4.8 Article

Mergeomics 2.0: a web server for multi-omics data integration to elucidate disease networks and predict therapeutics

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Psychology, Developmental

Epigenetic profiling of social communication trajectories and co-occurring mental health problems: a prospective, methylome-wide association study

Jolien Rijlaarsdam et al.

Summary: The study explored prospective associations between DNA methylation and trajectories of social communication deficits from childhood to adolescence using ALSPAC data. Differential DNA methylation at three loci in the genome differentiated children following high versus low trajectories of social communication deficits specifically in the neonatal period. However, further replication studies are needed to confirm these potentially novel findings.

DEVELOPMENT AND PSYCHOPATHOLOGY (2022)

Article Biochemical Research Methods

MiBiOmics: an interactive web application for multi-omics data exploration and integration

Johanna Zoppi et al.

Summary: MiBiOmics is a web-based application that facilitates multi-omics data visualization, exploration, integration, and analysis through interactive protocols. It helps mine complex biological systems and identify robust biomarkers linked to specific contextual parameters or biological states.

BMC BIOINFORMATICS (2021)

Article Environmental Sciences

Systems toxicogenomics of prenatal low-dose BPA exposure on liver metabolic pathways, gut microbiota, and metabolic health in mice

Graciel Diamante et al.

Summary: The study demonstrates that low-dose BPA exposure has significant effects on the liver transcriptome and gut microbial composition in offspring, leading to gender- and age-dependent differences in liver gene expression and changes in microbial composition associated with host disease risks.

ENVIRONMENT INTERNATIONAL (2021)

Article Biochemistry & Molecular Biology

Gene networks and pathways for plasma lipid traits via multitissue multiomics systems analysis

Montgomery Blencowe et al.

Summary: GWAS have identified genetic loci associated with plasma lipid traits, showing significant associations with gene subnetworks related to interferon signaling, autoimmune/immune activation, visual transduction, and protein catabolism. Specific gene subnetworks were also found for different lipid traits, with known and novel key regulator genes identified through tissue-specific gene regulatory networks. Knockdown of F2 gene in adipocytes altered lipid metabolism, suggesting a potential link between thrombin and lipid regulation.

JOURNAL OF LIPID RESEARCH (2021)

Article Biochemistry & Molecular Biology

Maternal anxiety during pregnancy and newborn epigenome-wide DNA methylation

Sara Sammallahti et al.

Summary: This study did not find consistent evidence of robust associations between maternal anxiety during pregnancy and genome-wide DNAm in umbilical cord blood. Larger studies and analysis of DNAm in other tissues may be needed to establish subtle or subgroup-specific associations between maternal anxiety and the foetal epigenome.

MOLECULAR PSYCHIATRY (2021)

Article Multidisciplinary Sciences

Genetic mechanisms of critical illness in COVID-19

Erola Pairo-Castineira et al.

Summary: In critically ill patients with COVID-19, host genetic variants associated with antiviral defense mechanisms and inflammatory organ damage were identified through a genome-wide association study. These genetic signals provide potential targets for therapeutic development and repurposing of existing drugs. Large-scale randomized clinical trials will be essential to confirm the effectiveness of targeted treatment strategies.

NATURE (2021)

Article Biochemistry & Molecular Biology

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets

Damian Szklarczyk et al.

Summary: The STRING database integrates various associations between proteins, including physical interactions and functional associations, by collecting evidence from sources such as literature, databases, computational predictions, and systematic transfers. STRING aims for wide coverage and provides extensive user interface features and querying methods for experimental data.

NUCLEIC ACIDS RESEARCH (2021)

Article Cardiac & Cardiovascular Systems

Sex-Stratified Gene Regulatory Networks Reveal Female Key Driver Genes of Atherosclerosis Involved in Smooth Muscle Cell Phenotype Switching

Robin J. G. Hartman et al.

Summary: By comparing sex-specific gene regulatory networks (GRNs), clear sex differences in network activity within atherosclerotic tissues were observed. Genes more active in women were associated with mesenchymal cells and endothelial cells, while genes more active in men were associated with the immune system.

CIRCULATION (2021)

Article Multidisciplinary Sciences

Identification of 38 novel loci for systemic lupus erythematosus and genetic heterogeneity between ancestral groups

Yong-Fei Wang et al.

Summary: The study revealed genetic differences in SLE among ancestral groups and identified ancestry-specific susceptibility loci, with better risk prediction using matched ancestral data.

