Unpaired t test was used to analyze expressions of PLCBs in tumor and non-tumor tissues. Box plots and survival plots were generated using GraphPad software version 7.0 (GraphPad Software, Inc., La Jolla, CA, USA). Survival analyses were performed using SPSS software version 16.0 (SPSS, Inc., Chicago, IL, USA). Median survival time and log-rank P-value were calculated by the Kaplan-Meier method, and the 95% confidence interval (CI) and hazard ratio (HR) were calculated by univariate and multivariate Cox proportional hazards regression models, respectively. P<0.05 was considered to indicate a statistically significant difference.
Software version 7
Manufactured by GraphPad
Sourced in United States
GraphPad software version 7.0 is a data analysis and graphing software package designed for scientific and research applications. The software provides tools for data organization, statistical analysis, and visualization. It offers a range of functionalities to support researchers in interpreting and presenting their findings.
Automatically generated - may contain errors
Lab products found in correlation
Spss software version 16, by IBM (3 mentions)
Spss statistics 23, by IBM (2 mentions)
Alexa fluor 488, by Thermo Fisher Scientific (2 mentions)
Spss version 22.0 for windows, by IBM (2 mentions)
Spss version 22, by IBM (2 mentions)
Spss version 24, by IBM (1 mentions)
Spss version 23, by GraphPad (1 mentions)
Spss statistical software version 22, by IBM (1 mentions)
Spss statistical software version 24, by IBM (1 mentions)
R software version 4, by R Project for Statistical Computing (1 mentions)
Spss software version 22, by IBM (1 mentions)
47 protocols using software version 7
1
Expression and Survival Analysis of PLCBs in Tumors
2
Statistical Analysis of Experimental Data
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GraphPad software (version 7.0) was used for statistical analysis. All data are expressed as the mean value and standard deviation (χ̄±s). We used the t test to compare differences between 2 groups. One-way analysis of variance was used for comparison among groups. Dunnett’s multiple comparisons test was performed for the post hoc comparison/test. P<0.05 was regarded as having statistical significance.
3
Statistical Analyses in Biological Research
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Significant differences between the groups were estimated by Student’s t-test. One-way analysis of variance (one-way ANOVA) was used for at least three groups. The overall survival curves were used to describe the survival distributions, and the log-rank test was applied for assessing statistical significance between different groups. The survival data were further processed by using univariate and multivariate Cox regression analysis. The Pearson correlation coefficient was used to analyze the correlations between variables. GO and KEGG Pathway analysis was performed using the DAVID website (http://david.abcc.ncifcrf.gov/home.jsp ). Statistically significant gene sets were visualized by Cytoscape, and GSEA was used to analyze biological processes. SsGSEA was used to calculate the enrichment score of every gene set for every sample64 (link). Heatmaps were constructed and produced using Gene Cluster 3.0 and Gene Tree View software. All results are expressed as the mean ± SD. A value of p < 0.05 was considered to be statistically significant. All statistical analyses were performed using GraphPad software version 7.0 (GraphPad Software, CA, USA) or IBM SPSS Statistics 23.0 (SPSS, Chicago, USA).
4
Comprehensive Bioinformatic Analysis of Genetic Markers
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All statistical analyses were performed with GraphPad software version 7.0 (GraphPad Software, San Diego, CA, USA) or IBM SPSS Statistics 23.0 software (SPSS, Chicago, IL, USA). The significance of the differences between groups was estimated with Student’s t test, chi-square test or one-way analysis of variance (ANOVA) as appropriate. The Kaplan–Meier method with the log-rank test was used to calculate the overall survival (OS) rate for comparison between different groups. The correlations between variables were analyzed with the Pearson correlation coefficient. GO and KEGG pathway analyses were performed on the DAVID website (https://david.ncifcrf.gov/ ). DIANA tools (http://diana.imis.athena-innovation.gr/ ) and miRcode (http://www.mircode.org/ ) were used to predict lncRNA-targeting miRNAs. All results are shown as the mean ± standard error of the mean (SEM) of three independent experiments. Statistical significance was considered to be represented by a value of p < 0.05. Additional file 5 (link): Table S5-7.
