Journal: STAR Protocols

Article Title: Analysis workflow of publicly available RNA-sequencing datasets

doi: 10.1016/j.xpro.2021.100478

Figure Lengend Snippet: Gene expression analysis based on SARS-CoV-2 positivity and age Dot plot for MX1 expression (i) and statistical output from RStudio (ii) for: (A) SARS-CoV-2 positive vs . negative patients (P-values correspond to Wilcoxon rank-sum test); (B) SARS-CoV-2 positive vs . negative patients categorized by age groups (P-values correspond to decreasing Jonckheere-Terpstra trend test. Alternative hypothesis: Median i > Median j > … > Median n , indicating that gene expression is significantly lower in SARS-CoV-2 patients when age is increased. Left panel: SARS-CoV-2 negative; right panel: SARS-CoV-2 positive). A.i and B.i were adapted with permission from Bizzotto et al., 2020 .

Article Snippet: Statistical significance: ∗ p < 0.05; ∗∗ p < 0.01; ∗∗∗ p < 0.001. (B) Scatter plot of MX1 and MX2 gene expression levels, color-coded by viral load (i) and Spearman correlation output in RStudio (ii).

Techniques: Gene Expression, Expressing

Journal: STAR Protocols

Article Title: Analysis workflow of publicly available RNA-sequencing datasets

doi: 10.1016/j.xpro.2021.100478

Figure Lengend Snippet: Correlation analysis (A) Pairwise Spearman correlation matrix analysis between all genes of interest ( MX1 , MX2 , ACE2 and TMPRSS2 ), considering different infection status (all patients together (Corr.), SARS-CoV-2 negative (HEALTHY), or SARS-CoV-2 positive patients (COVID19)). Alternative hypothesis: rho (ρ) ≠ 0, which indicates that there is a lineal correlation between the variables under study. Statistical significance: ∗ p < 0.05; ∗∗ p < 0.01; ∗∗∗ p < 0.001. (B) Scatter plot of MX1 and MX2 gene expression levels, color-coded by viral load (i) and Spearman correlation output in RStudio (ii). A and 3B.i were adapted with permission from Bizzotto et al., 2020 .

Article Snippet: Statistical significance: ∗ p < 0.05; ∗∗ p < 0.01; ∗∗∗ p < 0.001. (B) Scatter plot of MX1 and MX2 gene expression levels, color-coded by viral load (i) and Spearman correlation output in RStudio (ii).

Techniques: Infection, Gene Expression

Journal: STAR Protocols

Article Title: Analysis workflow of publicly available RNA-sequencing datasets

doi: 10.1016/j.xpro.2021.100478

Figure Lengend Snippet: Patient segregation based on gene expression (A) Principal component analysis (PCA) output in RStudio, showing the first two principal components explaining most part of the variance among samples. (B) PCA biplot of gene expression data showing a rough segregation of SARS-CoV-2 positive and negative samples. (C) 3D scatter plot for the expression of three genes of interest ( BSG , MX1 and ACE2 ). Samples are colored by SARS-CoV-2 status (positive or negative). Ellipsoids represent the 95% confidence interval. B and 4C were adapted with permission from Bizzotto et al., 2020 .

Article Snippet: Statistical significance: ∗ p < 0.05; ∗∗ p < 0.01; ∗∗∗ p < 0.001. (B) Scatter plot of MX1 and MX2 gene expression levels, color-coded by viral load (i) and Spearman correlation output in RStudio (ii).

Techniques: Gene Expression, Expressing

Journal: Antibiotics

Article Title: Molecular Characterization of Multidrug-Resistant and Extended-Spectrum β-Lactamases-Producing Salmonella enterica Serovars Enteritidis and Typhimurium Isolated from Raw Meat in Retail Markets

doi: 10.3390/antibiotics13070586

Figure Lengend Snippet: The scatter plot correlation matrix with a histogram showing the multiple antibiotic resistance index of Salmonella enterica serovars ( A ) S. Enteritidis, ( B ) S. Typhimurium, and ( C ) the multidrug resistance (MDR) profiles of the isolates in different livestock (cattle, goat, and chicken) meat samples investigated in the present study.

