Renormalized GSE3889 by using the parametric method
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE24948 | GEO | 2010/11/17
SECONDARY ACCESSION(S): PRJNA142721
REPOSITORIES: GEO
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Project description:Each of the channel data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). http://www.super-norm.com/eng/index.html ABS_CALL: A, affected severely by noise; M, marginal; P, plausible.
2010-11-17 | GSE24950 | GEO
Project description:Effects of soy isoflavones, genistein and daidzein, on the hepatic gene expression profile and indices for lipid metabolism were compared in rats. The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data.
2012-10-10 | GSE41420 | GEO
Project description:The effects of freeze-dried tofu, a traditional Japanese soy food, were compared with those of major active soy components, protein and isoflavone, by observing physiological differences and global transcriptomes in the liver of male rats. The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data.
2011-08-27 | GSE23748 | GEO
Project description:Effects of soy isoflavones, genistein and daidzein, on the hepatic gene expression profile and indices for lipid metabolism were compared in rats. The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data. Three groups of rats were fed with an experimental diet containing 2 g/kg of either genistein or daidzein, or a control diet free of isoflavone for 14 days. The basal composition of the experimental diet was (in g/kg): casein, 200; palm oil, 100; corn starch, 150; cellulose, 20; mineral mixture (AIN-93G), 35; vitamin mixture (AIN-93), 10; L-cystine, 3.0; choline bitartrate, 2.0 and sucrose to 1 kg.
2012-10-10 | E-GEOD-41420 | biostudies-arrayexpress
Project description:Soyfoods have been drawn the interrest in the roles that reducing risk of cardiovascular disease. Among various components, isoflavones have been come to the attention as beneficial soy ingredients. To evaluate the effectiveness of isoflavone content in dietary soybean (Glycine max) on modulating lipid metabolism, hepatic gene expressions involved in lipid metabolism were analyzed in rats. An isoflavone-rich cultivar (Yukipirika) and a conventional cultivar (Fukuyutaka) were employed. A principal component analysis (PCA) of microarray data was used to summarize characteristics of the experimental groups. As a result, the characteristics of the diets were largely explained by the first principal component (PC1). Soybean content in the diets distinctly separated in PC1. In contrast, isoflavone content had little effect on the mRNA expression. The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data.
2016-08-01 | GSE67782 | GEO
Project description:The effects of freeze-dried tofu, a traditional Japanese soy food, were compared with those of major active soy components, protein and isoflavone, by observing physiological differences and global transcriptomes in the liver of male rats. The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data. Rats were randomly divided into 6 groups of 5 samples and assigned experimental diets for 14 days. The experimental diets were as follows: casein diet (C); C containing isoflavone (CI) soy protein diet (S); S containing isoflavone (SI); a diet containing 100 g/kg each of protein derived from casein and freeze-dried tofu (T10); a diet containing 200 g/kg of protein derived from freeze-dried tofu (T20). CI and SI were supplemented with a mixture of isoflavones to match the isoflavone level of T20.
2011-08-26 | E-GEOD-23748 | biostudies-arrayexpress
Project description:Soybean and fish contains various active components that were reported to prevent cardiovasucular diseases. Epidemiological studies indicated that Asian eating patterns, consisting of daily seafood and/or soy consumption, confer protection against cardiovascular diseases. In this context, we expected that simultaneous intake of soybean and fish may be greatly beneficial in a manner different from the ingestion of the individual food. To understand the detailed mechanism for modulating the lipid metabolism by co-ingestion of a soy food (tofu) and fish oil, we investigated the global changes in hepatic mRNA expression in rats by using a microarray analysis. Generally, ingestion of tofu contributed to prevent the mRNA expressions involved in hepatic lipogenesis, whereas fish oil facilitated the mRNA expressions related to the degradation of hepatic fatty acids. In terms of mRNA expression, the interaction of two dietary factors was limited. The expression data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data.
