OBJECTIVES: To survey the gene expression profiles in pancreatic carcinoma by using cDNA microarray and detect target genes for further study. METHODS: Three mixed samples from 2 cases of normal pancreatic tissue and ...OBJECTIVES: To survey the gene expression profiles in pancreatic carcinoma by using cDNA microarray and detect target genes for further study. METHODS: Three mixed samples from 2 cases of normal pancreatic tissue and 4 cases of moderate-differentiated pancreatic carcinoma were studied by means of cDNA microarray consisting of 18 000 genes. RESULTS: 1484 and 1353 different expressed genes were observed in two cancer samples respectively. We identified 455 genes altered with the same tendency in both samples, including 102 up-regulated and 353 down-regulated genes. There were 274 known genes and 181 unknown genes; 27.8% and 52.0% genes respectively had an expression level in cancer that was 2-fold higher or lower than that in normal samples. Tumor suppressor genes, growth factors and receptor genes, signal conduction genes, transcription factor genes were identified. CONCLUSIONS: cDNA microarray is an efficient and high-throughout method to investigate gene expression profiles in pancreatic carcinoma. MBD1, EDG1 and gene hypermethylation mechanism would play an important role in the pathogenesis of pancreatic carcinoma.展开更多
In this study, we extracted total RNA from 15 intracranial aneurysms and 17 superficial temporal artery samples, then performed genome-wide expression profiling using the Affymetrix U133 Plus 2.0 GeneChip. Genes that ...In this study, we extracted total RNA from 15 intracranial aneurysms and 17 superficial temporal artery samples, then performed genome-wide expression profiling using the Affymetrix U133 Plus 2.0 GeneChip. Genes that were differentially expressed between intracranial aneurysms and arterial samples were identified using significance analysis for microarrays, and the expression patterns of three randomly-selected genes were verified by real-time polymerase chain reaction analysis. We identified 3 736 differentially-expressed genes out of the 47 000 assayed transcripts. A total of 179 genes showed a 〉10-fold change in expression between the aneurysms and the arterial samples. Genes involved in the proliferation, migration, and apoptosis of vascular muscle cells, atherosclerosis, extracellular matrix disruption, and inflammatory reactions were associated with the formation of intracranial aneurysms. There were no significant differences in gene expression profile between unruptured and ruptured aneurysms.展开更多
Differential gene expression profiles in Balb/cJ mouse model of acute hepatic failure infected with MHV-3 virus intervened by anti-hepatic failure compound （AHFC） and the changes of cytokines regulated by genes were...Differential gene expression profiles in Balb/cJ mouse model of acute hepatic failure infected with MHV-3 virus intervened by anti-hepatic failure compound （AHFC） and the changes of cytokines regulated by genes were investigated. The Balb/cj mice were divided into AHFC-intervened group and control group randomly. Acute hepatic failure model of Balb/cJ mice infected with MHV-3 virus was established. The survival rate in the two groups was observed. It was found that the survival rate in the AHFC-intervened group and control group was 90% and 50% respectively 48 h after intraperitoneal injection of MHV-3 （P〈0.05）. Before and after the experiment, the cytokines in peripheral blood of the survival mice were determined, and RNA was extracted from survival mouse liver tissue for the analysis of the differential gene expression by a 36 kb mouse oligonuleotide DNA array. In all the genes of microarray there were 332 genes expressed differently in the two groups, in which 234 genes were up-regulated and 78 genes down-regulated. Through clustering analysis, the differential expression of immune related genes, including TNF receptor superfamily, Kctd9, Bcl-2, Fgl2, IL-8, IL-6, IFN-7, TNF-α etc. might be related with the curative effectiveness of AHFC. It was suggested that AHFC can balance the immune state of mouse model of acute hepatic failure infected with MHV-3 virus mainly through regulating the expression of immune related genes, decrease the immune damage and inhibit liver cell apoptosis of mouse acute hepatic failure model obviously so as to increase the survival rate of mouse models of acute hepatic failure.展开更多
AIM： To investigate the role of inflammatory and anti-vira genes in the pathogenesis of SARS. METHODS： cDNA microarrays were used to screen the gene expression profiles of peripheral blood mononuclear cells （PBMCs...AIM： To investigate the role of inflammatory and anti-vira genes in the pathogenesis of SARS. METHODS： cDNA microarrays were used to screen the gene expression profiles of peripheral blood mononuclear cells （PBMCs） in two SARS patients （one in the acute severe phase and the other in the convalescent phase） and a healthy donor. In addition, real-time qualitative PCR was also performed to verify the reproducibility of the microarray results. The data were further analyzed. RESULTS： Many inflammatory and anti-viral genes were differentially expressed in SARS patients. Compared to the healthy control or the convalescent case, plenty of pro-inflammatory cytokines such as IL-1, TNF-α, IL-8, and MAPK signaling pathway were significantly upregulated in the acute severe case. However, anti-inflammatory agents such as IL-4 receptor, IL-13 receptor, IL-1Ra, and TNF-α-induced proteins 3 and 6 also increased dramatically in the acute severe case. On the contrary, a lot of IFN-stimulated genes like PKR, GBP-1 and 2, CXCL-10 and 11, and JAK/STAT signal pathway were downregulated in the acute severe case compared to the convalescent case. CONCLUSION： Gene expression in SAPS patients mirrors a host state of inflammation and anti-viral immunity at the transcription level, and understanding of gene expression profiles may make contribution to further studies of the SAPS pathogenesis.展开更多
Objective To characterize the immune reaction in SD rats exposed to trichloroethylene （TCE） and to identify the gene expression profiles involved in skin after TCE exposure. Methods Fifteen percent of TCE was inject...Objective To characterize the immune reaction in SD rats exposed to trichloroethylene （TCE） and to identify the gene expression profiles involved in skin after TCE exposure. Methods Fifteen percent of TCE was injected intradermally into the rat back （100 μL/120 g） at intervals of 7 days. Whole blood was collected 24 h after the fifth or seventh intradermic administration of TCE. The percentages of CD4＋ and CD8＋ of T lymphocytes were measured by a flow cytometer. The concentrations of IFN-gamma and 1L-4 in the serum were semi-quantified by ELISA. Total RNAs of skin samples at 3 h or 24 h after the seventh dose of TCE in SD rats were extracted, and gene expression proftles of these tissues were analyszed by rat toxicology U34 array of Affymetrix. Results Obvious decline of CD4＋ in T lymphocytes was observed in the TCE-administer group. No significant concentration differences in IFN-gamma and IL-4 were found between TCE-treated and control rats. Gadd45a and Mel were significantly up regulated in skin tissue 24 h after TCE exposure. The expression regulation of immune response factors was as active as proteins associated with lipid metabolism and synthesis process in these skin samples of SD rats exposed to TCE. Conclusion T-helper type 1 cells mediate immune response can not be elicited in TCE-treated SD rats, but certain immune disorder can be induced.展开更多
