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transcriptome analyses console  (Thermo Fisher)


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    Thermo Fisher transcriptome analyses console
    Differential rhythm analysis reveals changes in liver <t>transcriptome</t> rhythms that affect lipid and cholesterol metabolism in MMI mice. ( A ) Differential rhythm analysis was performed using CircaCompare and is represented as Venn diagrams. ( B ) UpSet plots show alterations in diurnal rhythm parameters (mesor, amplitude, phase). ( C ) Gene set enrichment analysis (GSEA) of the genes with either mesor, amplitude, or phase alterations was performed. Top-5 biological processes for each category are shown. ( D ) In-depth diurnal lipid metabolism analysis in response to low thyroid hormone state. Heatmaps show genes with mesor changes. Volcano plot and rose plot show alterations in amplitude and phase, respectively. ( E ) Normalized gene expression of selected genes participating in cholesterol uptake, biosynthesis, and degradation (bile acid secretion) in CON and MMI mice. ( F ) Quantification of cholesterol and TAG in serum or liver. Presence (R) or absence (NR) of significant circadian rhythm by CircaCompare ( p value < 0.05) is depicted. n = 3–4 for all ZTs and groups.
    Transcriptome Analyses Console, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/transcriptome+analyses+console/transcriptome+analysis+console/pmc10770409-230-4-7
    Average 90 stars, based on 1 article reviews
    transcriptome analyses console - by Bioz Stars, 2026-09
    90/100 stars

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    1) Product Images from "Tuning of liver circadian transcriptome rhythms by thyroid hormone state in male mice"

    Article Title: Tuning of liver circadian transcriptome rhythms by thyroid hormone state in male mice

    Journal: Scientific Reports

    doi: 10.1038/s41598-023-50374-z

    Differential rhythm analysis reveals changes in liver transcriptome rhythms that affect lipid and cholesterol metabolism in MMI mice. ( A ) Differential rhythm analysis was performed using CircaCompare and is represented as Venn diagrams. ( B ) UpSet plots show alterations in diurnal rhythm parameters (mesor, amplitude, phase). ( C ) Gene set enrichment analysis (GSEA) of the genes with either mesor, amplitude, or phase alterations was performed. Top-5 biological processes for each category are shown. ( D ) In-depth diurnal lipid metabolism analysis in response to low thyroid hormone state. Heatmaps show genes with mesor changes. Volcano plot and rose plot show alterations in amplitude and phase, respectively. ( E ) Normalized gene expression of selected genes participating in cholesterol uptake, biosynthesis, and degradation (bile acid secretion) in CON and MMI mice. ( F ) Quantification of cholesterol and TAG in serum or liver. Presence (R) or absence (NR) of significant circadian rhythm by CircaCompare ( p value < 0.05) is depicted. n = 3–4 for all ZTs and groups.
    Figure Legend Snippet: Differential rhythm analysis reveals changes in liver transcriptome rhythms that affect lipid and cholesterol metabolism in MMI mice. ( A ) Differential rhythm analysis was performed using CircaCompare and is represented as Venn diagrams. ( B ) UpSet plots show alterations in diurnal rhythm parameters (mesor, amplitude, phase). ( C ) Gene set enrichment analysis (GSEA) of the genes with either mesor, amplitude, or phase alterations was performed. Top-5 biological processes for each category are shown. ( D ) In-depth diurnal lipid metabolism analysis in response to low thyroid hormone state. Heatmaps show genes with mesor changes. Volcano plot and rose plot show alterations in amplitude and phase, respectively. ( E ) Normalized gene expression of selected genes participating in cholesterol uptake, biosynthesis, and degradation (bile acid secretion) in CON and MMI mice. ( F ) Quantification of cholesterol and TAG in serum or liver. Presence (R) or absence (NR) of significant circadian rhythm by CircaCompare ( p value < 0.05) is depicted. n = 3–4 for all ZTs and groups.

