java desktop software version 4.03 of gene set enrichment analysis  (Broad Institute Inc)

Journal: BMB Reports

Article Title: Oral administration of ginseng berry concentrate improves lactate metabolism and increases endurance performance in mice

doi: 10.5483/BMBRep.2023-0040

Figure Lengend Snippet: Unbiased gene set enrichment analysis (GSEA) and muscular nicotinamide adenine dinucleotide (NAD + ) levels. (A) Volcano plot summarizing the results of unbiased GSEA with the normalized enrichment score (NES) and nominal P-value [−log 10 (P-val)]. Pink dots indicates statistically significantly altered gene sets. (B) Bubble plot highlighting representative gene sets linked to lactate metabolism. It indicates that for each gene set, the depth of the purple color indicates the nominal P-value, and the size of the node indicates the size. (C) Representative enrichment plot generated by GSEA related with lactate metabolism. NES, nominal (Nom) P-values, and false discovery rate (FDR) Q values are indicated. (D) Heatmap displaying representative genes of three genes, lactate metabolism, Mitochondrial electron transport NADH to ubiquinone, and Inner mitochondrial membrane protein complex. (E) NAD + levels in gastrocnemius. All values are represented as mean ± standard deviation, and the P-values were determined by one-way ANOVA followed by Tukey’s test. P-values of < 0.01 (**), and < 0.0001 (****) were considered statistically significant.

Article Snippet: GSEA was conducted using the GSEA Java desktop software developed by the Broad Institute available for Windows at https://www.gsea-msigdb.org as described previously ( ).

Techniques: Generated, Membrane, Standard Deviation

Journal: The Journal of Pathology: Clinical Research

Article Title: CD24 is a surrogate for ‘immune‐cold’ phenotype in aggressive large B‐cell lymphoma

doi: 10.1002/cjp2.266

Figure Lengend Snippet: Characteristics of CD24‐high DLBCL. (A) Bar plot indicating that the numbers of CD24‐high and CD24‐low cases were comparable in GCB and ABC DLBCL. UNC, unclassified. (B–D) CD24‐high cases were enriched in MYC rearrangement cases (B), single‐ or double‐hit cases (C), and MHG cases (D). NA, not assessed. (E) Bar plot of the GSEA. NES, normalized enrichment score. (F) The most enriched gene set of the CD24‐high group was ‘hallmark_MYC_targets’. (G, H) The top two enriched gene sets in the CD24‐low group were related inflammatory genes, such as ‘Hallmark_inflammatory_response’ and ‘Hallmark_TNFa_signaling_via_NFkB’.

Article Snippet: The Broad Institute JAVA Desktop software Version 4.03 of GSEA was utilized.

Techniques:

Journal: Cancer Medicine

Article Title: METTL3 expression is associated with glycolysis metabolism and sensitivity to glycolytic stress in hepatocellular carcinoma

doi: 10.1002/cam4.2918

Figure Lengend Snippet: METTL3 expression was associated with altered glucose metabolism in HCC cases. A, Illustration of enzymes involved the key steps in glucose metabolic flux. B, Heatmap with cluster analysis of METT3 expression and glucose metabolism related genes revealed a co‐expression trend between METTL3 and genes involved in glycolysis. C, D, GSEA plot of two predefined gene sets based on the METTL3 expression revealed genes involved in normal glucose metabolism were significantly enriched in HCC cases with lower METTL3 expression, which suggesting that normal glucose metabolism was preserved in these cases. E, A heatmap displaying the Spearman rank correlation test results which implied positive correlation between METTL3 expression and glycolysis‐related genes and negative correlation between METTL3 expression and glycogenesis‐related genes, the bar indicates the value of spearman correlation coefficient

Article Snippet: Java GSEA Desktop Application software (V3.0, Broad Institute) was used.

Techniques: Expressing

Journal: Cancer Medicine

Article Title: METTL3 expression is associated with glycolysis metabolism and sensitivity to glycolytic stress in hepatocellular carcinoma

doi: 10.1002/cam4.2918

Figure Lengend Snippet: Correlation between METTL3 expression and activity of mTORC1 activity. A, GSEA plot of mTOR signal pathway based on METTL3 expression levels in TCGA cases. B, HCC cell lines were treated with siRNA oligonucleotides or not, then the indicated proteins were detected by WB. (C‐G) The HCC cell lines were treated with rapamycin or co‐treated with siRNA oligonucleotides, for 48 h followed by immunoblotting for mTOR phosphorylation levels (C), glucose uptake assays in HCC cells Huh‐7 (D) and SMMC‐7721 (E), and lactate production assays in Huh‐7 cell line (F) and SMMC‐7721 cell line (G). H, I, Gene‐specific m6A‐IP‐qPCR results showing the relative methylation levels of five RNAs in the HCC cell lines treated with siRNA oligonucleotides compared to those normal control cells

Article Snippet: Java GSEA Desktop Application software (V3.0, Broad Institute) was used.

Techniques: Expressing, Activity Assay, Western Blot, Phospho-proteomics, Methylation, Control

Journal: Scientific Reports

Article Title: Transcriptome analysis suggests a compensatory role of the cofactors coenzyme A and NAD + in medium-chain acyl-CoA dehydrogenase knockout mice

doi: 10.1038/s41598-019-50758-0

Figure Lengend Snippet: Up- and downregulated metabolic gene sets in KO compared to WT based on the GSEA method.

Article Snippet: Gene-set enrichment analysis (GSEA) was performed according to Subramanian et al . 2005 using the GSEA desktop Java application software (version 2.2.4, Broad Institute).

Techniques: Phospho-proteomics

Journal: Scientific Reports

Article Title: Transcriptome analysis suggests a compensatory role of the cofactors coenzyme A and NAD + in medium-chain acyl-CoA dehydrogenase knockout mice

doi: 10.1038/s41598-019-50758-0

Figure Lengend Snippet: Up- and downregulated metabolic gene sets in KO compared to WT based on the Alternative GSEA method.

Article Snippet: Gene-set enrichment analysis (GSEA) was performed according to Subramanian et al . 2005 using the GSEA desktop Java application software (version 2.2.4, Broad Institute).

Techniques: