User Manual

  ABOUT OpenXGR

  ABOUT

  We are pleased to introduce OpenXGR, an updated version of our previously established XGR software that has gained increasing popularity. OpenXGR is a newly designed web server that offers real-time enrichment and subnetwork analyses for a user-input list of genes, SNPs, or genomic regions, through leveraging ontologies, networks, and many other functional genomic datasets (such as e/pQTL, promoter capture Hi-C, and enhancer-gene maps). This new website is free and open to all users, and does not require users to log in.

  One of the major bottlenecks for genomics research is how to bridge the widening gap between generated genomic summary data and downstream knowledge discovery. We define genomic summary data as a list of genes or SNPs (more generally, genomic regions), along with their significance level (e.g. p-values). We are at the forefront of making sense of genomic summary data for knowledge discovery through developing approaches and tools that have been shown to be efficient and effective. These tools and approaches include XGR, Priority index, dnet, and dcGO; see below KEY PUBLICATIONS.

  OpenXGR builds upon our previous approaches (with most of citations received in the past two years) and the expanding knowledgebase of ontologies and networks. It includes six analysers, each doing specific interpretations tailored to genomic summary data at the gene, SNP, or genomic region level. These include three enrichment analysers that identify enriched ontology terms and three subnetwork analysers that identify gene subnetworks, described below:

  Please refer to  Source Code and  User Manual for step-by-step instructions on how to build and use OpenXGR, respectively. Looking further ahead, we are excited about exploring the use of large language models to support genomic summary data interpretation, either in ontology annotation and gene network generation or in providing outputs in a conversational way similar to ChatGPT (the product of OpenAI).

  CONTACT


    Hai FANG, PhD

      Professor of Bioinformatics

      fh12355@rjh.com.cn

      Google Scholar

      Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China

  FUNDINGS

    National Natural Science Foundation of China (32170663)

    2022 - 2025

    Innovative Research Team of High-Level Local Universities in Shanghai

    2022 - 2024

    Program for Professor of Special Appointment (Eastern Scholar) at Shanghai Institutions of Higher Learning

    2020 - 2022


  KEY PUBLICATIONS

    OpenXGR: a web-server update for genomic summary data interpretation

    Nucleic Acids Research 2023

    DOI: 10.1093/nar/gkad357

    XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits
    Access the recommendation on F1000Prime

    Genome Medicine 2016

    DOI: 10.1186/s13073-016-0384-y

    A genetics-led approach defines the drug target landscape of 30 immune-related traits
    Access the recommendation on F1000Prime

    Nature Genetics 2019

    DOI: 10.1038/s41588-019-0456-1

    The 'dnet' approach promotes emerging research on cancer patient survival

    Genome Medicine 2014

    DOI: 10.1186/s13073-014-0064-8

    dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

    Nucleic Acids Research 2013

    DOI: 10.1093/nar/gks1080

    SUPERFAMILY 1.75 including a domain-centric gene ontology method

    Nucleic Acids Research 2011

    DOI: 10.1093/nar/gkq1130

  SELECTED CITATIONS

    Prior anti-CTLA-4 therapy impacts molecular characteristics associated with anti-PD-1 response in advanced melanoma

    Cancer Cell 2023

    DOI: 10.1016/j.ccell.2023.03.010
    Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis

    Cell Genomics 2023

    DOI: 10.1016/j.xgen.2023.100306
    Brain Catalog: a comprehensive resource for the genetic landscape of brain-related traits

    Nucleic Acids Research 2023

    DOI: 10.1093/nar/gkac895
    The dcGO domain-centric ontology database in 2023: new website and extended annotations for protein structural domains

    Journal of Molecular Biology 2023

    DOI: 10.1016/j.jmb.2023.168093
    Proteomic characterization of atopic dermatitis blood from infancy to adulthood

    Journal of the American Academy of Dermatology 2023

    DOI: 10.1016/j.jaad.2022.12.050
    Inducible apelin receptor knockdown reduces differentiation efficiency and contractility of hESC-derived cardiomyocytes

    Cardiovascular Research 2023

    DOI: 10.1093/cvr/cvac065
    Klarigi: Characteristic explanations for semantic biomedical data

    Computers in Biology and Medicine 2023

    DOI: 10.1016/j.compbiomed.2022.106425
    Transcriptional reprogramming from innate immune functions to a pro-thrombotic signature by monocytes in COVID-19

    Nature Communications 2022

    DOI: 10.1038/s41467-022-35638-y
    IL7 genetic variation and toxicity to immune checkpoint blockade in patients with melanoma

    Nature Medicine 2022

    DOI: 10.1038/s41591-022-02095-5
    An immune dysfunction score for stratification of patients with acute infection based on whole-blood gene expression

    Science Translational Medicine 2022

    DOI: 10.1126/scitranslmed.abq4433
    Immune dysfunction signatures predict outcomes and define checkpoint blockade–unresponsive microenvironments in acute myeloid leukemia

    Journal of Clinical Investigation 2022

    DOI: 10.1172/jci159579
    Lineage-specific rearrangement of chromatin loops and epigenomic features during adipocytes and osteoblasts commitment

    Cell Death & Differentiation 2022

    DOI: 10.1038/s41418-022-01035-7
    Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity

    Nature Communications 2022

    DOI: 10.1038/s41467-022-31626-4
    Genome-wide association analysis and replication in 810,625 individuals with varicose veins

    Nature Communications 2022

    DOI: 10.3390/ijms23158503
    PiER: web-based facilities tailored for genetic target prioritisation harnessing human disease genetics, functional genomics and protein interactions

    Nucleic Acids Research 2022

    DOI: 10.1093/nar/gkac379
    Whole-genome sequencing reveals host factors underlying critical COVID-19

    Nature 2022

    DOI: 10.1038/s41586-022-04576-6
    Rapid synchronous type 1 IFN and virus-specific T cell responses characterize first wave non-severe SARS-CoV-2 infections

    Cell Reports Medicine 2022

    DOI: 10.1016/j.xcrm.2022.100557
    A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

    Cell 2022

    DOI: 10.1016/j.cell.2022.01.012
    GWAS of stool frequency provides insights into gastrointestinal motility and irritable bowel syndrome

    Cell Genomics 2021

    DOI: 10.1016/j.xgen.2021.100069
    Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma

    Cancer Cell 2021

    DOI: 10.1016/j.ccell.2021.10.001
    Human skeletal muscle CD90+ fibro-adipogenic progenitors are associated with muscle degeneration in type 2 diabetic patients

    Cell Metabolism 2021

    DOI: 10.1016/j.cmet.2021.10.001
    Immune checkpoint blockade sensitivity and progression-free survival associates with baseline CD8+ T cell clone size and cytotoxicity

    Science Immunology 2021

    DOI: 10.1126/sciimmunol.abj8825
    echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline

    Bioinformatics 2021

    DOI: 10.1093/bioinformatics/btab658
    High inflammation in hidradenitis suppurativa extends to perilesional skin and can be subdivided by lipocalin-2 expression

    Journal of Allergy and Clinical Immunology 2021

    DOI: 10.1016/j.jaci.2021.05.027
    In-Depth Analysis of the Hidradenitis Suppurativa Serum Proteome Identifies Distinct Inflammatory Subtypes

    Journal of Investigative Dermatology 2021

    DOI: 10.1016/j.jid.2021.02.742
    The molecular features of normal and atopic dermatitis skin in infants, children, adolescents, and adults

    Journal of Allergy and Clinical Immunology 2021

    DOI: 10.1016/j.jaci.2021.01.001