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proteomics toolset for integrative data analysis protigy  (Broad Institute Inc)

 
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    Broad Institute Inc proteomics toolset for integrative data analysis protigy
    Proteomics Toolset For Integrative Data Analysis Protigy, 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/data+integration/proteomics+toolset+for+integrative+data+analysis+protigy/pmc10070353-381-18-26
    Average 90 stars, based on 1 article reviews
    proteomics toolset for integrative data analysis protigy - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Multiplex sample analysis:

    Article Title: HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy.
    Article Snippet: .. Statistical analyses for TMT immunopeptidomics Proteomics Toolset for Integrative Data Analysis (Protigy, v1.1.4, Broad Institute, https://github.com/broadinstitute/protigy) was used to calculate moderated t-test P values. ll OPEN ACCESS e19 Cell 188, 1–21.e1–e23, April 3, 2025 Please cite this article in press as: Jiang et al., HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy, Cell (2025), https://doi.org/10.1016/j.cell.2025.01.046 Article ..

    Immunopeptidomics:

    Article Title: HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy.
    Article Snippet: .. Statistical analyses for TMT immunopeptidomics Proteomics Toolset for Integrative Data Analysis (Protigy, v1.1.4, Broad Institute, https://github.com/broadinstitute/protigy) was used to calculate moderated t-test P values. ll OPEN ACCESS e19 Cell 188, 1–21.e1–e23, April 3, 2025 Please cite this article in press as: Jiang et al., HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy, Cell (2025), https://doi.org/10.1016/j.cell.2025.01.046 Article ..

    T-Test:

    Article Title: Time-resolved proximity proteomics uncovers a membrane tension-sensitive caveolin-1 interactome at the rear of migrating cells
    Article Snippet: Moderated t- test was performed with Proteomics Toolset for Integrative Data Analysis (ProTIGY, Broad Institute, Proteomics Platform, https://github.com/broadinstitute/protigy), and a p- value <0.05 was considered statistically significant. .. Moderated t- test was performed with Proteomics Toolset for Integrative Data Analysis (ProTIGY, Broad Institute, Proteomics Platform, https://github.com/broadinstitute/protigy), and a p- value <0.05 was considered statistically significant. ..

    Significance Assay:

    Article Title: Time-resolved proximity proteomics uncovers a membrane tension-sensitive caveolin-1 interactome at the rear of migrating cells
    Article Snippet: Moderated t- test was performed with Proteomics Toolset for Integrative Data Analysis (ProTIGY, Broad Institute, Proteomics Platform, https://github.com/broadinstitute/protigy), and a p- value <0.05 was considered statistically significant. .. Moderated t- test was performed with Proteomics Toolset for Integrative Data Analysis (ProTIGY, Broad Institute, Proteomics Platform, https://github.com/broadinstitute/protigy), and a p- value <0.05 was considered statistically significant. ..

    other:

    Article Title: Bulk exocytosis of large intracellular apical precursor organelles establishes apical domain identity during de novo lumen formation
    Article Snippet: A moderated T-test was performed using the Proteomics Toolset for Integrative Data Analysis (ProTIGY, Broad Institute, Proteomics Platform, https://github.com/broadinstitute/protigy ).



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    Single-cell analysis of HCC TME and hepatocyte metabolic reprogramming. (A) UMAP dimensionality reduction plot showing 22 initial cell clusters. (B) Annotation of 7 major cell populations based on established marker genes. (C) Expression patterns of CD274 (PD-L1) and CTLA4 in various cell types before and after immunotherapy. (D) Cellular composition across samples. Sample H68 exhibits the highest proportion of Hepatocytes. (E) UMAP plot of hepatocyte subclustering analysis based on metabolic-related gene expression profiles, identifying 5 subpopulations (clusters 0-4). Cluster 1 is significantly enriched in post-treatment samples. (F) KEGG pathway enrichment analysis reveals functional clustering of hepatocyte subpopulations (clusters 0-4). (G) Hierarchical clustering of significantly enriched pathways within these clusters. (H) Expression patterns of core genes within the Pyruvate metabolism pathway across the five hepatocyte subpopulations. Genes in this pathway exhibit significantly elevated expression in Cluster 1.

    Journal: Frontiers in Immunology

    Article Title: The inhibitory effect of hepatic cancer energy metabolism on immune checkpoint therapy: perspectives from single-cell multi-omics analysis

    doi: 10.3389/fimmu.2026.1753670

    Figure Lengend Snippet: Single-cell analysis of HCC TME and hepatocyte metabolic reprogramming. (A) UMAP dimensionality reduction plot showing 22 initial cell clusters. (B) Annotation of 7 major cell populations based on established marker genes. (C) Expression patterns of CD274 (PD-L1) and CTLA4 in various cell types before and after immunotherapy. (D) Cellular composition across samples. Sample H68 exhibits the highest proportion of Hepatocytes. (E) UMAP plot of hepatocyte subclustering analysis based on metabolic-related gene expression profiles, identifying 5 subpopulations (clusters 0-4). Cluster 1 is significantly enriched in post-treatment samples. (F) KEGG pathway enrichment analysis reveals functional clustering of hepatocyte subpopulations (clusters 0-4). (G) Hierarchical clustering of significantly enriched pathways within these clusters. (H) Expression patterns of core genes within the Pyruvate metabolism pathway across the five hepatocyte subpopulations. Genes in this pathway exhibit significantly elevated expression in Cluster 1.

    Article Snippet: Integrated single-cell RNA-seq data (GEO, Mendeley) were analyzed using Seurat, AUCell, pySCENIC, CellChat, and Monocle.

    Techniques: Single-cell Analysis, Marker, Expressing, Gene Expression, Functional Assay