The difference of gene expression profile changes in Barrett＇s esophagus （BE） and cardia intestinal metaplasia （CIM） epithelium was studied and the novel associated genes were screened in the early stage by cDNA ...The difference of gene expression profile changes in Barrett＇s esophagus （BE） and cardia intestinal metaplasia （CIM） epithelium was studied and the novel associated genes were screened in the early stage by cDNA microarray. The cDNA retro-transcribed from equal quantity mRNA from BE and CIM epithelial tissues were labeled with Cy3 and Cy5 fluorescence as probes. The mixed probe was hybridized with three pieces BiostarH-40s double dot human whole gene chip. The chips were scanned with a ScanArray 4000. The acquired images were analyzed using GenePix Pro 3.0 software. It was found a total of 141 genes were screened out that exhibited differentially expression more than 2 times in all three chips. It was identified that in gene expression profiles of BE, 74 genes were up-regulated and 67 down-regulated as compared with CIM. The comparison between the difference of gene expression profile changes in BE and CIM epithelia revealed that there existed the difference between BE and CIM at gene level. 141 genes with the expression more than two time were probably related to the occurrence and development of BE and the promotion or progress in adenocarcinoma.展开更多
Objective： The aim of this study was to investigate the characteristics of gene changes from Barrett＇s esophagus （BE） to esophageal adenocarcinoma by cDNA microarray. Methods： The cDNA retro-transcribed from equa...Objective： The aim of this study was to investigate the characteristics of gene changes from Barrett＇s esophagus （BE） to esophageal adenocarcinoma by cDNA microarray. Methods： The cDNA retro-transcribed from equal quantity mRNA from esophageal carcinoma and BE tissues as well as control normal epithelium of esophagus which were from one patient with esophageal adenocarcinoma were labeled with Cy5 and Cy3 fluorescence as probes. The mixed probes were hybridized with two pieces gene chip respectively. It was scanned by laser scanner Scan Array 4000. The acquired images were analyzed by software GenePix Pro 3.0. Results： A total of 214 genes were screened out which expression levels were more than 2 times in hybridization of esophageal adenocarcinoma vs normal epithelium of esophagus, whereas 90 genes in hybridization of BE vs normal epithelium. A parallel comparison among these two gene profiles showed that a total of 45 genes with 24 downregulation and 21 up-regulation which expression levels were more than 2 times between the BE and the esophageal adenocarcinoma. Among these, there were 27 genes with 18 downregulafion and 9 up-regulation which implicated the tendencies progressing from BE to esophageal adenocarcinoma. Conclusion： These genes or their products which implicate the tendencies can be chosen as indicators of carcinogenesis with high risk index for BE.展开更多
Diet factors may be potential causes for atrophic gastritis.This study is to establish rat atrophic gastritis models under various hot and salt water conditions and to explore the associated molecular mechanisms.96 SD...Diet factors may be potential causes for atrophic gastritis.This study is to establish rat atrophic gastritis models under various hot and salt water conditions and to explore the associated molecular mechanisms.96 SD rats were divided randomly into 4 experimental groups and used to establish atrophic gastritis models.2 rats from each group were sacrificed every other week to collect gastric sinus tissues for pathological analysis.When atrophic lesion was identified in a given group,all remaining rats in that group were sacrificed and gastric sinus tissues were collected.The cDNA probes from sinus atrophic lesion or control sinus mucous were labeled with Cy5 or Cy3,respectively.These probes were mixed and hybridized with cDNA microarrays.Hot salt water group was pathologically confirmed to exhibit atrophic lesion in 10 weeks.Salt water group and hot water group were confirmed to exhibit atrophic lesion in 24 weeks.The atrophic lesions located mainly in gastric sinus.288 differentially expressed genes were identified between hot salt water group and normal control group.162 differentially expressed genes were identified between hot water group and normal control group.81 differentially expressed genes were identified between hot salt water group and salt water group.In conclusion,rat atrophic gastritis models induced by various hot and salt water conditions have been established.The corresponding gene expression profiles have been firstly established.This study shows that dietary factors such as temperature and salt concentration may play an important role in the development of atrophic gastritis.展开更多
Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive...Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive thyroid-related cell lines cultured under simulated microgravity.Methods:Five thyroid-related cell lines—normal thyrocytes(Nthy-ori 3-1),papillary thyroid cancer(PTC)cells(SNU-790,TPC-1),poorly differentiated thyroid cancer cell(BCPAP),and anaplastic thyroid cancer cell(SNU-80)—were cultured under simulated microgravity(10-3 g)using a clinostat.Differentially expressed genes(DEGs)were analyzed using cDNA microarray,followed by functional annotation and assessment of aggressiveness via Transwell migration and invasion assays.Results:DEG analysis under simulated microgravity revealed distinct gene expression profiles by gravity condition,with 2980 DEGs in SNU-790,1033 in BCPAP,562 in TPC-1,477 in Nthy-ori 3-1,and 246 in SNU-80,as confirmed by hierarchical clustering.In PTC cell lines(SNU-790,TPC-1),G2–M phase–related genes were upregulated.In non-PTC cell lines(BCPAP,SNU-80),genes associated with innate immune response,Toll-like receptor signaling,were upregulated,whereas Hypoxia-Inducible Factor 1-alpha(HIF-1α)signaling-related genes were downregulated.Additionally,under simulated microgravity,significant migration was observed in SNU-790(3×104 cells)and BCPAP(2×104 and 3×104),while significant invasion occurred in SNU-790,Nthy-ori 3-1,and BCPAP at a seeding density of 2×104.Other conditions showed no significant differences.Conclusion:This study comprehensively evaluates the effects of simulated microgravity using a diverse panel of thyroid-related cell lines.Thesefindings provide valuable insight into how microgravity could influence cancer biology,emphasizing the importance of further research on cancer behavior in space environments and its implications for human health during long-term space missions.展开更多
Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyz...Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyzed the global gene expression profile of adipose-derived mesenchymal stem cells(ASCs)using microarray analysis and compared it with stromal vascular fraction(SVF)cells.Results:Microarray analysis revealed that ASCs express elevated levels of genes related to the extracellular matrix(ECM;extracellular matrix)and collagen,which are critical components of tissue remodeling and wound healing.Additionally,genes associated with cell growth,differentiation,motility,and plasticity were highly expressed.When compared to stromal vascular fraction(SVF)cells,ASCs demonstrated enrichment of genes involved in anti-inflammatory responses,immune modulation,tissue repair,cell adhesion,and migration processes.Gene Set Enrichment Analysis(GSEA;Gene Set Enrichment Analysis)showed activation of pathways related to angiogenesis,such as vascular endothelial growth factor(VEGF),Integrin,Wnt signaling pathways,transforming growth factor-beta(TGF-β),extracellular matrix(ECM),and matrix metalloproteinase(MMP),highlighting the significant angiogenic potential of ASCs.Gene Ontology(GO;Gene Ontology)analysis further linked ASCs to biological processes associated with the regulation of cell proliferation and muscle cell differentiation.Conclusion:These findings collectively underscore the suitability of adipose-derived mesenchymal stem cells(ASCs)as a promising candidate for regenerative medicine,particularly in applications involving tissue repair,immune modulation,and promotion of angiogenesis.展开更多
