Tag: enrichr

Khan, S. et al. Role of recombinant DNA technology to improve life. Int. J. Genomics Proteomics 2016, 2405954 (2016). Google Scholar  Spolski, R., Li, P. & Leonard, W. J. Biology and regulation of IL-2: from molecular mechanisms to human therapy. Nat. Rev. Immunol. 18, 648–659 (2018). Article  CAS  PubMed  Google…

de Martel C, Georges D, Bray F, Ferlay J, Clifford GM. Global burden of cancer attributable to infections in 2018: a worldwide incidence analysis. Lancet Glob Health. 2020;8:e180–90. Article  PubMed  Google Scholar  McKaig RG, Baric RS, Olshan AF. Human papillomavirus and head and neck cancer: epidemiology and molecular biology. Head…

Adams, R. H. & Eichmann, A. Axon guidance molecules in vascular patterning. Cold Spring Harb. Perspect. Biol. 2, a001875 (2010). Article  PubMed  PubMed Central  Google Scholar  Fish, J. E. & Wythe, J. D. The molecular regulation of arteriovenous specification and maintenance. Dev. Dyn. 244, 391–409 (2015). Article  CAS  PubMed  Google…

Subjects The study was conducted in accordance with the Declaration of Helsinki and all subjects or their parents/guardian gave informed written consent for genetic testing. DNA testing and storage in the Beta Cell Research Bank was approved by the Wales Research Ethics Committee 5 Bangor (REC 17/WA/0327, IRAS project ID…

Dong, E., Du, H. & Gardner, L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect. Dis. 20, 533–534 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Tan, W. et al. A novel coronavirus genome identified in a cluster of pneumonia cases – Wuhan, China 2019–2020. China…

Help with Enrichr clustergram 0 Hi Biostars, I try to use Enrichr with the web version, when I provide background genes, I don’t have the option clustergram anymore. Do you have any idea why? I think it is helpful to know which genes involve in a pathway with clustergram. If…

PT-112’s mechanism of action promotes immunogenic cancer cell death through ribosomal biogenesis inhibition and organelle stress NEW YORK, Oct. 14, 2023 /PRNewswire/ — Promontory Therapeutics Inc., a clinical stage biotech company advancing immunogenic small molecule approaches in oncology, today presented data on its lead therapeutic candidate PT-112, detailing its early…

Farber, D. L., Netea, M. G., Radbruch, A., Rajewsky, K. & Zinkernagel, R. M. Immunological memory: lessons from the past and a look to the future. Nat. Rev. Immunol. 16, 124–128 (2016). Article  PubMed  Google Scholar  Netea, M. G. et al. Defining trained immunity and its role in health and…

Timmis, A. et al. European Society of Cardiology: Cardiovascular Disease Statistics 2017. Eur. Heart J. 39, 508–579 (2018). Article  PubMed  Google Scholar  Tsao, C. W. et al. Heart Disease and Stroke Statistics—2022 Update: a report from the American Heart Association. Circulation 145, e153–e639 (2022). Article  PubMed  Google Scholar  Libby, P.,…

Experimental procedures Plasmid design and cloning AAV genome plasmids (Fig. 1a and Extended Data Figs. 1a,g,h and 5a) were based on Addgene plasmid 60231 (ref. 12). To achieve widespread transgene expression, the hSyn promoter was replaced by the ubiquitous CBh promoter (pAS088). For the triple-colour experiments (Extended Data Fig. 1a),…

Running Enrichr in python using a background gene list 1 I am trying to run Enrichr in python using a background gene list as per gseapy.readthedocs.io/en/latest/gseapy_example.html (2.3.2.2. Enrichr Web Service (with background input)). I got the following to work without specifying a background: enr_bg = gp.enrichr(gene_list=”3383CCGs.txt”, gene_sets=[‘KEGG_2019_Mouse’], outdir=None ) But…

