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Contemporary high-throughput experimental and surveying techniques give rise to ultrahigh-dimensional supervised problems with sparse signals; that is, a limited number of observations (n), each with a very large number of covariates (p >> n), only a small share of which is truly associated with the response. In these settings, major concerns on computational burden, algorithmic stability, and statistical accuracy call for substantially reducing the feature space by eliminating redundant covariates before the use of any sophisticated statistical analysis. Along the lines of Sure Independence Screening (Fan and Lv, 2008) and other model- and correlation-based feature screening methods, we propose a model-free procedure called Covariate Information Number - Sure Independence Screening (CIS). CIS uses a marginal utility connected to the notion of the traditional Fisher Information, possesses the sure screening property, and is applicable to any type of response (features) with continuous features (response). Simulations and an application to transcriptomic data on rats reveal the comparative strengths of CIS over some popular feature screening methods.
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ObjectiveTo study the transcript atlas of cell immunity-associated genes in 8 liver cell types including hepatocytes, bile duct epithelial cells, oval cells, hepatic stellate cells, sinus endothelial cells, Kupffer cells, pit cells and dendritic cells from the rat regenerating liver. Methods The 8 liver cell types were isolated respectively by Percoll density gradient centrifugation combined with immune magnetic beads separation method. Their expression changes in the regenerating livers were detected by Rat Genome 230 2.0 Array, the expression patterns and the predicted physiological activities of cell immunity-associated genes were analyzed by Cluster program, and the methods of bioinformation and systematic biology. Results A total of 40 cell immunity-associated genes yielded the meaningful expression changes in liver regeneration, the corresponding gene numbers in 8 liver cell types were 19, 19, 9, 19, 19, 21, 22 and 21, respectively. It suggested that the formation of antigen peptide-MHC complexes, the NF-κB kinase activity and the production of cytokines like IL-2 were enhanced at the priming and progressing phases of liver regeneration. The biological activities, such as NF-κB-promoting cell differentiation and caspase-induced T cell apoptosis, were elevated at termination phase.Conclusion The rat liver regeneration is associated with cell immunity.
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ObjectiveTo explore the correlation of unknown gene AI408225 and humoral immunity involved in rat regenerating liver. MethodsIsolation of rat 8 liver cell types, detection of their genes expression change were accorded to Percoll density gradient centrifugation combined with immune magnetic beads separation method, and their genes sequence homoeology and coexpression relation were analyzed by Microsoft Excel, BLAST software, and the prediction physiological activities were analyzed by bioinformatics and systematic biology. Results A total of 93 humoral immunity-ass ociated genes yielded the meaningful expression changes in liver regeneration, the corresponding gene numbers in 8 liver cell types included hepatocytes, bile duct epithelial cells, oval cells, hepatic stellate cells, sinus endothelial cells, Kupffer cells, pit cells and dendritic cells were 33, 46, 17, 59, 48, 35, 53, 68. Among that AI408225 and cd4 are homology and coexpression.Conclusion The rat liver regeneration is closely associated with humoral immunity, and AI408225 participates in the formation of compound of MHC II-antigen peptide-CD4-TCR.
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ObjectiveTo study the transcript atlas of cell immunity-associated genes in 8 liver cell types including hepatocytes, bile duct epithelial cells, oval cells, hepatic stellate cells, sinus endothelial cells, Kupffer cells, pit cells and dendritic cells from the rat regenerating liver. Methods Isolation of rat 8 liver cell types, detection of their genes expression change and the prediction physiological activities were accorded to cluster program, and the methods of bioinformation and systematic biology, and their gene expression patterns were analyzed by Microsoft Excel software. Results A total of 40 blood coagulation-associated genes yielded the meaningful expression changes in liver regeneration. Serpine1, a2m in eight liver cell types, vwf, klkb1 in seven liver cell types other than Kupffer cells, and other genes in the two or more liver cell types yielded the meaningful expression changes. It suggested that the synthesis of kallikrein and prothrombin、the formation of thrombin were enhanced at the priming and progressing phases of liver regeneration. The biological activities, such as fibrin monomer aggregated into fibrin polymers, were elevated at termination phase.Conclusion The rat liver regeneration is closely associated with the blood coagulation.