    Techniques Used: Gene Expression

    Lowering thyroid hormone state has subtle effects on liver transcriptome rhythms. ( A ) Global DEG analysis (disregarding sampling time) is represented as a Venn diagram. ( B ) UpSet plots represent DEG analysis for each ZT separately. ( C ) Venn diagram represents all temporal DEGs (i.e., showing different expression levels of at least one ZT) identified in MMI and T 3 groups versus CON mice. ( D ) Selected examples of robust DEGs (37 in total) previously identified in T 3 -treated mice. Absolute fold change comparison of all 37 DEGs in T 3 and MMI mice are shown. Absolute fold changes were used as some genes were up- or downregulated across the groups. ( E ) Selective TH output genes and fold change of these genes. Comparisons were performed using two-way ANOVA (main treatment effect, p < 0.05). n = 3–4 for all ZTs and groups. Pair-wise comparisons were performed by Student’s t test with Welch correction. Presence (R) or absence (NR) of circadian rhythm by JTK cycle ( p value < 0.05). ***, **** represents a p value of < 0.001, and 0.0001, respectively.
    Figure Legend Snippet: Lowering thyroid hormone state has subtle effects on liver transcriptome rhythms. ( A ) Global DEG analysis (disregarding sampling time) is represented as a Venn diagram. ( B ) UpSet plots represent DEG analysis for each ZT separately. ( C ) Venn diagram represents all temporal DEGs (i.e., showing different expression levels of at least one ZT) identified in MMI and T 3 groups versus CON mice. ( D ) Selected examples of robust DEGs (37 in total) previously identified in T 3 -treated mice. Absolute fold change comparison of all 37 DEGs in T 3 and MMI mice are shown. Absolute fold changes were used as some genes were up- or downregulated across the groups. ( E ) Selective TH output genes and fold change of these genes. Comparisons were performed using two-way ANOVA (main treatment effect, p < 0.05). n = 3–4 for all ZTs and groups. Pair-wise comparisons were performed by Student’s t test with Welch correction. Presence (R) or absence (NR) of circadian rhythm by JTK cycle ( p value < 0.05). ***, **** represents a p value of < 0.001, and 0.0001, respectively.

    Techniques Used: Sampling, Expressing, Comparison

    Related Articles

    other:

    Article Title: Hepatocyte expression of fetal insulin receptor isoform contributes to the promotion of liver cancer through non-cell autonomous mechanisms
    Article Snippet: Raw data were normalized using the robust multichip algorithm (RMA) and TAC4.0 software (Thermo Fisher Scientific).

    Article Title: Senescence-associated alterations in histone H3 modifications, HP1 alpha levels and distribution, and in the transcriptome of vascular smooth muscle cells in different types of senescence.
    Article Snippet: Data was analyzed using Transcriptome Analysis Console (TAC) software (ThermoFisher Scientific).

    Article Title: Decoding the transcriptome from bulk RNA of infection-naïve versus imprinted patients with SARS-CoV-2 Omicron B.1.1.529.
    Article Snippet: Raw data were normalized and analyzed using Transcriptome Analysis Console (TAC) software 4.0.2.15 (Thermo Fisher Scientific, USA) with the human reference genome hg19 to generate the differential gene expression (DEG) list.

    Article Title: Comparative transcriptomic and molecular interaction analysis of olive polyphenols: Unraveling their mechanisms in immune regulation and metabolic processes in adipocytes.
    Article Snippet: After acquiring the raw image data from the scanning process, the data were processed using the Transcriptome Analysis Console (TAC) software, version 4.0.2 (Thermo Fisher Scientific, Waltham, MA, USA).

    Microarray:

    Article Title: Tacrolimus Modulates TGF-β Signaling-Related Genes and MicroRNAs in Human Retinal Pigment Epithelial Cells Activated by Lipopolysaccharide.
    Article Snippet: All ELISA kits were sourced from MyBioSource (San Diego, CA, USA), with the following catalog numbers: Human Mothers Against Decapentaplegic Homolog 4 (Smad4) ELISA Kit (MyBioSource; cat. no. MBS450115), Human Mothers Against Decapentaplegic Homolog 7 (Smad7) ELISA Kit (MyBioSource; cat. no. MBS162196), Transforming Growth Factor Beta-2 (TGF-β2) ELISA Kit (MyBioSource; cat. no. MBS8420054), and Interleukin-2 (IL-2) ELISA Kit (MyBioSource; cat. no. MBS2021996). .. The statistical evaluation of the microarray data was conducted using the Transcriptome Analysis Console (Thermo Fisher, Waltham, MA, USA) and Statplus software v. 1.1. ..



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    Differential rhythm analysis reveals changes in liver <t>transcriptome</t> rhythms that affect lipid and cholesterol metabolism in MMI mice. ( A ) Differential rhythm analysis was performed using CircaCompare and is represented as Venn diagrams. ( B ) UpSet plots show alterations in diurnal rhythm parameters (mesor, amplitude, phase). ( C ) Gene set enrichment analysis (GSEA) of the genes with either mesor, amplitude, or phase alterations was performed. Top-5 biological processes for each category are shown. ( D ) In-depth diurnal lipid metabolism analysis in response to low thyroid hormone state. Heatmaps show genes with mesor changes. Volcano plot and rose plot show alterations in amplitude and phase, respectively. ( E ) Normalized gene expression of selected genes participating in cholesterol uptake, biosynthesis, and degradation (bile acid secretion) in CON and MMI mice. ( F ) Quantification of cholesterol and TAG in serum or liver. Presence (R) or absence (NR) of significant circadian rhythm by CircaCompare ( p value < 0.05) is depicted. n = 3–4 for all ZTs and groups.
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    Image Search Results