Article Snippet: Additionally, a scatter plot correlation matrix with histograms was generated to display MARI value of Salmonella enterica serovars, utilizing Origin-Pro 2024 ( www.originlab.com , accessed on 15 March 2024).

Techniques:

Journal: Technology in Cancer Research & Treatment

Article Title: Prognostic Value of mRNA Expression of MAP4K Family in Acute Myeloid Leukemia

doi: 10.1177/1533033819873927

Figure Lengend Snippet: Metabolic gEne RApid Visualizer boxplots for MAP4K gene expression in normal hematopoietic and lymphoid tissue and primary AML tissue: (A) MAP4K1; (B) MAP4K2; (C) MAP4K3; (D) MAP4K4; (E) MAP4K5; and (F) MINK1. AML indicates acute myeloid leukemia; MAP4K, MAP kinase kinase kinase kinase.

Article Snippet: Vertical scatter plot of MAP4K mRNA expression and survival curves for MAP4K family were generated in GraphPad Prism v.7.0 (La Jolla, California).

Techniques: Gene Expression

Journal: Technology in Cancer Research & Treatment

Article Title: Prognostic Value of mRNA Expression of MAP4K Family in Acute Myeloid Leukemia

doi: 10.1177/1533033819873927

Figure Lengend Snippet: Transcript expression of MAP4K genes in multiple normal tissues and AML. The expression of MAP4K genes in AML is highlighted in red. (A) MAP4K1; (B) MAP4K3; (C) MAP4K4; (D) MAP4K5. AML indicates acute myeloid leukemia; MAP4K, MAP kinase kinase kinase kinase.

Article Snippet: Vertical scatter plot of MAP4K mRNA expression and survival curves for MAP4K family were generated in GraphPad Prism v.7.0 (La Jolla, California).

Techniques: Expressing

Journal: Technology in Cancer Research & Treatment

Article Title: Prognostic Value of mRNA Expression of MAP4K Family in Acute Myeloid Leukemia

doi: 10.1177/1533033819873927

Figure Lengend Snippet: A, Analysis of enriched GO terms and KEGG pathways for MAP4K genes by using Database for Annotation, Visualization, and Integrated Discovery. B, Gene interaction networks according to selected gene expression levels in GeneMANIA. C, Pearson correlation coefficients for MAP4K1, MAP4K2, MAP4K3, MAP4K4, MAP4K5, and MINK1 gene expression levels. ** P < .05. GO indicates Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; MAP4K, MAP kinase kinase kinase kinase.

Article Snippet: Vertical scatter plot of MAP4K mRNA expression and survival curves for MAP4K family were generated in GraphPad Prism v.7.0 (La Jolla, California).

Techniques: Gene Expression

Journal: Technology in Cancer Research & Treatment

Article Title: Prognostic Value of mRNA Expression of MAP4K Family in Acute Myeloid Leukemia

doi: 10.1177/1533033819873927

Figure Lengend Snippet: Prognostic value of MAP4K genes expression. A-F, Kaplan-Meier survival curves for all patients with AML according to MAP4K1 (A), MAP4K2 (B), MAP4K3 (C), MAP4K4 (D), MAP4K5 (E), and MINK1 (F) expression. AML indicates acute myeloid leukemia; MAP4K, MAP kinase kinase kinase kinase.

Article Snippet: Vertical scatter plot of MAP4K mRNA expression and survival curves for MAP4K family were generated in GraphPad Prism v.7.0 (La Jolla, California).

Techniques: Expressing

Journal: Technology in Cancer Research & Treatment

Article Title: Prognostic Value of mRNA Expression of MAP4K Family in Acute Myeloid Leukemia

doi: 10.1177/1533033819873927

Figure Lengend Snippet: Prognostic Survival Analysis for High or Low Expression of MAP4K Family Genes.