Background Early diagnosis and timely treatment are important for improving therapeutic efficiency of prostate cancer. DNA array is a new bio-technology for disease diagnosis. This study was conducted to diagnose pros...Background Early diagnosis and timely treatment are important for improving therapeutic efficiency of prostate cancer. DNA array is a new bio-technology for disease diagnosis. This study was conducted to diagnose prostate cancer with cDNA macroarray and analysis gene expression profiles of some selective genes in prostate cancer. Methods Total RNA was isolated from patients with prostate cancer and from normal people, and poly（A） RNA was further purified. Then it was analyzed for differentially expressed genes in prostate cancer and normal prostate by cDNA macroarray system. Results There were different expressions in the nine prostate-associated specific genes in prostate cancer as compared with normal prostate, in which, 7 were significantly upregulated and 2 were down-regulated. Conclusion As a diagnostic approach at molecular level, the cDNA macroarray is an effectively diagnostic method for orostate cancer.展开更多
Objective:To investigate the differential gene expression profiles in coronary heart disease(CHD) patients of blood-stasis syndrome(BSS) by oligonucleotide microarray technique,and the clinical significance of target ...Objective:To investigate the differential gene expression profiles in coronary heart disease(CHD) patients of blood-stasis syndrome(BSS) by oligonucleotide microarray technique,and the clinical significance of target gene.Methods:Subjects were assigned to CHD patients with BSS(n=8),CHD patients without BSS (n=8),and BSS patients without CHD(n=8) based on coronary angiography and the diagnostic criteria of BSS. The sex- and age-matched healthy volunteers(n=8) were enrolled as the control group.Venous blood s...展开更多
Clinical manifestations of rheumatoid arthritis(RA)are diversified,and based on the manifestations,the patients with RA could be classified into different patterns under traditional Chinese medicine.These patterns dec...Clinical manifestations of rheumatoid arthritis(RA)are diversified,and based on the manifestations,the patients with RA could be classified into different patterns under traditional Chinese medicine.These patterns decide the selection of herbal prescription,and thus they can help find a subset of rheumatoid arthritis patients for a type of therapy.In the present study,we combine genome-wide expression analysis with methods of systems biology to identify the functional gene networks for the sets of clinical symptoms that comprise the major information for pattern classification.Clinical manifestations in rheumatoid arthritis were clustered with factor analysis,and two factors(similar to cold and hot patterns in traditional Chinese medicine)were found.Microarray technology was used to reveal gene expression profiles in CD4^(+)T cells from 21 rheumatoid arthritis patients.Protein-protein interaction information for these genes from databases and literature data was searched.The highly-connected regions were detected to infer significant complexes or pathways in this protein-protein interaction network.The significant pathways and function were extracted from these subnetworks using the Biological Network Gene Ontology tool.The genes significantly related to hot and cold patterns were identified by correlations analysis.MAPK signalling pathway,Wnt signaling pathway,and insulin signaling pathway were found to be related to hot pattern.Purine metabolism was related to both hot and cold patterns.Alanine,aspartate,and tyrosine metabolism were related to cold pattern,and histindine metabolism and lysine degradation were related to hot pattern.The results suggest that cold and hot patterns in traditional Chinese medicine were related to different pathways,and the network analysis might be used for identifying the pattern classification in other diseases.展开更多
OBJECTIVE: To evaluate the clinical efficacy and safety of Shenzhu Guanxin recipe granules(参术冠心颗粒, SGR) in treating patients with intermediate coronary lesions(ICL), and to investigate the potential mechanism th...OBJECTIVE: To evaluate the clinical efficacy and safety of Shenzhu Guanxin recipe granules(参术冠心颗粒, SGR) in treating patients with intermediate coronary lesions(ICL), and to investigate the potential mechanism though a transcriptome sequencing approach. METHODS: ICL patients with Qi deficiency and phlegm stasis were adopted and randomly assigned to a case group or a control by random number generator in a 1∶1 randomization ratio to evaluate the clinical efficacy. RESULTS: There was no significant difference between the two groups in coronary computed tomography angiography related indexes in the two groups before and after intervention. Through the gene chip expression analysis, it is finally concluded that there are 355 differential mRNAs(190 up-regulated genes and 165 down regulated genes) when compared the SGR group and placebo group. Through protein-protein interaction network analysis of differentially expressed genes, 10 hub genes were finally obtained: CACNA2D2, CACNA2D3, DNAJC6, FGF12, SGSM2, CACNA1G, LRP6, KIF25, OXTR, UPB1. CONCLUSIONS: SGR combined with Western Medicine can be safely used to treat ICL patients with Qi deficiency and phlegm stasis. The possible mechanism of action and relevant gene loci and pathway were proposed.展开更多
Gene expression profiles of 14 common tumors and their counterpart normal tissues were analyzed with machine learning methods to address the problem of selection of tumor-specific genes and analysis of their different...Gene expression profiles of 14 common tumors and their counterpart normal tissues were analyzed with machine learning methods to address the problem of selection of tumor-specific genes and analysis of their differential expressions in tumor tissues.First,a variation of the Relief algorithm,"RFE_Relief algorithm"was proposed to learn the relations between genes and tissue types.Then,a support vector machine was employed to find the gene subset with the best classification performance for distinguishing cancerous tissues and their counterparts.After tissue-specific genes were removed,cross validation experiments were employed to demonstrate the common deregulated expressions of the selected gene in tumor tissues.The results indicate the existence of a specific expression fingerprint of these genes that is shared in different tumor tissues,and the hallmarks of the expression patterns of these genes in cancerous tissues are summarized at the end of this paper.展开更多
