Human Gene Set: GAVISH_3CA_METAPROGRAM_FIBROBLASTS_MHC_II_CYTOKINE


Standard name GAVISH_3CA_METAPROGRAM_FIBROBLASTS_MHC_II_CYTOKINE
Systematic name M46659
Brief description Genes upregulated in subsets of cells of a given type within various tumors
Full description or abstract In this study, an extensive analysis was conducted to define meta-programs (MPs) capturing intra-tumor heterogeneity across a spectrum of tumor types. The approach utilized non-negative matrix factorization (NMF) to analyze each cell type separately within individual tumor samples. This involved the analysis of malignant cells, macrophages, fibroblasts, endothelial cells, epithelial cells, T-cells, and B-cells. NMF was executed with varying parameter values (K=4, 5, 6, 7, 8, 9), thereby generating 39 programs for each cell type per sample. Each NMF program was summarized by the top 50 genes based on NMF coefficients.\nRobust MPs were then delineated for each cell type using a set of stringent criteria, including recurrence within the same tumor, similarity to programs in other tumors, and non-redundancy within a tumor. Subsequently, these robust NMF programs were clustered (per cell type) based on Jaccard similarity, leading to the identification of MPs associated with each cell type.\nTo enhance the quality of the MPs, a refinement steps were undertaken, involving the removal of MPs suspected of reflecting low-quality data (with an overrepresentation of ribosomal proteins or mitochondrial-encoded genes), single-study inclusion, or similarity to miss-annotated cell types.
Collection C4: Computational
      3CA: Curated Cancer Cell Atlas gene sets
Source publication Pubmed 37258682   Authors: Gavish A,Tyler M,Greenwald AC,Hoefflin R,Simkin D,Tschernichovsky R,Galili Darnell N,Somech E,Barbolin C,Antman T,Kovarsky D,Barrett T,Gonzalez Castro LN,Halder D,Chanoch-Myers R,Laffy J,Mints M,Wider A,Tal R,Spitzer A,Hara T,Raitses-Gurevich M,Stossel C,Golan T,Tirosh A,Suvā ML,Puram SV,Tirosh I
Exact source 3CA Download meta_programs_2023-07-13: Fibroblasts. MHC-II/Cytokine
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(show 2 gene sets from the same authors)
External links https://www.weizmann.ac.il/sites/3CA/
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Source species Homo sapiens
Contributed by Itay Tirosh (Weizmann Institute of Science)
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identifier namespace		 HUMAN_GENE_SYMBOL
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Version history 2024.1.Hs: Renamed from GAVISH_3CA_METAPROGRAM_FIBROBLASTS_CAF_3.

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