Selecting MOUSE gene set libraries in Enrichr 1 I see there are currently 212 gene set libraries available in Enrichr (maayanlab.cloud/Enrichr/index.jsp#). I am running Enrichr on the web and not in R. In scrolling through the 212 gene set libraries, I see there are mouse libraries available (i.e. KEGG_2019_Mouse) but…

Study participants and data collection The study participants were recruited from 2014 to 2016 during their annual health check-ups at the University of Tokyo Hospital. The individuals included both male and female Japanese individuals aged from 20 to 75 years. The exclusion criteria were as follows: established diagnosis of diabetes,…

EdgeR analysis in R for beginners using Ensembl ID 0 Hi there, I have been given a dataset of the raw counts, Ensembl ID and gene symbols in an excel spreadsheet. The experimental design is two groups (control v experimental), 6 time-points, 5 replicates per time point (therefore 60 samples…

Weinberg, R. A. The action of oncogenes in the cytoplasm and nucleus. Science 230, 770–776 (1985). Article  ADS  CAS  PubMed  Google Scholar  Davoli, T. et al. Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell 155, 948–962 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar  Sanchez-Vega,…

An important task of bulk rna-seq analysis is the different expression , which we can perform with omicverse. For different expression analysis, ov change the gene_id to gene_name of matrix first. When our dataset existed the batch effect, we can use the SizeFactors of DEseq2 to normalize it, and use…

Hunter, D. J. & Bierma-Zeinstra, S. Osteoarthritis. Lancet 393, 1745–1759 (2019). Article  CAS  PubMed  Google Scholar  Puig-Junoy, J. & Ruiz Zamora, A. Socio-economic costs of osteoarthritis: A systematic review of cost-of-illness studies. Semin. Arthritis Rheum. 44, 531–541 (2015). Article  PubMed  Google Scholar  Hunter, D. J., March, L. & Chew, M….

The Seibold Laboratory is a cutting-edge, NIH funded, laboratory focused on elucidating the pathobiological basis of asthma and other complex lung and allergic diseases. Our goal is to discover pathobiological subgroups of disease (termed disease endotypes) and the genetic, environmental, and immune factors driving their development. We are accomplishing these…

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…

Cho, N. H. et al. IDF Diabetes Atlas: global estimates of diabetes prevalence for 2017 and projections for 2045. Diabetes Res. Clin. Pract. 138, 271–281 (2018). Article  CAS  PubMed  Google Scholar  Lu, Y. et al. New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk. Nat….

hiPSC cell culture and differentiation hiPSCs were maintained on 1:40 matrigel (Corning, #354277) coated dishes in supplemented mTeSR-1 medium (StemCell Technologies, #85850) with 500 U ml−1 penicillin and 500 mg ml−1 streptomycin (Gibco, #15140122). For the differentiation of cortical neurons the protocol described previously21 was followed with slight modifications. Briefly, hiPSC colonies were seeded…

doi: 10.1093/nar/gkad393. Online ahead of print. Affiliations Expand Affiliation 1 Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, NY, NY, USA. Item in Clipboard John Erol Evangelista et al. Nucleic Acids Res. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1093/nar/gkad393….

Gene Set Enrichment Analysis 1 Once I come to Gene Set analysis, I have faced some confusing about the differences between ORA, GSEA, Pathway analysis . In addition about difference gene set databases: Which once shall I start first and using which tools ? for examples there are clusterProfile package,…

Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014). Article  PubMed  Google Scholar  Prüfer, K. et…

DOI: 10.18129/B9.bioc.TDbasedUFEadv   Advanced package of tensor decomposition based unsupervised feature extraction Bioconductor version: Release (3.17) This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. In contrast to TDbasedUFE which can perform simple the feature selection and the multiomics…

STAGEs is an interactive web app built using Streamlit (www.streamlit.io), and the running instance of the online app can be accessed via the website (kuanrongchan-stages-stages-vpgh46.streamlitapp.com/). The app can also run locally using the instructions detailed in GitHub (github.com/kuanrongchan/STAGES). Users can directly upload data from Excel spreadsheets, csv or txt files…

