Tag: MSigDB

Single-cell and single-nucleus RNA sequencing of sarcoma subtypes In this work, we studied sarcomas from varying tissue origins, including osteosarcoma (OS), Ewing sarcoma (ES), and desmoplastic small round cell tumor (DSRCT) (Fig. 1). We used different dissociation protocols: Miltenyi Tumor Dissociation Kit, cold-active protease derived from Bacillus licheniformis, and Nuclei EZ…

Standard name REACTOME_ACTIVATED_POINT_MUTANTS_OF_FGFR2 Systematic name M647 Brief description Genes involved in Activated point mutants of FGFR2 Full description or abstract   Collection ARCHIVED: Archived Founder gene sets that are referenced by current Hallmarks      C2_CP: ARCHIVED Canonical Pathways            C2_CP:REACTOME: ARCHIVED Reactome Pathways Source publication   Exact source R-HSA-2033519 Related gene sets   External…

Clinical and biochemical characteristics of parathyroid carcinoma In total, 50 thyroid tissues were collected from three groups, 12 parathyroid carcinomas, 28 parathyroid adenomas, and 10 normal parathyroid tissues, for genomic and transcriptomic profiling (Fig. 1). The detailed protocols and quality control procedures are described in the Materials and Methods section….

DOI: 10.18129/B9.bioc.mastR   Markers Automated Screening Tool in R Bioconductor version: Release (3.17) mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from…

Introduction Breast cancer is the second most common cancer and is the leading cause of cancer-related death among females worldwide with over 2 million newly diagnosed cases and more than 60 thousand deaths every year.Citation1 Despite advances in treatment, the mortality rate of breast cancer remains high, mainly due to…

Genomics-based consensus tumor purity estimates For TCGA samples, genomic-based consensus tumor purities were computed as a mean of predictions from ABSOLUTE17, AbsCNSeq18, ASCAT15, and PurBayes16 following the approach reported in Ghoshdastider et al. 41. AbsCNSeq and PurBayes estimates are based on mutation variant allele frequency data, and ASCAT and ABSOLUTE…

Bioinformatician position available at NIH (Bethesda, MD) We seek a bioinformatician/data scientist with a strong record of collaborative interactions with biologists. The successful candidate must have a M.S or Ph.D. degree in bioinformatics, computational biology, computer science, or a related field and have the ability to work independently or as…

Standard name RESPIRATORY_CHAIN_COMPLEX_I Systematic name M13440 Brief description Genes annotated by the GO term GO:0045271. Respiratory chain complex I is an enzyme of the respiratory chain. It consists of at least 34 polypeptide chains and is L-shaped, with a horizontal arm lying in the membrane and a vertical arm that…

Goddard, E. T., Bozic, I., Riddell, S. R. & Ghajar, C. M. Dormant tumour cells, their niches and the influence of immunity. Nat. Cell Biol. 20, 1240–1249 (2018). Article  CAS  PubMed  Google Scholar  Malladi, S. et al. Metastatic latency and immune evasion through autocrine inhibition of WNT. Cell 165, 45–60…

From GeneSetEnrichmentAnalysisWiki GSEA Home | Downloads | Molecular Signatures Database | Documentation | Contact Introduction With the release of MSigDB 2023.1 we have created a new SQLite database for the fully annotated gene sets in both the Human (2023.1.Hs) and the Mouse (2023.1.Ms) resources. Each ships as a single-file database…

Stephenson, W. et al. Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation. Nat. Commun. 9(1), 791 (2018). Article  ADS  PubMed  PubMed Central  Google Scholar  Schmidt, C. J. et al. Infection with Clostridioides difficile attenuated collagen-induced arthritis in mice and involved mesenteric Treg and Th2 polarization. Front. Immunol….

msigdbr returns the same genesets for mouse as in for human, 0 If we were to query the MSigDb database for mouse and human, respectively: mauz <-msigdbr::msigdbr(species=”Mus musculus”) hooman <-msigdbr::msigdbr(species = “Homo sapiens”) And counted the number of genesets from the C8 category, for instance, then both queries would yield…

Battery gene sets for CAMERA limma 1 @e1fb1374 Last seen 8 hours ago Germany Hi everyone, I’m confused with the results of my CAMERA analysis. For building indexes, I used the battery of gene sets from MSigDb. I transformed the gmt files to list and built indexes. The initial count…

Standard name MITOCHONDRIAL_RESPIRATORY_CHAIN Systematic name M19046 Brief description Genes annotated by the GO term GO:0005746. The protein complexes that form the mitochondrial electron transport system (the respiratory chain). Complexes I, III and IV can transport protons if embedded in an oriented membrane, such as an intact mitochondrial inner membrane. Full…

Edelmann L, Pandita RK, Morrow BE. Low-copy repeats mediate the common 3-Mb deletion in patients with velo-cardio-facial syndrome. Am J Hum Genet. 1999;64:1076–86. Article  CAS  PubMed  PubMed Central  Google Scholar  Shaikh TH, Kurahashi H, Saitta SC, O’Hare AM, Hu P, Roe BA, et al. Chromosome 22-specific low copy repeats and…

Background. Oxidative stress (OS) can either lead to leukemogenesis or induce tumor cell death by inflammation and immune response accompanying the process of OS through chemotherapy. However, previous studies mainly focus on the level of OS state and the salient factors leading to tumorigenesis and progression of acute myeloid leukemia…