5
Kaplan-Meier Survival Analysis Protocol
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Survival analyses were performed using SPSS software version 16.0 (IBM, Chicago, IL). Median survival time (MST) and log-rank P were calculated by Kaplan-Meier method, as well as 95% confidence interval (CI) and hazard ratio (HR) were calculated by univariate and multivariate Cox proportional hazards regression models. Box plots and survival plots were obtained using GraphPad software version 7.0. P value ≤ 0.05 was statistically significant.
6
Survival Analysis of Medical Interventions
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Kaplan-Meier and box plots were produced using GraphPad software version 7.0 (GraphPad Software, Inc.). Survival analysis was performed by using SPSS software version 16.0 (SPSS, Inc.). The median survival time and Log-rank P-values were calculated using the Kaplan-Meier method; 95% confidence interval (CI) and hazard ratio (HR) were calculated by univariate and multivariate Cox proportional hazards regression model. P≤0.05 was considered to indicate a statistically significant difference.
7
Quantitative Western Blotting Analysis
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All experiments were performed at least three times. Data are expressed as mean ± SEM. The acquisition of the Western blotting images was done through a scanner and the relative densities of the bands were analyzed with ImageJ software. Statistical analyses were performed using GraphPad Software version 7.0 (La Jolla, CA, USA). Statistical differences were determined by analysis of variance (ANOVA) followed, when significant, by an appropriate post hoc test as indicated in figure legends. For miRNA expression, we used linear mixed models, including treatments as fixed terms and plates as random effects, which allowed for different intercepts for each run. In miRNA figures, the points indicate the mean value while the bars represent the SEM. In all reported statistical analyses, effects were designated as significant with a p-value < 0.05. Statistical analyses were performed using R software version 3.4.1 (R Core Team, 2018 ).
8
Dietary Interventions and Exercise Effects
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Statistical analyses were performed using GraphPad software Version 7.0. Normally distributed data were expressed as mean ± SD. Non‐normally distributed data were expressed as median (interquartile range). Effects of dietary interventions (CHOW vs. HFD) and the differences between exercise conditions (untrained vs. END vs. HIIT) were calculated using a Two‐way ANOVA with Dunnet's and Sidak's pos‐hoc analysis. P values <0.05 were considered statistically significant.
9
Comprehensive Statistical Analysis Pipeline
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GraphPad software version 7.0 (GraphPad Software, La Jolla, CA, USA) was used for graph design and statistical analysis. One-way analysis of variance (ANOVA) followed by Tukey’s multiple comparisons test was performed to analyze the log2 fold-change of gene expression after Q-PCR. For RNA-seq analysis, the read count was adjusted by TMM, then differential expression analysis was performed by using the EdgeR R package. For microbiome analysis, the classification results were filtered through several statistical post-processing steps (K-mer-based classification, artifact filtering, and species-level abundance estimation [25 (link),26 (link)]) to eliminate false-positive results caused by contamination or sequencing artifacts.
10
Immunofluorescence Analysis of Renal Monocytes
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Paraffin‐embedded kidneys 4 μm in thickness were deparaffinized, as described above, for immunohistochemistry and immunofluorescence staining. The slides were incubated with primary antibodies cluster of differentiation (CD) 11b monoclonal antibody (M1/70), Alexa Fluor 488, and ICAM‐1 antibody (9HCLC), ABfinity Rabbit Oligoclonal (Thermo Scientific, Waltham, MA), overnight at 4°C, after blocking with 1% BSA for 1 hour at room temperature. Next, slides were washed with a tris‐buffered saline–Tween solution, followed by incubating with a secondary antibody for 2 hours at room temperature. The slides were then incubated with mounting medium containing 4′,6‐diamidino‐2‐phenylindole for nuclear staining and mounted with coverslip. Fluorescent signals were visualized using microscope. Ten images were taken from each slide. Immunofluorescence for presence of monocyte/macrophage was performed using rat anti‐monocyte/macrophage antibody (Abcam) as we have described.30 Data from 4 to 5 animals in each group were analyzed by GraphPad software version 7.0.
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