Objective: The effect of Chuanzhi Fang (ZGC) on the whole genome expression profile of RAW264.7 cells activated by lipopolysaccharide (LPS) was analyzed, and to explore the possible mechanism of action and core target...Objective: The effect of Chuanzhi Fang (ZGC) on the whole genome expression profile of RAW264.7 cells activated by lipopolysaccharide (LPS) was analyzed, and to explore the possible mechanism of action and core target of this formula on macrophage inflammatory injury at the overall level. Methods: A model of LPS-induced inflammation in RAW264.7 cells was constructed, and the effect of ZGC intervention on the genome-wide expression of inflammatory macrophages 3was examined by gene microarray technology, GO/KEGG enrichment analysis was performed for significantly differentially expressed genes among each group. Results: The results of genome-wide expression profiling microarray analysis showed that the ZGC intervention group upregulated the expression of 5 genes including C4bp and inhibited the expression of 22 genes including Mgat3, Psma6, and Siglecg relative to the LPS model group. KEGG signaling pathway analysis results showed that ZGC mainly acted through cytokine receptor interaction and the C-type lectin receptor signaling pathway. Conclusion: ZGC can interfere with the abnormal expression of 27 genes in inflammatory macrophages, and the related genes may exert corresponding anti-inflammatory effects by affecting cytokine receptor interactions, C-type lectin receptor signaling pathway, and TLR4/ NF-κB signaling pathway.展开更多
Objective： To study the effect of Tiantai No. 1 （天泰1号） on gene expression profile in hippocampus of Alzheimer＇s disease （AD） rat, molecular genetic target points of the effect of this drug were defined, its m...Objective： To study the effect of Tiantai No. 1 （天泰1号） on gene expression profile in hippocampus of Alzheimer＇s disease （AD） rat, molecular genetic target points of the effect of this drug were defined, its molecular genetic pharmacodynamic mechanism of anti-AD was further explored at molecular gene level, and a scientific basis was provided for its clinical availability and promotion. Methods： Thirty male Sprague- Dawley rats were divided into three groups with 10 rats per group： sham-operation group, model group and Tiantai No. 1 group. Sterile surgical procedure was applied, the model group with bilateral hippocampal injection of Aβ21-40 was established, and normal saline was used instead of Aβ1-40 in the sham-operation group. One week after the models was made, rats were administered by gastric lavage once every day for three consecutive weeks. The rats of the sham-operation group and the model group were daily fed with purified water by lavage; the rats of the Tiantai No.1 group treated group were administered with Tiantai No.1 by lavage. Total RNAs of hippocampus tissues were extracted with Trizol, the changes of hippocampus gene expression profiles in the above throe groups were analyzed by using Affymetrix rat whole genome expression profile microarray. Results： Microarray analysis showed that, compared with the sham-operation group, the hippocampus of the model group had 50 up-regulated genes with significant difference （fold change 〉2）, and 21 down-rogulated genes with significant difference （fold change 〈0.5）; compared with the hippocampus of the model group, the hippocampus of the Tiantai No. 1 group was found to have 5 up-regulated genes with significant difference （fold change 〉2） and 20 down-regulated genes with significant difference （fold change 〈0.5）. The functions of differonUally expressed genes of the groups were involved in nervous system＇s development, neuronic differentiation and function-regulation, cellular growth and differentiation and apoptosis, synaptic occurrence and plasticity, inflammation and immune response, ion channels/transporters, cellular signal transduction, cellular material/energy metabolism and so on. Conclusion： Tiantai No. 1 can regulate hippocampal function, and further regulate the brain function of animals in multiple gene target points by a number of ways.展开更多
[ Objective ] The aim of the research was to study the expression profile changes of genes involved in lipid metabolism pathway during liver regeneration in mice. [ Method] The CCI4 induced mouse model of liver regene...[ Objective ] The aim of the research was to study the expression profile changes of genes involved in lipid metabolism pathway during liver regeneration in mice. [ Method] The CCI4 induced mouse model of liver regeneration was established and the total RNA was isolated from liver tissue of mouse. Then the changes of genes involved in lipid metabolism pathway during different stages of liver regeneration were detected through micro-array chip gene technique and their specific functions were also analyzed. [ Result] Dudng the process of liver regeneration, the expression level of 98 genes involved in lipid metabolism pathway changed, which were divided into eight groups according to change trend. In the mass, the expression of genes was inhibited in the early stage and up-regulated in the late phase. And the gene expression associated with fatty acid synthesis pathway was mainly up-regulated while the catabolic pathway did not change significantly. Most of genes involved in bile acid synthesis pathway were suppressed before 4.5 d and up-regulated after 4.5 d or 7 d. [ Conclusion] During the process of liver regeneration, the genes associated with lipid metabolism are expressed in different trends, and this data should provide a specific range of genes for further studying the regulation effect of lipid metabolism related pathway on liver regeneration.展开更多
The detection of genes that show similar profiles under different experimental conditions is often an initial step in inferring the biological significance of such genes. Visualization tools are used to identify genes...The detection of genes that show similar profiles under different experimental conditions is often an initial step in inferring the biological significance of such genes. Visualization tools are used to identify genes with similar profiles in microarray studies. Given the large number of genes recorded in microarray experiments, gene expression data are generally displayed on a low dimensional plot, based on linear methods. However, microarray data show nonlinearity, due to high-order terms of interaction between genes, so alternative approaches, such as kernel methods, may be more appropriate. We introduce a technique that combines kernel principal component analysis （KPCA） and Biplot to visualize gene expression profiles. Our approach relies on the singular value decomposition of the input matrix and incorporates an additional step that involves KPCA. The main properties of our method are the extraction of nonlinear features and the preservation of the input variables （genes） in the output display. We apply this algorithm to colon tumor, leukemia and lymphoma datasets. Our approach reveals the underlying structure of the gene expression profiles and provides a more intuitive understanding of the gene and sample association.展开更多
文摘OBJECTIVES: To survey the gene expression profiles in pancreatic carcinoma by using cDNA microarray and detect target genes for further study. METHODS: Three mixed samples from 2 cases of normal pancreatic tissue and 4 cases of moderate-differentiated pancreatic carcinoma were studied by means of cDNA microarray consisting of 18 000 genes. RESULTS: 1484 and 1353 different expressed genes were observed in two cancer samples respectively. We identified 455 genes altered with the same tendency in both samples, including 102 up-regulated and 353 down-regulated genes. There were 274 known genes and 181 unknown genes; 27.8% and 52.0% genes respectively had an expression level in cancer that was 2-fold higher or lower than that in normal samples. Tumor suppressor genes, growth factors and receptor genes, signal conduction genes, transcription factor genes were identified. CONCLUSIONS: cDNA microarray is an efficient and high-throughout method to investigate gene expression profiles in pancreatic carcinoma. MBD1, EDG1 and gene hypermethylation mechanism would play an important role in the pathogenesis of pancreatic carcinoma.
