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gsea java desktop program gsea v. 4.1.0 for windows  (Broad Institute Inc)

 
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    Structured Review

    Broad Institute Inc gsea java desktop program gsea v. 4.1.0 for windows
    Unbiased transcriptomic analysis shows that pancreatic SCG5 expression is associated with the adipopenia phenotype. (A) Bubble plot summarizing the results of gene set enrichment analysis <t>(GSEA)</t> dissecting adipose transcriptomic profiles from donors of pancreatic SCG5 -high or -low groups. (B) Representative enrichment plots of cachexia and adipopenia-related gene sets. (C–F) Gene networks comparing correlations among top genes of each indicated gene set, human phenotype ontology (HP) Lipodystrophy (C) , HP Cachexia (D) , Gene Ontology biological process (GOBP) Mitochondrial respiratory chain complex assembly (E) , and GOBP Brown fat cell differentiation (F) .
    Gsea Java Desktop Program Gsea V. 4.1.0 For Windows, 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/gsea+java+desktop+program/gsea+software/pmc09428794-75-1-16
    Average 90 stars, based on 1 article reviews
    gsea java desktop program gsea v. 4.1.0 for windows - by Bioz Stars, 2026-09
    90/100 stars

    Images

    1) Product Images from "Machine learning-featured Secretogranin V is a circulating diagnostic biomarker for pancreatic adenocarcinomas associated with adipopenia"

    Article Title: Machine learning-featured Secretogranin V is a circulating diagnostic biomarker for pancreatic adenocarcinomas associated with adipopenia

    Journal: Frontiers in Oncology

    doi: 10.3389/fonc.2022.942774

    Unbiased transcriptomic analysis shows that pancreatic SCG5 expression is associated with the adipopenia phenotype. (A) Bubble plot summarizing the results of gene set enrichment analysis (GSEA) dissecting adipose transcriptomic profiles from donors of pancreatic SCG5 -high or -low groups. (B) Representative enrichment plots of cachexia and adipopenia-related gene sets. (C–F) Gene networks comparing correlations among top genes of each indicated gene set, human phenotype ontology (HP) Lipodystrophy (C) , HP Cachexia (D) , Gene Ontology biological process (GOBP) Mitochondrial respiratory chain complex assembly (E) , and GOBP Brown fat cell differentiation (F) .
    Figure Legend Snippet: Unbiased transcriptomic analysis shows that pancreatic SCG5 expression is associated with the adipopenia phenotype. (A) Bubble plot summarizing the results of gene set enrichment analysis (GSEA) dissecting adipose transcriptomic profiles from donors of pancreatic SCG5 -high or -low groups. (B) Representative enrichment plots of cachexia and adipopenia-related gene sets. (C–F) Gene networks comparing correlations among top genes of each indicated gene set, human phenotype ontology (HP) Lipodystrophy (C) , HP Cachexia (D) , Gene Ontology biological process (GOBP) Mitochondrial respiratory chain complex assembly (E) , and GOBP Brown fat cell differentiation (F) .

    Techniques Used: Expressing, Cell Differentiation

    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 GSEA Java desktop program was downloaded from the Broad Institute (http:// www.broadinstitute.org/gsea/index.jsp) For microRNA - bcl2fastq software (version 0.10.1; Illumina, Inc.). ..

    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. .. GSEA software (v4.1.0; Broad Institute, MIT; UCSD) was used to identify enriched signaling pathways and biological functions associated with a specific treatment. ..

    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 GSEA software (version 3.0).

    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 GSEA software (version 3.0). ..

    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. .. GSEA software (v4.1.0; Broad Institute, MIT; UCSD) was used to identify enriched signaling pathways and biological functions associated with a specific treatment. ..

    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 GSEA software (version 3.0).

    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 GSEA software (version 3.0). ..



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    Broad Institute Inc gsea java desktop program gsea v. 4.1.0 for windows
    Unbiased transcriptomic analysis shows that pancreatic SCG5 expression is associated with the adipopenia phenotype. (A) Bubble plot summarizing the results of gene set enrichment analysis <t>(GSEA)</t> dissecting adipose transcriptomic profiles from donors of pancreatic SCG5 -high or -low groups. (B) Representative enrichment plots of cachexia and adipopenia-related gene sets. (C–F) Gene networks comparing correlations among top genes of each indicated gene set, human phenotype ontology (HP) Lipodystrophy (C) , HP Cachexia (D) , Gene Ontology biological process (GOBP) Mitochondrial respiratory chain complex assembly (E) , and GOBP Brown fat cell differentiation (F) .
    Gsea Java Desktop Program Gsea V. 4.1.0 For Windows, 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/gsea+java+desktop+program/gsea+software/pmc09428794-75-1-16
    Average 90 stars, based on 1 article reviews
    gsea java desktop program gsea v. 4.1.0 for windows - by Bioz Stars, 2026-09
    90/100 stars
      Buy from Supplier

    Image Search Results


    Unbiased transcriptomic analysis shows that pancreatic SCG5 expression is associated with the adipopenia phenotype. (A) Bubble plot summarizing the results of gene set enrichment analysis (GSEA) dissecting adipose transcriptomic profiles from donors of pancreatic SCG5 -high or -low groups. (B) Representative enrichment plots of cachexia and adipopenia-related gene sets. (C–F) Gene networks comparing correlations among top genes of each indicated gene set, human phenotype ontology (HP) Lipodystrophy (C) , HP Cachexia (D) , Gene Ontology biological process (GOBP) Mitochondrial respiratory chain complex assembly (E) , and GOBP Brown fat cell differentiation (F) .

    Journal: Frontiers in Oncology

    Article Title: Machine learning-featured Secretogranin V is a circulating diagnostic biomarker for pancreatic adenocarcinomas associated with adipopenia

    doi: 10.3389/fonc.2022.942774

    Figure Lengend Snippet: Unbiased transcriptomic analysis shows that pancreatic SCG5 expression is associated with the adipopenia phenotype. (A) Bubble plot summarizing the results of gene set enrichment analysis (GSEA) dissecting adipose transcriptomic profiles from donors of pancreatic SCG5 -high or -low groups. (B) Representative enrichment plots of cachexia and adipopenia-related gene sets. (C–F) Gene networks comparing correlations among top genes of each indicated gene set, human phenotype ontology (HP) Lipodystrophy (C) , HP Cachexia (D) , Gene Ontology biological process (GOBP) Mitochondrial respiratory chain complex assembly (E) , and GOBP Brown fat cell differentiation (F) .

    Article Snippet: The GSEA Java desktop program (GSEA v. 4.1.0 for Windows) was downloaded from the website of Broad Institute ( https://www.gsea-msigdb.org ).

    Techniques: Expressing, Cell Differentiation