Sigmaplot v13

Manufactured by Merck Group

Sourced in United States

SigmaPlot v13 is a data analysis and graphing software product from the Merck Group. It provides tools for data visualization, statistical analysis, and scientific and technical graphing. The software is designed to help users easily create high-quality plots and charts from their data.

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SigmaPlot (794 citations)

27 protocols using sigmaplot v13

Quantifying microRNA Expression Patterns

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MicroRNA expression was assessed using SDS2.4 software (Life Technologies) and fold change was determined as for comparative Ct method (26 (link)). Statistical analyses were carried out using SPSS v19.0, Sigmaplot v13 or GraphPad Prism v6.0. Differences between groups were assed using the independent t-test, one-way ANOVA, or one-way ANOVA repeated measure analysis. Following a significant ANOVA result, differences between pairs of groups were detrmined via the Tukey post-hoc test (Prism v6.0). Receiver operating characteristic (ROC) analysis was performed using marker expression on a continuous scale as the test variable and disease status as the state variable (Sigmaplot v13). For the ROC analyses, pre-test prior-probability was set to 0.5 and Cost Ratio to 1.0 (27 (link)). The optimal cutoff value to dichotomise microRNA expression was computed from sensitivity and specificity using the slope m by finding the cutoff that maximizes the function: sensitivity-m(1-specificity) (Sigmaplot v13) (28 (link)). The accuracy of the test was defined by the area under the curve (AUC), whereby AUC = 0.5 means no diagnostic ability and AUC = 1 means perfect diagnostic ability.

Crossland R.E., Norden J., Ghimire S., Juric M.K., Pearce K.F., Lendrem C., Collin M., Mischak-Weissinger E., Holler E., Greinix H.T, & Dickinson A.M. (2021). Profiling Tissue and Biofluid miR-155-5p, miR-155*, and miR-146a-5p Expression in Graft vs. Host Disease. Frontiers in Immunology, 12, 639171.

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Cardiac Morphology and Function Assessment

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Data are expressed as mean±SEM unless otherwise stated. mRNA and protein expression levels were normalized to glyceraldehyde 3-phosphate dehydrogenase (GAPDH). A linear transformation was performed to set the result of control group (usually Ntg without TAM chow) to 1, by dividing each group with the average obtained for their control group. Shapiro-Wilk and Brown-Forsythe tests were performed to examine data normality and variance equality using SigmaPlot V13. The number of mice needed to meet the statistical power (β=0.8) was also calculated using SigmaPlot V13. The following tests were performed using Graphpad (Prism 7). Student’s t-test was performed for two group comparisons. A paired t-test was performed to determine the significance of fractional shortening changes of the same mouse before and after tamoxifen chow treatment. One-way ANOVA with Tukey’s post hoc analysis was performed for multiple group comparisons as well as to determine the adjusted P value between group comparisons. Kaplan-Meier curves using the Log-rank test were generated to detect changes in survival probabilities. Between group differences were determined using the Holm-Šídák post hoc test. Statistical significance was defined as *P<0.05, **P<0.01, ***P<0.001.

Meng Q., Bhandary B., Shenuarin Bhuiyan M., James J., Osinska H., Valiente-Alandi I., Shay-Winkler K., Gulick J., Molkentin J.D., Blaxall B.C, & Robbins J. (2018). Myofibroblast Specific TGFβ Receptor II Signaling in the Fibrotic Response to Cardiac Myosin Binding Protein C-Induced Cardiomyopathy. Circulation research, 123(12), 1285-1297.

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Evaluating NGS-based Cancer IVDs

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The ddPCR assay was performed in triplicate, and the results were assessed by one-way ANOVA to calculate the uniformity of each mutation. The relevance of the results between ddPCR and NGS was analyzed by linear regression and Wilcoxon signed rank test. The general performance of NGS-based cancer IVDs for detecting the cfDNA RMs at an allelic frequency was evaluated by calculating the CV of the results of all participants testing the same sample. The CV was defined as the ratio of the standard deviation to the mean expressing the dispersion of the distribution of allelic frequencies detected by the participants. One sample t-test was performed to examine the differences in allelic frequencies detected by the NGS assay compared with those detected by the ddPCR assay. Significance was defined when the P value was less than 0.05. Statistical analyses and data visualization were performed using SPSS v19.0, GraphPad Prism v5.0, and SigmaPlot v13.0.

