pearson's correlation coefficient prism 5.0  (GraphPad Software Inc)

Journal: Molecules and Cells

Article Title: Epigenetic Activation of Tensin 4 Promotes Gastric Cancer Progression

doi: 10.14348/molcells.2023.2148

Figure Lengend Snippet: (A) Quantitative RT-PCR analysis for TNS4 mRNA in GC cell lines (mean ± SD; n = 3 independent samples). (B) Western blotting for TNS4 expression in GC cell lines. GAPDH was used as the loading control. (C) Distribution of TNS4 dependency of GC cell lines divided into TNS4-high (13 cell lines) and TNS4-low (17 cell lines) groups. Dots depict TNS4 effect scores. A lower effect score indicates that TNS4 was more likely to be essential for a given cell line. Data were downloaded from the DepMap web portal ( https://depmap.org/portal/ ) based on the CRISPR Public 22Q2 dataset. (D) Pearson’s correlation analyses between TNS4 expression and TNS4 effect scores for the GC cell lines from the DepMap data. (E) Gene ontology analysis of differentially expressed genes between TNS4-high (SNU-601, SNU-620, and AGS) and -low (SNU-16, SNU-216, and SNU-668) GC cell lines using CCLE RNA-seq data.

Article Snippet: Statistical analysis of correlations between expression and methylation was performed using Pearson’s correlation coefficient (Prism 5.0; GraphPad Software, USA).

Techniques: Quantitative RT-PCR, Western Blot, Expressing, Control, CRISPR, RNA Sequencing

Journal: Molecules and Cells

Article Title: Epigenetic Activation of Tensin 4 Promotes Gastric Cancer Progression

doi: 10.14348/molcells.2023.2148

Figure Lengend Snippet: (A) Bisulfite sequencing (BS-seq) of gastric cancer (GC) cell lines and paired normal and tumor tissue samples. Methylation status of the TNS4 promoter in GC cell lines with high or low expression of TNS4 . BS-seq regions are also indicated in . These regions include the infinium human methylation 450 K BeadChip CpG probes cg08074477, cg20468081, and cg09303236. Black circles, methylated; white circles, unmethylated. Total methylation percentages are indicated. (B) TNS4 mRNA levels in GC cells treated with 5-aza-dC and/or trichostatin A (TSA). n = 8 independent experiments; mean ± SD; *** P < 0.001 (Mann–Whitney U-test). (C) The methylation level of the TNS4 promoter in normal gastric tissue (n = 11) and GC tumor tissue (n = 250) from TCGA data using Infinum Human BeadChip 450K. BS-seq regions in are indicated with gray shading. TSS, transcription start site. Each box plot shows the median and 25th and 75th percentiles. Statistical significance between normal and tumor tissues was inferred by using the Mann–Whitney U-test; ** P < 0.01, *** P < 0.001. (D) Pearson’s correlation analyses between TNS4 CpG methylation and TNS4 expression levels for the indicated probes from TCGA data.

Article Snippet: Statistical analysis of correlations between expression and methylation was performed using Pearson’s correlation coefficient (Prism 5.0; GraphPad Software, USA).

Techniques: Methylation Sequencing, Methylation, Expressing, MANN-WHITNEY, CpG Methylation Assay