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transcriptome analyses console version 4.0  (Thermo Fisher)


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    Thermo Fisher transcriptome analyses console version 4.0
    Transcriptome Analyses Console Version 4.0, 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+software/pm38182610-292-4-7
    Average 90 stars, based on 1 article reviews
    transcriptome analyses console version 4.0 - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    other:

    Article Title: Cell-of-origin and genetic drivers define advanced bladder cancer subtypes and potential therapeutic response in mouse models
    Article Snippet: Data analysis was conducted using Transcriptome Analysis Console (TAC) v4.0.2 (Thermo Fisher Scientific).

    Article Title: Inhibiting the TGF-β1 Pathway Reduces the Aggressiveness of Intrahepatic CCA HuCCT1 CD90-Positive Cells.
    Article Snippet: Differential expression analyses were performed in the Transcriptome Analysis Console 4.0 software (Thermo Fisher Scientific, Waltham, MA, USA).

    Article Title: Effects of Dairy Matrix on the Intestinal, Liver, and Bone Transcriptome of Healthy Rats.
    Article Snippet: The resulting data were analyzed using the Transcriptome Analysis Console software 4.0.2 (Applied Biosystems, Thermo Fisher Scientific Inc., Waltham, MA, USA) with an FDR threshold of <0.1.

    Software:

    Article Title: Transcriptomic analysis of bone transport reveals different functions between both ends
    Article Snippet: .. Raw data of the transcriptomes was based on Affymetrix Rat Transcriptome Array 1.0, which was read and normalized on Transcriptome Analysis Console software (v4.0.3.14, Thermo Fisher Scientific). .. The values of the probes were output and re-edited in RStudio (v2023.06.1 Build 524), with probes converted into gene symbols and the expression levels calculated using the average method.

    Article Title: Transcriptomic Profile of Early Antral Follicles: Predictive Somatic Gene Markers of Oocyte Maturation Outcome.
    Article Snippet: .. The statistical analysis was conducted as follows: The Microarray GeneChip assays were performed through a One-Way ANOVA, followed by an empirical Bayes correction for differential expression using the Transcriptome Analysis Console (TAC software; version 4.0.1, Thermo Fisher Scientific, Waltham, MA, USA). .. For the analyses related to oocyte maturation performance, embryonic developmental competence, and qPCR validation, One-Way ANOVA was performed with GraphPad Prism 10.1.1 (https://www.graphpad.com/, accessed on 2 May 2024), with p-values less than 0.05 considered statistically significant.

    Article Title: Prognostic gene expression signatures for HPV-negative head and neck squamous cell carcinoma.
    Article Snippet: Background: Head and neck squamous cell carcinoma (HNSCC) is a leading cause of cancer-related deaths worldwide, with HPV-negative cases being particularly aggressive.. These cases often show poor prognosis and low responsiveness to radiotherapy.. Improved prognostic tools and treatment strategies are needed to enhance outcomes.

    Article Title: Identification of a Growth-Promoting Gene Cluster in the Region 2q24 as a Driver of Tumorigenesis in Childhood Hepatoblastoma.
    Article Snippet: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 ajp.amjpathol.org 63 64 65 66 67 68 69 70 71 72 73 74 Identification of a Growth-Promoting Gene 75 76 Cluster in the Region 2q24 as a Driver of 77 78 79 80 81 82 Tumorigenesis in Childhood Hepatoblastoma Martin M. Rodemann,* Verena Dreschmann,* Evelyn Dörner,* Anette Sommer,y Joern Kraetzschmar,y Ludger Klein-Hitpass,z Genta Nagae,x Eiso Hiyama,{k Dietrich von Schweinitz,** Roland Kappler,** Christian Vokuhl,yy and Torsten Pietsch*

    Article Title: Modelling the Liver’s Regenerative Capacity across Different Clinical Conditions
    Article Snippet: 197 198 Transcriptome Analysis 199 Total RNA extracted from liver tissues was profiled utilizing the Affymetrix Mouse Gene 2.0 200 ST array provided by ThermoFisher Scientific. .. The data obtained were pre-processed, 201 annotated, and statistically analyzed using the Transcriptome Analysis Console software 202 (ThermoFisher Scientific). .. For pathway analysis, differentially expressed genes identified from 203 this process were analyzed using Ingenuity Pathway Analysis (IPA) software (Qiagen).

    Microarray:

    Article Title: Transcriptomic Profile of Early Antral Follicles: Predictive Somatic Gene Markers of Oocyte Maturation Outcome.
    Article Snippet: .. The statistical analysis was conducted as follows: The Microarray GeneChip assays were performed through a One-Way ANOVA, followed by an empirical Bayes correction for differential expression using the Transcriptome Analysis Console (TAC software; version 4.0.1, Thermo Fisher Scientific, Waltham, MA, USA). .. For the analyses related to oocyte maturation performance, embryonic developmental competence, and qPCR validation, One-Way ANOVA was performed with GraphPad Prism 10.1.1 (https://www.graphpad.com/, accessed on 2 May 2024), with p-values less than 0.05 considered statistically significant.

    Quantitative Proteomics:

    Article Title: Transcriptomic Profile of Early Antral Follicles: Predictive Somatic Gene Markers of Oocyte Maturation Outcome.
    Article Snippet: .. The statistical analysis was conducted as follows: The Microarray GeneChip assays were performed through a One-Way ANOVA, followed by an empirical Bayes correction for differential expression using the Transcriptome Analysis Console (TAC software; version 4.0.1, Thermo Fisher Scientific, Waltham, MA, USA). .. For the analyses related to oocyte maturation performance, embryonic developmental competence, and qPCR validation, One-Way ANOVA was performed with GraphPad Prism 10.1.1 (https://www.graphpad.com/, accessed on 2 May 2024), with p-values less than 0.05 considered statistically significant.

    Gene Expression:

    Article Title: Prognostic gene expression signatures for HPV-negative head and neck squamous cell carcinoma.
    Article Snippet: Background: Head and neck squamous cell carcinoma (HNSCC) is a leading cause of cancer-related deaths worldwide, with HPV-negative cases being particularly aggressive.. These cases often show poor prognosis and low responsiveness to radiotherapy.. Improved prognostic tools and treatment strategies are needed to enhance outcomes.



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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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    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