基金supported by a grant from the National Natural Science Foundation of China(30830101/H0928)
文摘In this study, we extracted total RNA from 15 intracranial aneurysms and 17 superficial temporal artery samples, then performed genome-wide expression profiling using the Affymetrix U133 Plus 2.0 GeneChip. Genes that were differentially expressed between intracranial aneurysms and arterial samples were identified using significance analysis for microarrays, and the expression patterns of three randomly-selected genes were verified by real-time polymerase chain reaction analysis. We identified 3 736 differentially-expressed genes out of the 47 000 assayed transcripts. A total of 179 genes showed a 〉10-fold change in expression between the aneurysms and the arterial samples. Genes involved in the proliferation, migration, and apoptosis of vascular muscle cells, atherosclerosis, extracellular matrix disruption, and inflammatory reactions were associated with the formation of intracranial aneurysms. There were no significant differences in gene expression profile between unruptured and ruptured aneurysms.
基金This project was supported by a grant from Hubei Province Natural Sciences Foundation of China (No2007ABA114)
文摘Differential gene expression profiles in Balb/cJ mouse model of acute hepatic failure infected with MHV-3 virus intervened by anti-hepatic failure compound （AHFC） and the changes of cytokines regulated by genes were investigated. The Balb/cj mice were divided into AHFC-intervened group and control group randomly. Acute hepatic failure model of Balb/cJ mice infected with MHV-3 virus was established. The survival rate in the two groups was observed. It was found that the survival rate in the AHFC-intervened group and control group was 90% and 50% respectively 48 h after intraperitoneal injection of MHV-3 （P〈0.05）. Before and after the experiment, the cytokines in peripheral blood of the survival mice were determined, and RNA was extracted from survival mouse liver tissue for the analysis of the differential gene expression by a 36 kb mouse oligonuleotide DNA array. In all the genes of microarray there were 332 genes expressed differently in the two groups, in which 234 genes were up-regulated and 78 genes down-regulated. Through clustering analysis, the differential expression of immune related genes, including TNF receptor superfamily, Kctd9, Bcl-2, Fgl2, IL-8, IL-6, IFN-7, TNF-α etc. might be related with the curative effectiveness of AHFC. It was suggested that AHFC can balance the immune state of mouse model of acute hepatic failure infected with MHV-3 virus mainly through regulating the expression of immune related genes, decrease the immune damage and inhibit liver cell apoptosis of mouse acute hepatic failure model obviously so as to increase the survival rate of mouse models of acute hepatic failure.
基金Supported by the Grants From Shanghai Commission of Science and TechnologyShanghai Bureau of Health, No. 024Y32the grants from the Sino-German Center for Research Promotion, No.GZNr. 239(202/12)
文摘AIM： To investigate the role of inflammatory and anti-vira genes in the pathogenesis of SARS. METHODS： cDNA microarrays were used to screen the gene expression profiles of peripheral blood mononuclear cells （PBMCs） in two SARS patients （one in the acute severe phase and the other in the convalescent phase） and a healthy donor. In addition, real-time qualitative PCR was also performed to verify the reproducibility of the microarray results. The data were further analyzed. RESULTS： Many inflammatory and anti-viral genes were differentially expressed in SARS patients. Compared to the healthy control or the convalescent case, plenty of pro-inflammatory cytokines such as IL-1, TNF-α, IL-8, and MAPK signaling pathway were significantly upregulated in the acute severe case. However, anti-inflammatory agents such as IL-4 receptor, IL-13 receptor, IL-1Ra, and TNF-α-induced proteins 3 and 6 also increased dramatically in the acute severe case. On the contrary, a lot of IFN-stimulated genes like PKR, GBP-1 and 2, CXCL-10 and 11, and JAK/STAT signal pathway were downregulated in the acute severe case compared to the convalescent case. CONCLUSION： Gene expression in SAPS patients mirrors a host state of inflammation and anti-viral immunity at the transcription level, and understanding of gene expression profiles may make contribution to further studies of the SAPS pathogenesis.
基金This work was supported by "973" Project (No. 2002CB512903) and Shenzhen Bureau of Science and Technology, China (No. 200204121 No. 200304156).
文摘Objective To characterize the immune reaction in SD rats exposed to trichloroethylene （TCE） and to identify the gene expression profiles involved in skin after TCE exposure. Methods Fifteen percent of TCE was injected intradermally into the rat back （100 μL/120 g） at intervals of 7 days. Whole blood was collected 24 h after the fifth or seventh intradermic administration of TCE. The percentages of CD4＋ and CD8＋ of T lymphocytes were measured by a flow cytometer. The concentrations of IFN-gamma and 1L-4 in the serum were semi-quantified by ELISA. Total RNAs of skin samples at 3 h or 24 h after the seventh dose of TCE in SD rats were extracted, and gene expression proftles of these tissues were analyszed by rat toxicology U34 array of Affymetrix. Results Obvious decline of CD4＋ in T lymphocytes was observed in the TCE-administer group. No significant concentration differences in IFN-gamma and IL-4 were found between TCE-treated and control rats. Gadd45a and Mel were significantly up regulated in skin tissue 24 h after TCE exposure. The expression regulation of immune response factors was as active as proteins associated with lipid metabolism and synthesis process in these skin samples of SD rats exposed to TCE. Conclusion T-helper type 1 cells mediate immune response can not be elicited in TCE-treated SD rats, but certain immune disorder can be induced.