    Differential rhythm analysis reveals changes in liver transcriptome rhythms that affect lipid and cholesterol metabolism in MMI mice. ( A ) Differential rhythm analysis was performed using CircaCompare and is represented as Venn diagrams. ( B ) UpSet plots show alterations in diurnal rhythm parameters (mesor, amplitude, phase). ( C ) Gene set enrichment analysis (GSEA) of the genes with either mesor, amplitude, or phase alterations was performed. Top-5 biological processes for each category are shown. ( D ) In-depth diurnal lipid metabolism analysis in response to low thyroid hormone state. Heatmaps show genes with mesor changes. Volcano plot and rose plot show alterations in amplitude and phase, respectively. ( E ) Normalized gene expression of selected genes participating in cholesterol uptake, biosynthesis, and degradation (bile acid secretion) in CON and MMI mice. ( F ) Quantification of cholesterol and TAG in serum or liver. Presence (R) or absence (NR) of significant circadian rhythm by CircaCompare ( p value < 0.05) is depicted. n = 3–4 for all ZTs and groups.

    Journal: Scientific Reports

    Article Title: Tuning of liver circadian transcriptome rhythms by thyroid hormone state in male mice

    doi: 10.1038/s41598-023-50374-z

    Figure Lengend Snippet: Differential rhythm analysis reveals changes in liver transcriptome rhythms that affect lipid and cholesterol metabolism in MMI mice. ( A ) Differential rhythm analysis was performed using CircaCompare and is represented as Venn diagrams. ( B ) UpSet plots show alterations in diurnal rhythm parameters (mesor, amplitude, phase). ( C ) Gene set enrichment analysis (GSEA) of the genes with either mesor, amplitude, or phase alterations was performed. Top-5 biological processes for each category are shown. ( D ) In-depth diurnal lipid metabolism analysis in response to low thyroid hormone state. Heatmaps show genes with mesor changes. Volcano plot and rose plot show alterations in amplitude and phase, respectively. ( E ) Normalized gene expression of selected genes participating in cholesterol uptake, biosynthesis, and degradation (bile acid secretion) in CON and MMI mice. ( F ) Quantification of cholesterol and TAG in serum or liver. Presence (R) or absence (NR) of significant circadian rhythm by CircaCompare ( p value < 0.05) is depicted. n = 3–4 for all ZTs and groups.

    Article Snippet: Data were analyzed using Transcriptome Analyses Console (Thermo Fisher Scientific, version 4.0) and expressed in log 2 values.

    Techniques: Gene Expression

    Lowering thyroid hormone state has subtle effects on liver transcriptome rhythms. ( A ) Global DEG analysis (disregarding sampling time) is represented as a Venn diagram. ( B ) UpSet plots represent DEG analysis for each ZT separately. ( C ) Venn diagram represents all temporal DEGs (i.e., showing different expression levels of at least one ZT) identified in MMI and T 3 groups versus CON mice. ( D ) Selected examples of robust DEGs (37 in total) previously identified in T 3 -treated mice. Absolute fold change comparison of all 37 DEGs in T 3 and MMI mice are shown. Absolute fold changes were used as some genes were up- or downregulated across the groups. ( E ) Selective TH output genes and fold change of these genes. Comparisons were performed using two-way ANOVA (main treatment effect, p < 0.05). n = 3–4 for all ZTs and groups. Pair-wise comparisons were performed by Student’s t test with Welch correction. Presence (R) or absence (NR) of circadian rhythm by JTK cycle ( p value < 0.05). ***, **** represents a p value of < 0.001, and 0.0001, respectively.

    Journal: Scientific Reports

    Article Title: Tuning of liver circadian transcriptome rhythms by thyroid hormone state in male mice

    doi: 10.1038/s41598-023-50374-z

    Figure Lengend Snippet: Lowering thyroid hormone state has subtle effects on liver transcriptome rhythms. ( A ) Global DEG analysis (disregarding sampling time) is represented as a Venn diagram. ( B ) UpSet plots represent DEG analysis for each ZT separately. ( C ) Venn diagram represents all temporal DEGs (i.e., showing different expression levels of at least one ZT) identified in MMI and T 3 groups versus CON mice. ( D ) Selected examples of robust DEGs (37 in total) previously identified in T 3 -treated mice. Absolute fold change comparison of all 37 DEGs in T 3 and MMI mice are shown. Absolute fold changes were used as some genes were up- or downregulated across the groups. ( E ) Selective TH output genes and fold change of these genes. Comparisons were performed using two-way ANOVA (main treatment effect, p < 0.05). n = 3–4 for all ZTs and groups. Pair-wise comparisons were performed by Student’s t test with Welch correction. Presence (R) or absence (NR) of circadian rhythm by JTK cycle ( p value < 0.05). ***, **** represents a p value of < 0.001, and 0.0001, respectively.

    Article Snippet: Data were analyzed using Transcriptome Analyses Console (Thermo Fisher Scientific, version 4.0) and expressed in log 2 values.

    Techniques: Sampling, Expressing, Comparison