Different results between clusterProfiler and Enrichr 0 Hi, I first used enrichr and found an intesresting pathway enriched in my geneset. Then I wanted to use clusterProfiler with the same geneset but this time including background genes. My issue is that clusterProfiler gives completely different results compared to enrichr even…

Excel file with tabs containing pathways or terms identified across Nasosorption FX-i datasets and publicly accessible nasal proteomes as described in Chapter 2 of the thesis entitled: “The Nasal Proteome as a Source of Biomarkers for SARS-CoV-2 and Lung Cancer”. Nasal mucus from Nasosorption FX-i devices from patients with COPD,…

To install R-enrichR, paste this in macOS terminal after installing MacPorts sudo port install R-enrichR Copy More instructions Report an issue with this port If not done already, install MacPorts. To install R-enrichR, run the following command in macOS terminal (Applications->Utilities->Terminal) sudo port install R-enrichR Copy To see what files…

1Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China; 2Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China Background: Ulcerative colitis (UC) is a chronic inflammatory disease of the colon and rectum that has no exact cause and…

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…

Enrichr Seurat – 2023 …

Introduction Osteoarthritis (OA) is a chronic musculoskeletal disease with a polygenic and heterogeneous nature that involves movable joints. The set of features that take place during the development of the disease lead to consider OA as a severe disease of the whole joint as an organ.1–3 The aetiology of knee…

Herald:The Biostar Herald for Tuesday, March 28, 2023 0 The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by…

Bioinformatics pipeline Aiming to genetically separate, characterize, and individually identify persons who contributed to multi-person blood mixtures from single-cell transcriptome sequencing (scRNA-seq) data, we have developed a bioinformatics pipeline called de-goulash (Fig. 1a)24. We applied de-goulash on scRNA-seq datasets that we de-novo generated from multi-person blood mixtures and on in silico…

How to interpret dotplot from enrichment analysis with gseapy? 0 Hello, I used gseapy for enrichment analysis and I am trying to understand the dotplot figure that is generated. This is what the object after enrichment analysis looks like: Below is the figure they produced. I am trying to understand…

Showing : enrichr • reset updated 11 hours ago by ATpoint ★ 2.2k • written 1 day ago by marinaw ▴ 10 5 months ago angkoo ▴ 10 updated 5.3 years ago by thokall ▴ 160 • written 5.3 years ago by Nithisha ▴ 10 3 results • Page 1…

Understanding “gene ratio” when using plotEnrich(c()) 1 @9c8b15cf Last seen 1 hour ago Canada Hi all, I’ve been using the function enrichr(c(). The output is exactly what I wanted (for my purposes) but I have one question regarding the plotEnrich(c()) function: you can plot the output either as y =…

Download stats for experiment package enrichR This page was generated on 2023-02-03 22:50:00 -0500 (Fri, 03 Feb 2023). Note that enrichR doesn’t belong to the current release or devel version of Bioconductor anymore. Number of downloads for experiment package enrichR, year by year, from 2023 back to 2009 (years with…

Faraone, S. V. et al. Attention-deficit/hyperactivity disorder. Nat. Rev. Dis. Prim. 1, 15020 (2015). Article  Google Scholar  Franke, B. et al. The genetics of attention deficit/hyperactivity disorder in adults, a review. Mol. Psychiatry 17, 960–987 (2012). Article  CAS  Google Scholar  Dalsgaard, S., Leckman, J. F., Mortensen, P. B., Nielsen, H….

Amiel, D., Frank, C., Harwood, F., Fronek, J. & Akeson, W. Tendons and ligaments: a morphological and biochemical comparison. J. Orthop. Res. 1, 257–265 (1984). PubMed  CAS  Google Scholar  Lipps, D. B., Wojtys, E. M. & Ashton-Miller, J. A. Anterior cruciate ligament fatigue failures in knees subjected to repeated simulated…

Villanueva, A. Hepatocellular carcinoma. N. Engl. J. Med. 380, 1450–1462 (2019). CAS  PubMed  Article  Google Scholar  Affo, S., Yu, L. X. & Schwabe, R. F. The role of cancer-associated fibroblasts and fibrosis in liver cancer. Annu. Rev. Pathol. 12, 153–186 (2017). CAS  PubMed  Article  Google Scholar  Mederacke, I. et al….