文摘The difference of gene expression profile changes in Barrett＇s esophagus （BE） and cardia intestinal metaplasia （CIM） epithelium was studied and the novel associated genes were screened in the early stage by cDNA microarray. The cDNA retro-transcribed from equal quantity mRNA from BE and CIM epithelial tissues were labeled with Cy3 and Cy5 fluorescence as probes. The mixed probe was hybridized with three pieces BiostarH-40s double dot human whole gene chip. The chips were scanned with a ScanArray 4000. The acquired images were analyzed using GenePix Pro 3.0 software. It was found a total of 141 genes were screened out that exhibited differentially expression more than 2 times in all three chips. It was identified that in gene expression profiles of BE, 74 genes were up-regulated and 67 down-regulated as compared with CIM. The comparison between the difference of gene expression profile changes in BE and CIM epithelia revealed that there existed the difference between BE and CIM at gene level. 141 genes with the expression more than two time were probably related to the occurrence and development of BE and the promotion or progress in adenocarcinoma.
文摘Objective： The aim of this study was to investigate the characteristics of gene changes from Barrett＇s esophagus （BE） to esophageal adenocarcinoma by cDNA microarray. Methods： The cDNA retro-transcribed from equal quantity mRNA from esophageal carcinoma and BE tissues as well as control normal epithelium of esophagus which were from one patient with esophageal adenocarcinoma were labeled with Cy5 and Cy3 fluorescence as probes. The mixed probes were hybridized with two pieces gene chip respectively. It was scanned by laser scanner Scan Array 4000. The acquired images were analyzed by software GenePix Pro 3.0. Results： A total of 214 genes were screened out which expression levels were more than 2 times in hybridization of esophageal adenocarcinoma vs normal epithelium of esophagus, whereas 90 genes in hybridization of BE vs normal epithelium. A parallel comparison among these two gene profiles showed that a total of 45 genes with 24 downregulation and 21 up-regulation which expression levels were more than 2 times between the BE and the esophageal adenocarcinoma. Among these, there were 27 genes with 18 downregulafion and 9 up-regulation which implicated the tendencies progressing from BE to esophageal adenocarcinoma. Conclusion： These genes or their products which implicate the tendencies can be chosen as indicators of carcinogenesis with high risk index for BE.
基金supported by Chinese foundamental basic research Project(2010CB933901and 2011CB933100)863 Key Project(2007AA022004)+2 种基金New Century Excellent Talent of Ministry of Education of China(NCET-08-0350 and No.20070248050)Special Infection Diseases Key Project of China(2009ZX10004-311)Shanghai Science and Technology Fund(10XD1406100 and 1052nm04100).
文摘Diet factors may be potential causes for atrophic gastritis.This study is to establish rat atrophic gastritis models under various hot and salt water conditions and to explore the associated molecular mechanisms.96 SD rats were divided randomly into 4 experimental groups and used to establish atrophic gastritis models.2 rats from each group were sacrificed every other week to collect gastric sinus tissues for pathological analysis.When atrophic lesion was identified in a given group,all remaining rats in that group were sacrificed and gastric sinus tissues were collected.The cDNA probes from sinus atrophic lesion or control sinus mucous were labeled with Cy5 or Cy3,respectively.These probes were mixed and hybridized with cDNA microarrays.Hot salt water group was pathologically confirmed to exhibit atrophic lesion in 10 weeks.Salt water group and hot water group were confirmed to exhibit atrophic lesion in 24 weeks.The atrophic lesions located mainly in gastric sinus.288 differentially expressed genes were identified between hot salt water group and normal control group.162 differentially expressed genes were identified between hot water group and normal control group.81 differentially expressed genes were identified between hot salt water group and salt water group.In conclusion,rat atrophic gastritis models induced by various hot and salt water conditions have been established.The corresponding gene expression profiles have been firstly established.This study shows that dietary factors such as temperature and salt concentration may play an important role in the development of atrophic gastritis.
文摘Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive thyroid-related cell lines cultured under simulated microgravity.Methods:Five thyroid-related cell lines—normal thyrocytes(Nthy-ori 3-1),papillary thyroid cancer(PTC)cells(SNU-790,TPC-1),poorly differentiated thyroid cancer cell(BCPAP),and anaplastic thyroid cancer cell(SNU-80)—were cultured under simulated microgravity(10-3 g)using a clinostat.Differentially expressed genes(DEGs)were analyzed using cDNA microarray,followed by functional annotation and assessment of aggressiveness via Transwell migration and invasion assays.Results:DEG analysis under simulated microgravity revealed distinct gene expression profiles by gravity condition,with 2980 DEGs in SNU-790,1033 in BCPAP,562 in TPC-1,477 in Nthy-ori 3-1,and 246 in SNU-80,as confirmed by hierarchical clustering.In PTC cell lines(SNU-790,TPC-1),G2–M phase–related genes were upregulated.In non-PTC cell lines(BCPAP,SNU-80),genes associated with innate immune response,Toll-like receptor signaling,were upregulated,whereas Hypoxia-Inducible Factor 1-alpha(HIF-1α)signaling-related genes were downregulated.Additionally,under simulated microgravity,significant migration was observed in SNU-790(3×104 cells)and BCPAP(2×104 and 3×104),while significant invasion occurred in SNU-790,Nthy-ori 3-1,and BCPAP at a seeding density of 2×104.Other conditions showed no significant differences.Conclusion:This study comprehensively evaluates the effects of simulated microgravity using a diverse panel of thyroid-related cell lines.Thesefindings provide valuable insight into how microgravity could influence cancer biology,emphasizing the importance of further research on cancer behavior in space environments and its implications for human health during long-term space missions.
基金supported through National Research Foundation(NRF)of Korea grants funded by the Korean Government(No.NRF-2022R1F1A1064405)the research fund of Catholic Kwandong University and Catholic Kwandong University International St.Mary’s Hospital for S.-W Kim.