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Objective To investigate the possible contribution of PPAR-? coupled signaling pathways to rat liver regeneration (LR) at transcription level.Methods The above signaling pathways-related genes were obtained by collecting database data and retrieving pertinent literatures. The gene expression during LR was checked by Rat Genome 230 2.0 array, and LR-associated genes were identified by comparing difference between partial hepatectomy (PH) and operation control (OC) groups.Results Sixty four genes were found to be LR-associated. The number of initially and totally expressed genes occurring in initiation phase of LR, G0/G1 transition, cell proliferation, cell differentiation and structure-function reconstruction was 28, 4, 34, 2 and 72, 41, 247, 90 respectively. Classification of their expression patterns into 11 groups reflected diversity and complexity of gene expression alteration in LR. Conclusion PPAR-? coupled signaling pathways may promote glycogen synthesis in forepart, prophase and anaphase of LR, cell proliferation and migration in the whole LR, while inhibits inflammation during LR.
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Objective To study the function of liver stem cells during at liver regeneration(LR) at transcriptional level.Methods The liver stem cell growth-and differentiation-related genes were obtained by data collection and literature review,and the gene expressions in rat regenerating liver were checked by Rat Genome 230 2.0 array.The relativity of the LR-associated genes was identified by comparing the discrepancy of gene expression changes between partial hepatectomy(PH) group and sham operation(SO) group.Results Fifty genes were found to be related with liver regeneration.The initial and total expressing gene numbers occurring in the initiation phase of liver regeneration(0.5-4 hours after PH),G_0/G_1 transition(4-6 hours after PH),cell proliferation(6-66 hours after PH),cell differentiation and structure-function reconstruction(72-168 hours after PH) were 24,10,21,2 and 24,23,46,26 respectively,indicating that the related genes were mainly triggered during the initiation phase,and worked at different phases.The total frequencies of their up-and down-regulation expression were 153 and 123 respectively,demonstrating that the expression of the major genes increased,and the minority decreased.Their expression profiles were classified into 6 types,indicating that the activities mentioned above were diverse and complicated during liver regeneration.Conclusion The growth and differentiation of liver stem cells are enhanced during liver regeneration.
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Objective To investigate the actions of apoptotic pathways in rat liver regeneration(LR) at the transcription level.Methods The apoptosis genes were obtained by referring to the putative literatures and databases.Apoptotic-related genes expression profiles in rat LR were checked by Rat Genome 230 2.0 array.Identification of LR-associated genes was made by comparing the discrepancies of genes expression between partial hepatectomied(PH) and sham operatied(SO) rats.Results 252 genes were found to be related to liver regeneration.The initial and total expressing gene numbers occurring in the initiation phase of liver regeneration(0.5-4hours after PH),G_0/G_1 transition(4-6hours after PH),cell proliferation(6-66hours after PH),cell differentiation and structure-function reconstruction(72-168hours after PH) were 81,23,155,16 and 161,100,733,192 respectively.This demonstrated that LR-related genes primarily started their expression in the initiation phase,and worked in the different phases.The total times of their up-and down-regulated expression were 795 and 291,demonstrating that expression of most genes was enhanced in LR.Their expression patterns could be classified into 35 types,indicating the expressions of apoptosis-related genes in LR were diverse and complicated.Conclusion There are fifteen kinds of apoptosis pathways that associate to apoptosis regulation in the regenerating liver.
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Objective To study the function of the genes regulating sex determination and differentiation during liver regeneration at transcriptional level.Methods The genes regulating sex determination and differentiation were obtained by referring to the theses and collecting the data of databases at NCBI,GENMAPP,KEGG,BIOCARTA and RGD,and their function and expression changes in rat liver regeneration were analysized by the Rat Genome 230 2.0 array.Results The initial and total expressed gene numbers in the starting phase of liver regeneration [half to four hours after partial hepatectomy(PH)],G_0/G_1 transition(4 to 6 hours after PH),cell proliferation 6 to 66 hours after PH),cell differentiation and tissue structural function reconstruction(72 to 160 hours after PH) were 41,6,18,3 and 41,25,57,41 respectively,which showed that the related genes were mainly triggered in the starting phase,and worked in different phases.Their expression similarity was classified into 5 groups:only up-,predominantly up-,only down-predominantly down-,up-/down-regulation,involving 22,9,15,9 and 7 genes respectively,and the total frequencies of their up-and down-regulation expressions were 231 and 146 respectively,demonstrating that the expression of the major genes was increased,and the minority decreased.Their expression time relevance was classified into 15 groups,showing that the cellular physiological and biochemical activities were phase related during liver regeneration.The gene expression patterns were classified into 20 types,indicating the diversity and complexity of the cellular physiological and biochemical activity.Conclusion The genes regulating male determination,male and female differentiation are enhanced mainly in the late early phase and prophase of liver regeneration,and the genes regulating female determination are enhanced mainly in the prophase.The function of the genes is closely related to liver regeneration.