NATURE COMMUNICATIONS (2021)

Review Biochemistry & Molecular Biology

Multi-omics data integration considerations and study design for biological systems and disease

Stefan Graw et al.

Summary: This article discusses the increasing demand for merging biological features to study a system as a whole, due to advancements in next-generation sequencing and mass spectrometry. Technological limitations such as sample preparation steps, material amount required for sequencing, and sequencing depth requirements need to be addressed. The development of data integration methods, considerations for each data feature, limitations in gene and protein abundance, and the influence of the microbiome on gene and protein expression are important aspects in studying multi-omics data integration.

MOLECULAR OMICS (2021)

Article Biochemistry & Molecular Biology

Differential metabolic and multi-tissue transcriptomic responses to fructose consumption among genetically diverse mice

Guanglin Zhang et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2020)

Article Biochemistry & Molecular Biology

Genome-wide gene-environment analyses of major depressive disorder and reported lifetime traumatic experiences in UK Biobank

Jonathan R. I. Coleman et al.

MOLECULAR PSYCHIATRY (2020)

Review Biochemistry & Molecular Biology

Multitissue Multiomics Systems Biology to Dissect Complex Diseases

Xia Yang

TRENDS IN MOLECULAR MEDICINE (2020)

Article Substance Abuse

Assessing the Role of Long Noncoding RNA in Nucleus Accumbens in Subjects With Alcohol Dependence

John Drake et al.

ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH (2020)

Article Multidisciplinary Sciences

The GTEx Consortium atlas of genetic regulatory effects across human tissues

Francois Aguet et al.

SCIENCE (2020)

Article Multidisciplinary Sciences

Pan-cancer study detects genetic risk variants and shared genetic basis in two large cohorts

Sara R. Rashkin et al.

NATURE COMMUNICATIONS (2020)

Review Biochemistry & Molecular Biology

Psoriasis Pathogenesis and Treatment

Adriana Rendon et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

Article Multidisciplinary Sciences

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

Yingyao Zhou et al.

NATURE COMMUNICATIONS (2019)

Article Cardiac & Cardiovascular Systems

Spatiotemporal Gene Coexpression and Regulation in Mouse Cardiomyocytes of Early Cardiac Morphogenesis

Yang Liu et al.

JOURNAL OF THE AMERICAN HEART ASSOCIATION (2019)

Article Mathematical & Computational Biology

Multi-omics integration reveals molecular networks and regulators of psoriasis

Yuqi Zhao et al.

BMC SYSTEMS BIOLOGY (2019)

Article Biochemistry & Molecular Biology

The Gene Ontology Resource: 20 years and still GOing strong

S. Carbon et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

Annalisa Buniello et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Mathematical & Computational Biology

iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery

Hiromi W. L. Koh et al.

NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2019)

Article Cardiac & Cardiovascular Systems

Integrative Genomics Analysis Unravels Tissue-Specific Pathways, Networks, and Key Regulators of Blood Pressure Regulation

Yuqi Zhao et al.

FRONTIERS IN CARDIOVASCULAR MEDICINE (2019)

Article Biochemistry & Molecular Biology

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

Denise N. Slenter et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

The Reactome Pathway Knowledgebase

Antonio Fabregat et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemical Research Methods

Network-based integration of multi-omics data for prioritizing cancer genes

Christos Dimitrakopoulos et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

EWAS: epigenome-wide association study software 2.0

Jing Xu et al.

BIOINFORMATICS (2018)

Article Gastroenterology & Hepatology

The Genetic Architecture of Diet-Induced Hepatic Fibrosis in Mice

Simon T. Hui et al.

HEPATOLOGY (2018)

Article Biochemistry & Molecular Biology

PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data

Rafael Hernandez-de-Diego et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Multidisciplinary Sciences

Network-based approach to prediction and population-based validation of in silico drug repurposing

Feixiong Cheng et al.

NATURE COMMUNICATIONS (2018)

Article Psychiatry

GWAS on family history of Alzheimer's disease

Riccardo E. Marioni et al.

TRANSLATIONAL PSYCHIATRY (2018)

Article Biochemical Research Methods

mixOmics: An R package for 'omics feature selection and multiple data integration

Florian Rohart et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles

Aravind Subramanian et al.

Article Biochemical Research Methods

Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data

Qianqian Shi et al.

BIOINFORMATICS (2017)

Review Biochemistry & Molecular Biology

An Expanded View of Complex Traits: From Polygenic to Omnigenic

Evan A. Boyle et al.

