java gsea desktop application software  (Broad Institute Inc)

Journal: Antibiotics

Article Title: Antibiogram, Prevalence of OXA Carbapenemase Encoding Genes, and RAPD-Genotyping of Multidrug-Resistant Acinetobacter baumannii Incriminated in Hidden Community-Acquired Infections

doi: 10.3390/antibiotics9090603

Figure Lengend Snippet: RAPD genotyping of the strains. ( a ) Combined RAPD patterns of 23 clinical Acinetobacter isolates obtained after electrophoresis of the PCRs with five different primers individually. For each primer, five RAPD gels were combined into one image. ( b ) RAPD dendrogram was constructed with GelJ cluster analysis software by Unweighted Pair Group Method with Arithmetic Mean UPGMA). Percentages of similarity and primers used as presented in on the top line of the dendrogram. RAPD type and strain code as in and strain numbers as presented in a appear on the right (between parenthesis).

Article Snippet: For cluster analysis, a DNA fingerprint java application analysis software (GelJ) was used (downloaded from https://sourceforge.net/projects/gelj/ ) [ ].

Techniques: Electrophoresis, Construct, Software

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:

Journal: PLoS ONE

Article Title: Asymmetric Regulation of Peripheral Genes by Two Transcriptional Regulatory Networks

doi: 10.1371/journal.pone.0160459

Figure Lengend Snippet: (A) Principal component analysis of monocyte- and fibroblast-specific gene expression. (B) Heatmap diagram of monocyte- and fibroblast-specific gene expression. (C–E) The enrichment plot in the monocytic gene set of KDOE, OE-only, and KD-only. (F–H) Gene set enrichment analysis in the fibroblastic gene set of KDOE, KD-only, and OE-only.

Article Snippet: We used the java GSEA Desktop Application software from the Broad Institute Gene Set Enrichment Analysis website ( http://software.broadinstitute.org/gsea/downloads.jsp ).

Techniques: Gene Expression