文摘Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyzed the global gene expression profile of adipose-derived mesenchymal stem cells(ASCs)using microarray analysis and compared it with stromal vascular fraction(SVF)cells.Results:Microarray analysis revealed that ASCs express elevated levels of genes related to the extracellular matrix(ECM;extracellular matrix)and collagen,which are critical components of tissue remodeling and wound healing.Additionally,genes associated with cell growth,differentiation,motility,and plasticity were highly expressed.When compared to stromal vascular fraction(SVF)cells,ASCs demonstrated enrichment of genes involved in anti-inflammatory responses,immune modulation,tissue repair,cell adhesion,and migration processes.Gene Set Enrichment Analysis(GSEA;Gene Set Enrichment Analysis)showed activation of pathways related to angiogenesis,such as vascular endothelial growth factor(VEGF),Integrin,Wnt signaling pathways,transforming growth factor-beta(TGF-β),extracellular matrix(ECM),and matrix metalloproteinase(MMP),highlighting the significant angiogenic potential of ASCs.Gene Ontology(GO;Gene Ontology)analysis further linked ASCs to biological processes associated with the regulation of cell proliferation and muscle cell differentiation.Conclusion:These findings collectively underscore the suitability of adipose-derived mesenchymal stem cells(ASCs)as a promising candidate for regenerative medicine,particularly in applications involving tissue repair,immune modulation,and promotion of angiogenesis.
文摘Background Early diagnosis and timely treatment are important for improving therapeutic efficiency of prostate cancer. DNA array is a new bio-technology for disease diagnosis. This study was conducted to diagnose prostate cancer with cDNA macroarray and analysis gene expression profiles of some selective genes in prostate cancer. Methods Total RNA was isolated from patients with prostate cancer and from normal people, and poly（A） RNA was further purified. Then it was analyzed for differentially expressed genes in prostate cancer and normal prostate by cDNA macroarray system. Results There were different expressions in the nine prostate-associated specific genes in prostate cancer as compared with normal prostate, in which, 7 were significantly upregulated and 2 were down-regulated. Conclusion As a diagnostic approach at molecular level, the cDNA macroarray is an effectively diagnostic method for orostate cancer.
基金Supported by the Major Research Plan of National Natural Science Foundation of China(No.90409021)
文摘Objective:To investigate the differential gene expression profiles in coronary heart disease(CHD) patients of blood-stasis syndrome(BSS) by oligonucleotide microarray technique,and the clinical significance of target gene.Methods:Subjects were assigned to CHD patients with BSS(n=8),CHD patients without BSS (n=8),and BSS patients without CHD(n=8) based on coronary angiography and the diagnostic criteria of BSS. The sex- and age-matched healthy volunteers(n=8) were enrolled as the control group.Venous blood s...
基金supported in part by the projects from the Ministry of Sciences and Technology(International Collaboration Project)(No.2006DFA31731)the National Natural Science Foundation of China(Grant No.90709007,No.30825047)by the E-institutes of Shanghai Municipal Education Commission(No.E03008).
文摘Clinical manifestations of rheumatoid arthritis(RA)are diversified,and based on the manifestations,the patients with RA could be classified into different patterns under traditional Chinese medicine.These patterns decide the selection of herbal prescription,and thus they can help find a subset of rheumatoid arthritis patients for a type of therapy.In the present study,we combine genome-wide expression analysis with methods of systems biology to identify the functional gene networks for the sets of clinical symptoms that comprise the major information for pattern classification.Clinical manifestations in rheumatoid arthritis were clustered with factor analysis,and two factors(similar to cold and hot patterns in traditional Chinese medicine)were found.Microarray technology was used to reveal gene expression profiles in CD4^(+)T cells from 21 rheumatoid arthritis patients.Protein-protein interaction information for these genes from databases and literature data was searched.The highly-connected regions were detected to infer significant complexes or pathways in this protein-protein interaction network.The significant pathways and function were extracted from these subnetworks using the Biological Network Gene Ontology tool.The genes significantly related to hot and cold patterns were identified by correlations analysis.MAPK signalling pathway,Wnt signaling pathway,and insulin signaling pathway were found to be related to hot pattern.Purine metabolism was related to both hot and cold patterns.Alanine,aspartate,and tyrosine metabolism were related to cold pattern,and histindine metabolism and lysine degradation were related to hot pattern.The results suggest that cold and hot patterns in traditional Chinese medicine were related to different pathways,and the network analysis might be used for identifying the pattern classification in other diseases.
基金the project of Traditional Chinese Medicine Bureau of Guangdong Province:Research on the Mechanism of Shen Shu Guan Xin Fang in Reducing Hypoxia Induced Myocardial Cell Injury by Regulating miR-24 (No. 20221108)Science and Technology Projects in Guangzhou:Exploring the Intervention of Shenzhu Guanxin Formula on Myocardial Ischemia Based on MiR-24 Mediated Bim/Caspase Apoptosis Signal Pathway Mechanism Research (No. 202201010521)+1 种基金the Science and Technology Innovation Projects of Shenzhen:to Study the Mechanism of Hesperidin in Improving Heart Failure Based on Myocardial Inflammation Mediated by MtDNAs GAS-STING Signaling Pathway (No. JCYJ20220530144212026)Futian Healthcare Research Project:To Study the Anti-atherosclerosis Effects and Mechanism of Shenzhu Guanxin Decoction on Inhibiting Platelet-mediated Inflammation Based on the Theory of "Phlegm-stasis Interjunction"(No. FTWS2022012)。
文摘OBJECTIVE: To evaluate the clinical efficacy and safety of Shenzhu Guanxin recipe granules(参术冠心颗粒, SGR) in treating patients with intermediate coronary lesions(ICL), and to investigate the potential mechanism though a transcriptome sequencing approach. METHODS: ICL patients with Qi deficiency and phlegm stasis were adopted and randomly assigned to a case group or a control by random number generator in a 1∶1 randomization ratio to evaluate the clinical efficacy. RESULTS: There was no significant difference between the two groups in coronary computed tomography angiography related indexes in the two groups before and after intervention. Through the gene chip expression analysis, it is finally concluded that there are 355 differential mRNAs(190 up-regulated genes and 165 down regulated genes) when compared the SGR group and placebo group. Through protein-protein interaction network analysis of differentially expressed genes, 10 hub genes were finally obtained: CACNA2D2, CACNA2D3, DNAJC6, FGF12, SGSM2, CACNA1G, LRP6, KIF25, OXTR, UPB1. CONCLUSIONS: SGR combined with Western Medicine can be safely used to treat ICL patients with Qi deficiency and phlegm stasis. The possible mechanism of action and relevant gene loci and pathway were proposed.
基金supported in part by the National Natural Science Foundation of China(Grant No.60234020).
文摘Gene expression profiles of 14 common tumors and their counterpart normal tissues were analyzed with machine learning methods to address the problem of selection of tumor-specific genes and analysis of their differential expressions in tumor tissues.First,a variation of the Relief algorithm,"RFE_Relief algorithm"was proposed to learn the relations between genes and tissue types.Then,a support vector machine was employed to find the gene subset with the best classification performance for distinguishing cancerous tissues and their counterparts.After tissue-specific genes were removed,cross validation experiments were employed to demonstrate the common deregulated expressions of the selected gene in tumor tissues.The results indicate the existence of a specific expression fingerprint of these genes that is shared in different tumor tissues,and the hallmarks of the expression patterns of these genes in cancerous tissues are summarized at the end of this paper.
基金Chinese Academy of Traditional Chinese Medicine Autonomous Topic Selection Project(No.ZZ2018017)Research Development Fund Project of the Medical Experimental Center of the Chinese Academy of Traditional Chinese Medicine(No.FZ2023003)。
文摘Objective: The effect of Chuanzhi Fang (ZGC) on the whole genome expression profile of RAW264.7 cells activated by lipopolysaccharide (LPS) was analyzed, and to explore the possible mechanism of action and core target of this formula on macrophage inflammatory injury at the overall level. Methods: A model of LPS-induced inflammation in RAW264.7 cells was constructed, and the effect of ZGC intervention on the genome-wide expression of inflammatory macrophages 3was examined by gene microarray technology, GO/KEGG enrichment analysis was performed for significantly differentially expressed genes among each group. Results: The results of genome-wide expression profiling microarray analysis showed that the ZGC intervention group upregulated the expression of 5 genes including C4bp and inhibited the expression of 22 genes including Mgat3, Psma6, and Siglecg relative to the LPS model group. KEGG signaling pathway analysis results showed that ZGC mainly acted through cytokine receptor interaction and the C-type lectin receptor signaling pathway. Conclusion: ZGC can interfere with the abnormal expression of 27 genes in inflammatory macrophages, and the related genes may exert corresponding anti-inflammatory effects by affecting cytokine receptor interactions, C-type lectin receptor signaling pathway, and TLR4/ NF-κB signaling pathway.
基金Supported by the National Natural Science Foundation of China(No.39770890)Shenzhen Major Project of Science and Technology Planning,China(No.JCYJ20130401115231337)
文摘Objective： To study the effect of Tiantai No. 1 （天泰1号） on gene expression profile in hippocampus of Alzheimer＇s disease （AD） rat, molecular genetic target points of the effect of this drug were defined, its molecular genetic pharmacodynamic mechanism of anti-AD was further explored at molecular gene level, and a scientific basis was provided for its clinical availability and promotion. Methods： Thirty male Sprague- Dawley rats were divided into three groups with 10 rats per group： sham-operation group, model group and Tiantai No. 1 group. Sterile surgical procedure was applied, the model group with bilateral hippocampal injection of Aβ21-40 was established, and normal saline was used instead of Aβ1-40 in the sham-operation group. One week after the models was made, rats were administered by gastric lavage once every day for three consecutive weeks. The rats of the sham-operation group and the model group were daily fed with purified water by lavage; the rats of the Tiantai No.1 group treated group were administered with Tiantai No.1 by lavage. Total RNAs of hippocampus tissues were extracted with Trizol, the changes of hippocampus gene expression profiles in the above throe groups were analyzed by using Affymetrix rat whole genome expression profile microarray. Results： Microarray analysis showed that, compared with the sham-operation group, the hippocampus of the model group had 50 up-regulated genes with significant difference （fold change 〉2）, and 21 down-rogulated genes with significant difference （fold change 〈0.5）; compared with the hippocampus of the model group, the hippocampus of the Tiantai No. 1 group was found to have 5 up-regulated genes with significant difference （fold change 〉2） and 20 down-regulated genes with significant difference （fold change 〈0.5）. The functions of differonUally expressed genes of the groups were involved in nervous system＇s development, neuronic differentiation and function-regulation, cellular growth and differentiation and apoptosis, synaptic occurrence and plasticity, inflammation and immune response, ion channels/transporters, cellular signal transduction, cellular material/energy metabolism and so on. Conclusion： Tiantai No. 1 can regulate hippocampal function, and further regulate the brain function of animals in multiple gene target points by a number of ways.
文摘[ Objective ] The aim of the research was to study the expression profile changes of genes involved in lipid metabolism pathway during liver regeneration in mice. [ Method] The CCI4 induced mouse model of liver regeneration was established and the total RNA was isolated from liver tissue of mouse. Then the changes of genes involved in lipid metabolism pathway during different stages of liver regeneration were detected through micro-array chip gene technique and their specific functions were also analyzed. [ Result] Dudng the process of liver regeneration, the expression level of 98 genes involved in lipid metabolism pathway changed, which were divided into eight groups according to change trend. In the mass, the expression of genes was inhibited in the early stage and up-regulated in the late phase. And the gene expression associated with fatty acid synthesis pathway was mainly up-regulated while the catabolic pathway did not change significantly. Most of genes involved in bile acid synthesis pathway were suppressed before 4.5 d and up-regulated after 4.5 d or 7 d. [ Conclusion] During the process of liver regeneration, the genes associated with lipid metabolism are expressed in different trends, and this data should provide a specific range of genes for further studying the regulation effect of lipid metabolism related pathway on liver regeneration.
文摘The detection of genes that show similar profiles under different experimental conditions is often an initial step in inferring the biological significance of such genes. Visualization tools are used to identify genes with similar profiles in microarray studies. Given the large number of genes recorded in microarray experiments, gene expression data are generally displayed on a low dimensional plot, based on linear methods. However, microarray data show nonlinearity, due to high-order terms of interaction between genes, so alternative approaches, such as kernel methods, may be more appropriate. We introduce a technique that combines kernel principal component analysis （KPCA） and Biplot to visualize gene expression profiles. Our approach relies on the singular value decomposition of the input matrix and incorporates an additional step that involves KPCA. The main properties of our method are the extraction of nonlinear features and the preservation of the input variables （genes） in the output display. We apply this algorithm to colon tumor, leukemia and lymphoma datasets. Our approach reveals the underlying structure of the gene expression profiles and provides a more intuitive understanding of the gene and sample association.