Biological materials RAW264.7, 293T and HeLa cells were obtained from ATCC. RAW264.7 cells with Tnf-mCherry reporter and relA-GFP fusion protein (RAW-G9 clone) were kindly provided by I.D.C. Fraser (National Institutes of Health). The IBA cell line derived from the stromal vascular fraction of interscapular brown adipose tissue of young male…

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…

Sallusto, F. & Lanzavecchia, A. Heterogeneity of CD4+ memory T cells: functional modules for tailored immunity. Eur. J. Immunol. 39, 2076–2082 (2009). CAS  PubMed  Article  Google Scholar  Swain, S. L., McKinstry, K. K. & Strutt, T. M. Expanding roles for CD4+ T cells in immunity to viruses. Nat. Rev. Immunol….

I’ve noticed 10 issues related to”EnrichR website not responding”. Is it possible to output some more details about the connection errors when running listEnrichrSites or setEnrichrSite? For example, httr::GET below might return the problem and this would be a much better message than “EnrichR website not responding”. I’m sure there…

Verleden, S. E. et al. Small airways pathology in idiopathic pulmonary fibrosis: a retrospective cohort study. Lancet Respir. Med. 8, 573–584 (2020). CAS  PubMed  PubMed Central  Google Scholar  Hogg, J. C., Macklem, P. T. & Thurlbeck, W. M. The resistance of small airways in normal and diseased human lungs. Aspen…

The protocol presented here describes a complete pipeline to analyze RNA-sequencing transcriptome data from raw reads to functional analysis, including quality control and preprocessing steps to advanced statistical analytical approaches. Welcome to the protocol of high-throughput transcriptome analysis for investigating host-pathogen interactions. This protocol is divided in the following steps….

Cluster Profiler output not the same as Enrichr output 0 @angkoo-23537 Last seen 18 hours ago United Kingdom Hi there, I have am getting different outputs after running enrichGO on cluster profiler when I put the same genes into enrichR (by Maayan Lab) website. Example here using Biological Process 2021…

INTRODUCTION Dengue is the most common mosquito-borne viral disease globally (1). This acute disease, which can be life-threatening, is caused by four different dengue viruses (DENVs) (DENV-1, DENV-2, DENV-3, and DENV-4). An estimated 390 million people are infected with these DENVs annually (2), and populations throughout the tropics face frequent…

Introduction Thyroid carcinoma (THCA) is the most common type of endocrine malignancy and its incidence is increasing.1 Based on its histopathological characteristics, thyroid carcinoma can be classified into multiple subtypes, such as papillary thyroid carcinoma (PTC), follicular thyroid carcinoma, and anaplastic thyroid carcinoma.2 PTC is the most common subtype of…

Integration of APC scRNA-seq data reveals heterogeneity of adipocyte progenitor cells In a previous study9, we defined Lin−Sca1+CD142+ APCs as adipogenesis regulatory (Areg) cells and demonstrated that these cells are both refractory toward adipogenesis and control adipocyte formation of APCs through paracrine signaling. In contrast, Merrick et. al.4 observed that Lin−CD142+ cells…

Hi, I am using EnrichR to analyze my DEGs gotten from limma. I extracted subsets of significant DEGs with their IDs and t-statistics that have been scaled, like the following example: CHI3L1 1.0000000 ARPC1B 0.9605097 SH3D21 0.9303946 FCGBP 0.9165999 MFNG 0.8830144 C2 0.8153162 CTA-398F10.2 0.8459803 CTSD 0.7543101 GRN 0.7503898 CTSB…

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,…

Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…

I am not sure what is the proper way to carry out over-representation analysis (and also gene set enrichment analysis) for RNAseq data. Ideally, the analysis can be performed in R, otherwise, if the software/ platform can export the output file (also include all the non-statistical-significant term) will also be…