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Objective To elucidate the action of carbohydrates metabolism-associated genes on rat liver regeneration(LR). Methods We obtained the above genes through collecting website data and retrieving related articles,and detected their expression changes in rat LR with Rat Genome 230 2.0 array,then determined LR-associated genes by comparison of gene expression discrepancy between partial hepatectomy(PH) group and sham operation(SO) group. Results 118 carbohydrates metabolism genes were proved to be LR-associated.Number of the initial and total expressing genes occurring in forepart(0.5-4 hours after PH),prophase(6-12 hours after PH),metaphase(16-66 hours after PH) and anaphase(72-168 hours after PH),were 33,6,68,7 and 68,44,210,83,respectively,demonstrating that expression of these genes were triggered mainly at the initial stage of LR,and functioned in different phases.The number of their up-regulation and down-regulation was 205 and 200,and their expression patterns were classified into 12 types,implying that the cellular Carbohydrate metabolism during LR were characterized by diversity and complication.Monosaccharides and glycogen metabolism-associated genes,glycoprotein and glycosphingolipid(mainly gangliosides) biosynthesis-associated genes were up-regulated almost in the whole LR.In contrast,oligosaccharides and glycosaminoglycans biosynthesisassociated genes,glycoprotein and glycosphingolipid degradation-associated genes were down regulated.Conclusion Liver regeneration was closely related to carbohydrate metabolism.
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Objective To realize the expression changes and patterns of lipid metabolism and transport-related genes in rat liver regeneration(LR) at transcriptional level. Methods Genes involved in lipid metabolism and transport were obtained by retrieving the databases data and the related papers.The gene expression changes during LR was checked by Rat Genome 230 2.0 array,and LR-associated genes were identified by comparing gene expression difference between partial hepatectomy(PH) and sham operation(SO) groups. Results One hundred ninety three genes were found to be LR-associated.The number of initially and totally expressed genes occurring in forepart(0.5-4 hours after PH) of LR,prophase(6-12 hours after PH),metaphase(12-66 hours after PH),and anaphase(72-168 hours after PH) was 113,20,66,1 and 250,205,796,293,respectively.The number of their up-regulation and down-regulation was 852 and 630 times,and their expression profiles were classified into 27 types.The subdued transcription levels occur to the bile acid metabolism-involved genes in forepart and prophase of LR;the elevated transcription levels occur to the glucocorticoid catabolism-involved genes in forepart and anaphase;phospholipids synthesis-involved genes were up-regulated in prophase and metaphase,while phospholipids catabolism-involved genes were down-expressed;fatty acid,leukotriene and glycosphingolipid synthesis-involved genes,triglyceride and phosphatidylinositol metabolism-involved genes were up-regulated in metaphase,while glycosphingolipid catabolism-involved genes were down-expressed;the elevated transcription levels occur to the prostaglandin synthesis and fatty acid catabolism-involved genes in metaphase and anaphase;during almost the whole period of LR,genes participating in sex hormone,glucocorticoid and progesterone synthesis,sphingomyelin metabolism and lipid transport were up-regulated,while cholesterol metabolism-involved genes were down-expressed.Conclusion Lipid metabolism and transport during LR were diverse,and they were tightly related with LR.
