The Molecular Signatures Database (MSigDB) hallmark gene set collection

By Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir, Mahmoud Ghandi, Jill P. Mesirov, Pablo Tamayo. 2015

9,497 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/93d5369a0be3134c6018373d5290923f3d718815

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In Molecular Biology

Citations in the corpus

Integrative molecular and clinical modeling of clinical outcomes to PD-1 blockade in metastatic melanoma patients (2019, positive): “GSEA and ssGSEA— Gene Set Enrichment Analysis 32 (GSEA) was performed using the Cancer Hallmarks genesets 33 from MSigDB at https://cloud.genepattern.org/.”
CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models (2017, methodology): “…stroma, including epithelial to mesenchymal transition (EMT), extracellular matrix organization and angiogenesis, which ranked 1 st , 2 nd and 8 th in terms of significance among 2038 unselected gene sets from reactome.org 30 and MSigDB Hallmarks 31 (hypergeometric test, Supplementary Table 2).”
Targeting KRAS Mutant Cancers with a Covalent G12C-Specific Inhibitor. (2018, methodology): “…to transformation by oncogenic KRAS (Barbie et al., 2009; Chiaradonna et al., 2006; Liberzon et al., 2015), such as E2F transcription factors (Liberzon et al., 2015), a MYC regulatory network (Bild et al., 2006), ERK activation (Dry et al., 2010; Kwong et al., 2015), and KRAS-dependency…”
Interrogation of the Microenvironmental Landscape in Brain Tumors Reveals Disease-Specific Alterations of Immune Cells (2020, positive): “In the Molecular Signature Database (MSigDB; Liberzon et al., 2015) ‘‘hallmark’’ collection of major biological categories, T-MG and T-MDMs showed pathway enrichment in (1) modeling of the TME (‘‘Angiogenesis,’’ ‘‘Hypoxia’’), (2) inflammation (‘‘Inflammatory Response,’’ ‘‘Allograft Rejection’’), and”
Modulation of Myelopoiesis Progenitors Is an Integral Component of Trained Immunity (2018, methodology): “Regarding metabolic pathways, gene set enrichment analysis (GSEA) using the Molecular Signatures Database (MSigDB) hallmark gene set collection (Liberzon et al., 2015) showed a significant positive correlation with glycolysis and cholesterol homeostasis gene sets in LT-HSCs from b-glucan-treated…”
Quantitative Proteomics of the Cancer Cell Line Encyclopedia (2020, methodology): “A primary tool for several analyses in this work are various gene set databases taken fromMSigDB (Liberzon et al., 2011, 2015).”
Multimodal Co-Attention Transformer for Survival Prediction in Gigapixel Whole Slide Images (2021, methodology): “In our implementation, we use N = 6 functional categories obtained from [32] to deﬁne the following genomic embeddings: 1) Tumor Supression, 2) Oncogenesis, 3) Protein Kinases, 4) Cellular Differentiation, 5) Transcription, and 6) Cytokines and Growth.”
Integrative Clinical Genomics of Metastatic Cancer (2017, neutral): “Next, we looked at transcriptional signatures associated with perturbed cancer-related genes 25,26 .”