Article Psychology, Developmental

A Genome-Wide Association Meta-Analysis of Attention-Deficit/Hyperactivity Disorder Symptoms in Population-Based Pediatric Cohorts

Christel M. Middeldorp et al.

JOURNAL OF THE AMERICAN ACADEMY OF CHILD AND ADOLESCENT PSYCHIATRY (2016)

Article Multidisciplinary Sciences

The genetic architecture of type 2 diabetes

Christian Fuchsberger et al.

NATURE (2016)

Article Biochemical Research Methods

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

Daniel Marbach et al.

NATURE METHODS (2016)

Article Medicine, General & Internal

Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders

Qingying Meng et al.

EBIOMEDICINE (2016)

Article Multidisciplinary Sciences

A global reference for human genetic variation

David M. Altshuler et al.

NATURE (2015)

Article Multidisciplinary Sciences

Genetic studies of body mass index yield new insights for obesity biology

Adam E. Locke et al.

NATURE (2015)

Article Genetics & Heredity

Understanding multicellular function and disease with human tissue-specific networks

Casey S. Greene et al.

NATURE GENETICS (2015)

Article Biochemical Research Methods

Multiscale Embedded Gene Co-expression Network Analysis

Won-Min Song et al.

PLOS COMPUTATIONAL BIOLOGY (2015)

Article Biochemical Research Methods

Integrative Multi-omics Module Network Inference with Lemon-Tree

Eric Bonnet et al.

PLOS COMPUTATIONAL BIOLOGY (2015)

Article Biochemistry & Molecular Biology

The Molecular Signatures Database Hallmark Gene Set Collection

Arthur Liberzon et al.

CELL SYSTEMS (2015)

Letter Dermatology

Pityriasis rosea and activation of latent herpesvirus infections Reply

Alan Menter

JOURNAL OF THE AMERICAN ACADEMY OF DERMATOLOGY (2014)

Article Multidisciplinary Sciences

Biological insights from 108 schizophrenia-associated genetic loci

Stephan Ripke et al.

NATURE (2014)

Article Biochemical Research Methods

Similarity network fusion for aggregating data types on a genomic scale

Bo Wang et al.

NATURE METHODS (2014)

Article Biochemical Research Methods

Bayesian consensus clustering

Eric F. Lock et al.

BIOINFORMATICS (2013)

Article Genetics & Heredity

Discovery and refinement of loci associated with lipid levels

Cristen J. Willer et al.

NATURE GENETICS (2013)

Article Substance Abuse

Convergence of Genome-Wide Association and Candidate Gene Studies for Alcoholism

Emily Olfson et al.

ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH (2012)

Article Biochemistry & Molecular Biology

Annotation of functional variation in personal genomes using RegulomeDB

Alan P. Boyle et al.

GENOME RESEARCH (2012)

Article Dermatology

A Subset of Methylated CpG Sites Differentiate Psoriatic from Normal Skin

Elisha D. O. Roberson et al.

JOURNAL OF INVESTIGATIVE DERMATOLOGY (2012)

Article Multidisciplinary Sciences

Integrative Subtype Discovery in Glioblastoma Using iCluster

Ronglai Shen et al.

PLOS ONE (2012)

Article Biochemical Research Methods

Patient-Specific Data Fusion Defines Prognostic Cancer Subtypes

Yinyin Yuan et al.

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Biochemical Research Methods

integrOmics: an R package to unravel relationships between two omics datasets

Kim-Anh Le Cao et al.

BIOINFORMATICS (2009)

Article Genetics & Heredity

Genome-wide scan reveals association of psoriasis with IL-23 and NF-κB pathways

Rajan P. Nair et al.

NATURE GENETICS (2009)

Article Biochemical Research Methods

WGCNA: an R package for weighted correlation network analysis

Peter Langfelder et al.

BMC BIOINFORMATICS (2008)

Article Multidisciplinary Sciences

Genetics of gene expression and its effect on disease

Valur Emilsson et al.

NATURE (2008)

Article Biochemistry & Molecular Biology

Mapping the genetic architecture of gene expression in human liver

Eric E. Schadt et al.

PLOS BIOLOGY (2008)

Article Biochemistry & Molecular Biology

KEGG for linking genomes to life and the environment

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemistry & Molecular Biology

Tissue-specific expression and regulation of sexually dimorphic genes in mice

Xia Yang et al.

GENOME RESEARCH (2006)