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Objective To study the expression changes and profiles of nuclear structure and biogenesis-related genes in rat liver regeneration(LR). Methods Genes involved in nuclear structure and biogenesis were obtained by data collection and literature review.The gene expression changes during LR were checked by Rat Genome 230 2.0 array,and LR-related genes were identified by comparing gene expression difference between partial hepatectomy(PH) and sham operation(SO) groups.Results 406 genes were found to be LR-related.The numbers of initially and totally expressed genes occurring in the forepart(0.5-4 hours after PH) of LR,the prophase(6-12 hours after PH),the metaphase(12-66 hours after PH),and the anaphase(72-168 hours after PH) were 200,29,179,5 and 374,290,1?876,603,respectively.The numbers of their up-regulation and down-regulation were 1?224 and 496 times.The elevated transcription levels occur red to the nuclear organization and biogenesis-involved genes in the prophase and the metaphase of LR and to the nuclear membrane,nuclear matrix and nucleoplasm-involved genes in the metaphase;nuclear chromosome,nucleolus and nuclear functional protein complex-involved genes were up-regulated in the metaphase and the anaphase.Conclusion The expression of nuclear structure and biogenesis-related genes was active during LR,and it was tightly related with LR.
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Objective To study the expression changes of transcription factor genes and their underlying involvement in rat liver regeneration(LR) at transcription level. Methods The transcription factor genes and their function were collected by referring to the putative literatures and databases.Then,their expression in rat LR were checked by Rat Genome 230 2.0 array.LR-related genes were identified through the comparison of discrepancies in gene expression between partial hepatectomy(PH) and sham-operation(SO) groups. Results 320 genes were determined to be LR-related,which were involved in 16 biological processes,such as cellular metabolism,proliferation,differentiation,apoptosis,etc.Expression profiles of above genes were classified into 41 categories according to their functions and expression trends,implying their diversity and complexity during LR.The expression of transcription factor genes that were involved in carbohydrate biosynthesis,lipid metabolism,and inflammatory response was enhanced in the forepart(0.5-4 hours after PH) and prophase(6-12 hours after PH) of LR.Cellular proliferation,growth,differentiation and apoptosis related transcription factor genes were promoted in the metaphase(16-66 hours after PH) and anaphase(72-168 hours after PH).Conclusion Physiological and biochemical activities in LR were regulated by multiple transcription factor genes,and e2f1,fos,copeb,etc.played key roles in it.
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Objective To study the expression changes and patterns of nucleic acid and their derivative metabolism,processing and transport-related genes in rat liver regeneration(LR) at transcriptional level. Methods The related genes were obtained by online data collection and literature review,and gene expression patterns in rat regenerated liver were checked by Rat Genome 230 2.0 array.LR-related genes were identified through the comparison of discrepancles in gene expression between partial hepatectomy(PH) and sham operation(SO) groups. Results 240 genes were determined to be related with liver regeneration.The number of initially expressive genes in the forepart of liver regeneration(0.5-4 hours after PH),prophase(6-12 hours after PH),metaphase(16-66 hours after PH),anaphase(72-168 hours after PH) were 65,14,150,11 respectively and the total expression numbers were 133,87,627,169 respeitirely.There were 6,5,22 and 9 expression patterns.Frequencies of up-regulation and down-regulation were 768 and 248.mRNA catabolism in prophase and metaphase,DNA recombination,modification and transcript,mRNA processing and transport in prophase,metaphase and anaphase,and nucleotides and their derivatives metabolism,as well as DNA replication,packaging and catabolism during the whole LR,were enhanced.Conclusion LR-related genes were mainly triggered in the forepart of liver regeneration,and funclioned at different phases.
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Objective To address the expression correlation of ribosome-related genes in rat regeneration liver(RL) and those in liver tumor at transcriptional level.Methods Genes involved in ribosome biogenesis,assembly and function,as well as their expression changes in liver tumor,were obtained by online data collection and literature review,and their expression profiles in rat regenerating liver were detected by Rat Genome 230 2.0 array.Expression similarities and differences of the above genes were analyzed using statistical methods. Results A total of 75 genes were found to be RL-related.In regenerated liver and liver tumor,the expressions of 18 genes increased and 6 genes decreased,and no significant expression changes were found in 51 genes in liver tumor.Conclusion The expression profiles of the ribosome-related genes in regenerated liver cells and liver tumor cells have both similarities and differences,and the former exhibit properties of more gradualness and complexity.
