-enriched module of interest. GSnet provides a new framework for gene set analysis by integrating a priori knowledge of a biological network with functional enrichment analysis.