2015-09-01 | GSE66371 | GEO
Project description:Soyfoods have been drawn the interrest in the roles that reducing risk of cardiovascular disease. Among various components, isoflavones have been come to the attention as beneficial soy ingredients. To evaluate the effectiveness of isoflavone content in dietary soybean (Glycine max) on modulating lipid metabolism, hepatic gene expressions involved in lipid metabolism were analyzed in rats. An isoflavone-rich cultivar (Yukipirika) and a conventional cultivar (Fukuyutaka) were employed. A principal component analysis (PCA) of microarray data was used to summarize characteristics of the experimental groups. As a result, the characteristics of the diets were largely explained by the first principal component (PC1). Soybean content in the diets distinctly separated in PC1. In contrast, isoflavone content had little effect on the mRNA expression. The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data. Male Splague-Dawley rats were randomly divided into 4 groups and fed an experimental diet for 21 days. The experimental diets were as follows: a diet containing 200 g/kg casein (Cas, n=7); a diet containing two proteins derived equally from casein and Fukuyutaka (conventional cultiver soybean) (F10, n=7); a diet containing two proteins derived from casein and Yukipirika (high-isoflavone soybean) in the proportion of three parts to one (Y05, n=7); a diet containing two proteins derived equally from casein and Yukipirika (Y10, n=8). In each of the groups, five rats with average food intake were used for microarray analysis.
2016-08-01 | E-GEOD-67782 | biostudies-arrayexpress
Project description:Soybean and fish contains various active components that were reported to prevent cardiovasucular diseases. Epidemiological studies indicated that Asian eating patterns, consisting of daily seafood and/or soy consumption, confer protection against cardiovascular diseases. In this context, we expected that simultaneous intake of soybean and fish may be greatly beneficial in a manner different from the ingestion of the individual food. To understand the detailed mechanism for modulating the lipid metabolism by co-ingestion of a soy food (tofu) and fish oil, we investigated the global changes in hepatic mRNA expression in rats by using a microarray analysis. Generally, ingestion of tofu contributed to prevent the mRNA expressions involved in hepatic lipogenesis, whereas fish oil facilitated the mRNA expressions related to the degradation of hepatic fatty acids. In terms of mRNA expression, the interaction of two dietary factors was limited. The expression data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data. Rats were divided into four groups each with similar average body weights and assigned experimental diets for 21 days as follows: casein and soybean oil diet (CS); casein and fish oil diet (CF); tofu and soybean oil diet (TS); tofu and fish oil diet (TF). Total protein and fat content of each diet was 200 and 150 g/kg, respectively. Soybean oil diets (CS and TS) contain 150 g/kg diet of soybean-derived fat (i.e. soybean oil and freeze-dried tofu), and 50 g/kg of fish oil was replaced with the same amount of soybean-derived fat for fish oil diets (CF and TF). Animals were allowed free access to food and water.
2015-09-01 | E-GEOD-66371 | biostudies-arrayexpress
Project description:Although principal component analysis is frequently used in multivariate/ analysis, it has disadvantages when applied to experimental or diagnostic data. First, the identified principal components have poor generality; since the size and directions of the components are dependent on the particular data set, the components are valid only within the set. Second, the method is sensitive to experimental noise and bias between sample groups, since it cannot reflect the design of experiments; rather, it estimates the same weight and independence of all the samples in the matrix. Third, the resulting components are often difficult to interpret. To address these issues, several options were introduced to the methodology. The resulting components were scaled to unify their size unit. Also, the principal axes were identified using training data sets and shared among experiments. This training data reflects the design of experiments, and its preparation allows noise to be reduced and group bias to be removed. The effects of these options were observed in microarray experiments, and showed an improvement in the separation of groups and robustness to noise. Additionally, unknown samples were appropriately classified using pre-arranged axes, and principal axes well reflected the characteristics of groups in the experiments. The summarized levels the genes are presented in the Matrix form.
2011-08-12 | GSE31291 | GEO