Gicquel, C., El-Osta, A. & Le Bouc, Y. Epigenetic regulation and fetal programming. Best Pract. Res. Clin. Endocrinol. Metab. 22, 1–16 (2008). CAS  Google Scholar  Godfrey, K. M. & Barker, D. J. Fetal programming and adult health. Public Health Nutr. 4, 611–624 (2001). CAS  Google Scholar  Encinias, H. B., Lardy,…

GSEA on nonmodel organisms 2 Hi, I want to do GSEA analysis in R on significantly differentially expressed genes on nonmodel species (five in total). My research is based on cross-species comparative transcriptomics. And this is what I am doing: I already have species-specific: de novo assemblies, annotations (across 7…

Mechanisms of sepsis severity and mortality in COVID-19 patients To identify COVID-19 specific severity mechanisms, we initially compared the whole blood gene expression profiles associated with defined severity groups from a cohort of 124 patients recruited at various times relative to hospital admission. Patient severity was assessed using two measures,…

Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed Central  Article  CAS  Google Scholar  Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central …

Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central  Article  Google Scholar  Hekselman, I. & Yeger-Lotem, E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat. Rev. Genet. 21, 137–150 (2020)….

lncRNA expression according to breast cancer clinicopathological subtypes To identify lncRNAs expressed by specific breast cancer subtypes or associated with clinicopathological features, we analyzed RNA-sequencing data from two large independent breast cancer cohorts: SCAN-B (n = 3455)17 and TCGA-BRCA (n = 1095). We focused on lncRNAs annotated in the Ensembl18 v93 non-coding reference transcriptome…

Cell-type annotation scRNA-seq data were filtered to discard low-quality cells and doublets (Supplementary Fig. 1, Extended Data Fig. 1 and Methods). Supervised clustering (Reference Component Analysis v2 (RCA2)) at low resolution grouped cells into 11 major cell types (Extended Data Fig. 1). To identify epithelial cell subtypes, we initially analyzed…

Dataset MSigDB Cancer Gene Co-expression Modules Category transcriptomics Type co-expressed gene Description tumor necrosis factor (ligand) superfamily, member 10|The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This protein preferentially induces apoptosis in transformed and tumor cells, but does not…

Introduction Lung cancer is the major leading cause of tumour-related deaths throughout the world, while lung squamous cell carcinoma (LUSC) as the second most common histological type of lung cancer.1 Each year, almost 1.8 million people are diagnosed with lung cancer worldwide and 400,000 of these die from LUSC.2,3 Due to…

Overview of the transcriptomics-guided drug discovery strategy.(A) Schematic outline of the drug screening strategy. (B) Heatmap shows the gene expression pattern of the druggable genes (www.dgidb.org) identified both in CS-exposed mice and patient with COPD databases. (C) Reactome pathway enrichment analysis of genes differentially expressed from patients with COPD (8)…

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article  Google Scholar  2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…

This article was originally published here Front Cell Dev Biol. 2021 Nov 25;9:762478. doi: 10.3389/fcell.2021.762478. eCollection 2021. ABSTRACT Objective: Resistance to immune checkpoint inhibitors (ICIs) has been a massive obstacle to ICI treatment in metastatic urothelial carcinoma (MUC). Recently, increasing evidence indicates the clinical importance of the association between hypoxia…

Standard name KINNEY_DNMT1_METHYLATION_TARGETS Systematic name M2508 Brief description Hypomethylated genes in prostate tissue from mice carrying hypomorphic alleles of DNMT1 [GeneID=1786]. Full description or abstract Previous studies have shown that tumor progression in the transgenic adenocarcinoma of mouse prostate (TRAMP) model is characterized by global DNA hypomethylation initiated during early-stage…

Background Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer. Despite the dramatic improvement in breast cancer prognosis due to recent therapeutic advances, such as more effective adjuvant and neo-adjuvant chemotherapies, together with more radical and safer surgery, advances in early diagnosis and treatment over the…

Introduction Coronary artery disease (CAD) is a complex pathology associated with behavioral and environmental factors.1–3 CAD shows high prevalence and is associated with a high fatality rate among cardiovascular diseases. The main manifestations of CAD are stable or unstable angina pectoris and identifiable or unrecognized myocardial infarction.4 The main risk…

Filtering relevant Gene Ontology (GO) results from Gene Set Enrichment Analysis (GSEA) 1 Hi all, I am new to bioinformatics and am currently learning how to use GSEA. Background: I analyzed my RNA-Seq results using DESeq2, and am now learning to perform GSEA. For my project, in broad terms, I…

Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…

Error in loading files into the GSEA software 0 Hi everyone I have some trouble with my RNA-seq file when I try to upload it for analysis with GSEA. I am getting the following error: Can anyone help me fix it? many thanks! —- Full Error Message —- There were…

DOI: 10.18129/B9.bioc.SingscoreAMLMutations     Using singscore to predict mutations in AML from transcriptomic signatures Bioconductor version: Release (3.13) This workflow package shows how transcriptomic signatures can be used to infer phenotypes. The workflow begins by showing how the TCGA AML transcriptomic data can be downloaded and processed using the TCGAbiolinks…

working with .gmt files 3 Hi! I have downloaded a pathway data set in .gmt format form the GSEA website. I’m wondering how can I properly read this data set in R. Could anyone help me? Thank you!   myposts • 9.5k views • link updated 2 hours ago by…

Performing GSEA using MSigDB gene sets in R 2 I am trying to perform a gene set enrichment analysis in r using the gene sets available from msigdb and a list of gene names from my own data set. I am able to to use the msigdbr library to import…