gsea java desktop software (Broad Institute Inc)
Structured Review
![Unbiased gene set enrichment analysis <t>(GSEA)</t> 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.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_5566/pmc10315566/pmc10315566__bmb-56-6-353-f4.jpg)
Gsea Java Desktop Software, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/java+desktop+software/gsea+software/pmc10315566-108-5-12
Average 90 stars, based on 1 article reviews
Images
1) Product Images from "Oral administration of ginseng berry concentrate improves lactate metabolism and increases endurance performance in mice"
Article Title: Oral administration of ginseng berry concentrate improves lactate metabolism and increases endurance performance in mice
Journal: BMB Reports
doi: 10.5483/BMBRep.2023-0040
Figure Legend 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.
Techniques Used: Generated, Membrane, Standard Deviation
Related Articles
Software:Article Title: Article Snippet: Microsoft Excel for Mac, Version 16.54 QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA), version 01-20-04 Palantir Foundry platform (Palantir Technologies), version 5.341.0 For Whole blood transcriptome - Trimmomatic (version 0.36) - STAR aligner (version 2.5.3a) - HTSeq (version 0.9.1) - R package edgeR (version 3.30.3) - R package LIMMA (version 3.44.3) - Molecular Signatures Database gene sets (version 6.1). .. The Article Title: Colocalized inhibition of TGF-β and PD-L1 Article Snippet: DEGs identified between treatment groups were evaluated using the “investigate gene sets” function at the Molecular Signature Database (MSigDB v7.3; Broad Institute, MIT; UC San Diego; https://www.gsea-msigdb.org/gsea/msigdb/index.jsp) to compute overlaps between the list of genes and gene sets in MSigDB, which is a collection of curated gene signatures for the evaluation of biological functions. .. Article Title: Machine learning-based integration develops a hypoxia-derived signature for improving outcomes in glioma Article Snippet: .. Exploring the fundamental signaling pathways of the two subtypes was carried out utilizing Article Title: Machine learning-based integration develops a hypoxia-derived signature for improving outcomes in glioma Article Snippet: Exploring the fundamental signaling pathways of the two subtypes was carried out utilizing GSEA software (version 3.0) acquired from the Broad Institute ( http://www.broadinstitute.org/gsea ). .. The gene expression profile of the two subtypes in the TCGA cohort, along with the hallmark gene sets from the MSigDB datasets provided by the Broad Institute, were imported into the other:Article Title: Supporting Information Article Snippet: Gene set enrichment analysis (GSEA) was performed using GSEA version 4.1.0 software (Broad Institute) as previously described[13]. Article Title: Targeting mitochondria mitigates chemotherapy-induced bone marrow dysfunction Article Snippet: Gene-set enrichment analysis (GSEA) was conducted using the Broad-Institute GSEA tool (V4.4.0) ( , ), employing the classic enrichment score calculation, 1.000 gene-set based permutations, and the signal2noise metric for gene ranking. Article Title: Engineered regulatory T cells Article Snippet: We then carried out Gene Set Enrichment Analysis (GSEA) pathway analysis using GSEA v3.0 from the Broad Institute and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Article Title: Engineered regulatory T cells Article Snippet: We made these filtered lists for each donor and comparison and used the CPMs to carry out gene set enrichment analysis (GSEA) with the GSEA v3.0 software from the Broad Institute. Protein-Protein interactions:Article Title: Colocalized inhibition of TGF-β and PD-L1 Article Snippet: DEGs identified between treatment groups were evaluated using the “investigate gene sets” function at the Molecular Signature Database (MSigDB v7.3; Broad Institute, MIT; UC San Diego; https://www.gsea-msigdb.org/gsea/msigdb/index.jsp) to compute overlaps between the list of genes and gene sets in MSigDB, which is a collection of curated gene signatures for the evaluation of biological functions. .. Article Title: Machine learning-based integration develops a hypoxia-derived signature for improving outcomes in glioma Article Snippet: .. Exploring the fundamental signaling pathways of the two subtypes was carried out utilizing Gene Expression:Article Title: Machine learning-based integration develops a hypoxia-derived signature for improving outcomes in glioma Article Snippet: Exploring the fundamental signaling pathways of the two subtypes was carried out utilizing GSEA software (version 3.0) acquired from the Broad Institute ( http://www.broadinstitute.org/gsea ). .. The gene expression profile of the two subtypes in the TCGA cohort, along with the hallmark gene sets from the MSigDB datasets provided by the Broad Institute, were imported into the |