Liu D., Zhang X., Zhou H., Lin X., Shi D., Shen S., Tian Y., Du B., Zhang H., Wang H., Wang Y, & Zhang C. (2018). Multiplex Cell-Free DNA Reference Materials for Quality Control of Next-Generation Sequencing-Based In Vitro Diagnostic Tests of Colorectal Cancer Tolerance. Journal of Cancer, 9(20), 3812-3823.

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Age-Dependent Alterations in αCaMKII

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Two-way ANOVA was conducted for all animal groups and Tukey post-hoc analysis was undertaken to signify specific differences in total, phosphorylated and ratio of phosphorylated:total αCaMKII, between young and aged mice in different brain regions. For the ratio of phosphorylated:total αCaMKII in CA3 hippocampus, lateral and central amygdala, original data was not normally distributed and instead a two-way ANOVA was conducted further to log transformation. All other outcome variables were found to be normally distributed and of equal variance. Statistical tests were carried out on SigmaPlot v13.0, US.

Fang T., Kasbi K., Rothe S., Aziz W, & Giese K.P. (2017). Age-dependent changes in autophosphorylation of alpha calcium/calmodulin dependent kinase II in hippocampus and amygdala after contextual fear conditioning. Brain Research Bulletin, 134, 18-23.

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Kinetic Characterization of BDH Enzyme

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The oxidation reaction mixture contained 30 μg/ml enzyme, 50 mM Tris-HCl at pH 7.5, 1 mM NAD⁺ and 1 mM substrate at 30 °C. The reaction was started by the addition of enzyme. The reduction reaction mixture contained 500 μg/ml enzyme, 50 mM citrate-phosphate buffer at pH 5.0, 1 mM NADH, and 1 mM substrate at 30 °C for the enzyme analysis. The screening of engineered enzyme variants was done in 50 mM Tris-HCl at pH 7.5, 1 mM NADH with 12.5 mM formate, and 1 mg/ml formate dehydrogenase. The reaction was started by the addition of BDH enzyme. For determination of pH optimum, the enzyme was desalted in the corresponding buffer and activity measured as described. The temperature optimum was determined by incubation of the assay solutions before and during the reaction at the corresponding temperature. Kinetic analysis was done at optimal pH and temperature values. The K_m and k_cat of NAD⁺ were determined in the presence of 1 mM substrate and 0.01, 0.02, 0.04, 0.08, 0.1, 0.2, 0.4, 0.6, 0.8, and 1 mM cofactor. The K_m and k_cat for (+)-borneol and (−)-borneol were determined in the presence of 1 mM NAD⁺ and 0.02, 0.04, 0.08, 0.1, 0.2, 0.4, 0.6, 0.8, 1, and 2 mM substrate. For data analysis, the enzyme kinetics module of SigmaPlot v13.0 was used.

Hofer M., Diener J., Begander B., Kourist R, & Sieber V. (2021). Engineering of a borneol dehydrogenase from P. putida for the enzymatic resolution of camphor. Applied Microbiology and Biotechnology, 105(8), 3159-3167.

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Evaluation of [Ca2+]i and Vm Data

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[Ca2+]i and V_m data at either fixed time points, or as “area under the curve” (AUC), were compared using student's t‐test, or paired t‐test as appropriate. For regression analysis, where a dose response was expected, a Sigmoidal fit was used. Other datasets were analyzed using a linear or nonlinear regression based on the equation which best fit the data (all tests performed in SigmaPlot V13.0). Differences in P‐value <0.05 were considered significant.

Alvarez R.E., Boeldt D.S., Pattnaik B.R., Friedman H.L, & Bird I.M. (2017). Pregnancy‐adapted uterine artery endothelial cell Ca2+ signaling and its relationship with membrane potential. Physiological Reports, 5(21), e13452.

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Multivariate Analysis of Research Data

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Unless otherwise specified, statistical analyses were performed using SigmaPlot v13.0. Hierarchical clustering and heatmaps were generated with Morpheus, https://software.broadinstitute.org/morpheus, accessed on 12 January 2021 [40 ]. Clustered correlation plots were generated in R (https://www.r-project.org/, accessed on 1 October 2020) using the R packages “corrplot” and “hclust” and partitioning around medoids (PAM) K-medoids clustering plots were generated with the R packages ‘factoextra’ and “cluster” [41 ]. FreeViz multivariate plots were generated with Orange [42 ]. p values less than 0.05 were considered statistically significant.

De Velasco M.A., Kura Y., Ando N., Sako N., Banno E., Fujita K., Nozawa M., Yoshimura K., Sakai K., Yoshikawa K., Nishio K, & Uemura H. (2021). Context-Specific Efficacy of Apalutamide Therapy in Preclinical Models of Pten-Deficient Prostate Cancer. Cancers, 13(16), 3975.

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Evaluation of Cancer Diagnostic Assays

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The ddPCR assay was performed in quadruplicate and the results were assessed by one-way ANOVA test for calculation of uniformity of each mutation. The differences between the results of ddPCR and ARMS-PCR were analyzed by Wilcoxon signed rank test. The general performance of NGS-based cancer IVDs detecting the reference material at a particular allelic frequency was evaluated by calculating the CV of the results of all participants testing the same sample. The CV was defined as the ratio of the standard deviation to the mean expressing the dispersion of the distribution of allelic frequencies detected by the participants. One sample t-test was performed to examine the differences of allelic frequencies detected by the NGS assay compared with those by the ddPCR assay. Significance was defined when P value was less than 0.05. Statistical analyses and data visualization were performed using SPSS v19.0, GraphPad Prism v5.0, and SigmaPlot v13.0.

Liu D., Zhou H., Shi D., Shen S., Tian Y., Wang L., Lou J., Cong R., Lu J., Zhang H., Zhao M., Zhu S., Cao Z., Jin R., Wang Y., Zhang X., Yang G., Wang Y, & Zhang C. (2018). Quality Control of Next-generation Sequencing-based In vitro Diagnostic Test for Onco-relevant Mutations Using Multiplex Reference Materials in Plasma. Journal of Cancer, 9(9), 1680-1688.

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Statistical Analysis with SigmaPlot

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SigmaPlot v13.0 was employed to render results graphically, compute linear regression plots and compute statistical parameters.

, & Brown J.C. (2020). Involvement of promoter/enhancers in a feedback loop to regulate human gene expression. Heliyon, 6(9), e04934.

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Assessing Weekly Patterns in Information Seeking Behavior

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In order to assess whether ISB waveforms observed were consistent throughout every day of the week, we conducted linear regression analyses using the daily amplitudes. If the amount of Google information seeking increased dramatically on certain days, such as the weekend, then the amplitude should exhibit a significant increase on Saturday and Sunday (when oriented as Monday–Sunday). Alternatively, the absence of a significant regression would indicate that information seeking remained constant. Cosinor-based analyses are readily employed for the analyses of time series in chronobiology [23 (link)]. Amplitude of circadian waveforms was determined using Cosinor software developed by Roberto Refinetti (http://www.circadian.org/softwar.html). A linear regression was then conducted using SigmaPlot v. 13.0 to assess whether the level of food-related ISB terms changed over the week. Significance was determined at p < 0.001.

Scrutton Alvarado N, & Stevenson T.J. (2018). Appetitive information seeking behaviour reveals robust daily rhythmicity for Internet-based food-related keyword searches. Royal Society Open Science, 5(7), 172080.

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