Article Snippet: Vertical scatter plot of MAP4K mRNA expression and survival curves for MAP4K family were generated in GraphPad Prism v.7.0 (La Jolla, California).

Techniques: Expressing

Journal: Technology in Cancer Research & Treatment

Article Title: Prognostic Value of mRNA Expression of MAP4K Family in Acute Myeloid Leukemia

doi: 10.1177/1533033819873927

Figure Lengend Snippet: Joint effect analysis for MAP4K genes expression with stratified OS according to 2 selected MAP4K genes among MAP4K1, MAP4K3, MAP4K4, and MAP4K5. (A) MAP4K1 and MAP4K3, (B) MAP4K1 and MAP4K4, (C) MAP4K1 and MAP4K5, (D) MAP4K3 and MAP4K4, (E) MAP4K3 and MAP4K5, and (F) MAP4K4 and MAP4K5. Group A, low MAP4K1 + high MAP4K3; group C, high MAP4K1 + low MAP4K3; group D, low MAP4K1 + high MAP4K4; group F, high MAP4K1 + low MAP4K4; group G, low MAP4K1 + high MAP4K5; group I, high MAP4K1 + low MAP4K5; group J, high MAP4K3 + high MAP4K4; group L, low MAP4K3 + low MAP4K4; group M, high MAP4K3 + high MAP4K5; group O, low MAP4K3 + low MAP4K5; group P, high MAP4K4 + high MAP4K5; group R, low MAP4K4 + low MAP4K5; groups B, E, H, K, N, and Q correspond to other combinations of genes as detailed in . MAP4K indicates MAP kinase kinase kinase kinase; OS, overall survival.

Article Snippet: Vertical scatter plot of MAP4K mRNA expression and survival curves for MAP4K family were generated in GraphPad Prism v.7.0 (La Jolla, California).

Techniques: Expressing

Journal: Technology in Cancer Research & Treatment

Article Title: Prognostic Value of mRNA Expression of MAP4K Family in Acute Myeloid Leukemia

doi: 10.1177/1533033819873927

Figure Lengend Snippet: Joint effect analysis for MAP4K genes expression with stratified OS according to 3 or 4 selected MAP4K genes among MAP4K1, MAP4K3, MAP4K4, and MAP4K5. (A) MAP4K1, MAP4K3, and MAP4K4; (B) MAP4K1, MAP4K3, and MAP4K5; (C) MAP4K1, MAP4K4, and MAP4K5; (D) MAP4K3, MAP4K4, and MAP4K5; (E) MAP4K1, MAP4K3, MAP4K4, and MAP4K5. Group i, Low MAP4K1 + high MAP4K3 + high MAP4K4; group iii, High MAP4K1 + low MAP4K3 + low MAP4K4; group iv, Low MAP4K1 + high MAP4K3 + high MAP4K5; group vi, High MAP4K1 + low MAP4K3 + low MAP4K5; group vii, Low MAP4K1 + high MAP4K4 + high MAP4K5; group ix, High MAP4K1 + low MAP4K4 + low MAP4K5; group x, High MAP4K3 + high MAP4K4 + high MAP4K5; group xii, Low MAP4K3 + low MAP4K4 + low MAP4K5. Group ii, v, viii, and xi correspond to other combinations of genes as detailed in . Group 1, low MAP4K1 + high MAP4K3 + high MAP4K4 + high MAP4K5; group 3, High MAP4K1 + low MAP4K3 + low MAP4K4 + low MAP4K5. 2 correspond to other combinations of genes as detailed in . MAP4K indicates MAP kinase kinase kinase kinase; OS, overall survival.

Article Snippet: Vertical scatter plot of MAP4K mRNA expression and survival curves for MAP4K family were generated in GraphPad Prism v.7.0 (La Jolla, California).

Techniques: Expressing