In complex diseases, various combinations of genomic perturbations often lead to the same phenotype. On a molecular level, combinations of genomic perturbations are assumed to dys-regulate the same cellular pathways. Such a pathway-centric perspective is fundamental to understanding the mechanisms of complex diseases and the identification of potential drug targets. In order to provide an integrated perspective on complex disease mechanisms, we developed a novel computational method to simultaneously identify causal genes and dys-regulated pathways. First, we identified a representative set of genes that are differentially expressed in cancer compared to non-tumor control cases. Assuming that disease-associated gene expression changes are caused by genomic alterations, we determined potential paths from such genomic causes to target genes through a network of molecular interactions. Applying our method to sets of genomic alterations and gene expression profiles of 158 Glioblastoma multiforme (GBM) patients we uncovered candidate causal genes and causal paths that are potentially responsible for the altered expression of disease genes. We discovered a set of putative causal genes that potentially play a role in the disease. Comb...Continue Reading
Deletion-mutant epidermal growth factor receptor in human gliomas: effects of type II mutation on receptor function
Response of malignant glioma cell lines to epidermal growth factor and platelet-derived growth factor in a serum-free medium
Cloning and characterization of a novel gene (TM7SF1) encoding a putative seven-pass transmembrane protein that is upregulated during kidney development
GBAS, a novel gene encoding a protein with tyrosine phosphorylation sites and a transmembrane domain, is co-amplified with EGFR
Molecular classification of cancer: class discovery and class prediction by gene expression monitoring
MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data
Characterization of CEBPA mutations in acute myeloid leukemia: most patients with CEBPA mutations have biallelic mutations and show a distinct immunophenotype of the leukemic cells
High-resolution global genomic survey of 178 gliomas reveals novel regions of copy number alteration and allelic imbalances
High TGFbeta-Smad activity confers poor prognosis in glioma patients and promotes cell proliferation depending on the methylation of the PDGF-B gene
The role of versican isoforms V0/V1 in glioma migration mediated by transforming growth factor-beta2
Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle
Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality
Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity
Integrated functional, gene expression and genomic analysis for the identification of cancer targets
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis
Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases
PI3K/PTEN/Akt pathway status affects the sensitivity of high-grade glioma cell cultures to the insulin-like growth factor-1 receptor inhibitor NVP-AEW541
Sequence variants in four candidate genes (NIPSNAP1, GBAS, CHCHD1 and METT11D1) in patients with combined oxidative phosphorylation system deficiencies
Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation
Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae
Determining molecular predictors of adverse drug reactions with causality analysis based on structure learning
An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer
SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways
Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem
Pathways-driven sparse regression identifies pathways and genes associated with high-density lipoprotein cholesterol in two Asian cohorts
Genome-wide association study in a Chinese population identifies a susceptibility locus for type 2 diabetes at 7q32 near PAX4.
Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach
Combined analysis of genome-wide expression and copy number profiles to identify key altered genomic regions in cancer
A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity
Testis-Specific Y-Centric Protein-Protein Interaction Network Provides Clues to the Etiology of Severe Spermatogenic Failure
Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework
Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination
Cancer systems biology in the genome sequencing era: part 2, evolutionary dynamics of tumor clonal networks and drug resistance
Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles
Identifying core gene modules in glioblastoma based on multilayer factor-mediated dysfunctional regulatory networks through integrating multi-dimensional genomic data
Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties
Network-based survival analysis reveals subnetwork signatures for predicting outcomes of ovarian cancer treatment
Systematic genetic analysis identifies Cis-eQTL target genes associated with glioblastoma patient survival
Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets
Systems-based analyses of brain regions functionally impacted in Parkinson's disease reveals underlying causal mechanisms
Knowledge-Based Neuroendocrine Immunomodulation (NIM) Molecular Network Construction and Its Application
NERI: network-medicine based integrative approach for disease gene prioritization by relative importance
Compendium of skin molecular signatures identifies key pathological features associated with fibrosis in systemic sclerosis
Prioritization of SNPs for genome-wide association studies using an interaction model of genetic variation, gene expression, and trait variation
A dynamic programing approach to integrate gene expression data and network information for pathway model generation
The prediction of candidate genes for cervix related cancer through gene ontology and graph theoretical approach
IndividualizedPath: identifying genetic alterations contributing to the dysfunctional pathways in glioblastoma individuals
Graph- and rule-based learning algorithms: a comprehensive review of their applications for cancer type classification and prognosis using genomic data.
Integrated systems analysis of salivary gland transcriptomics reveals key molecular networks in Sjögren's syndrome
Identification of common key genes and pathways between type 1 diabetes and multiple sclerosis using transcriptome and interactome analysis.
3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients
Genotype distribution-based inference of collective effects in genome-wide association studies: insights to age-related macular degeneration disease mechanism
Network-based analysis of differentially expressed genes in cerebrospinal fluid (CSF) and blood reveals new candidate genes for multiple sclerosis
Pathway centrality in protein interaction networks identifies putative functional mediating pathways in pulmonary disease
Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes
ACE2 Interaction Networks in COVID-19: A Physiological Framework for Prediction of Outcome in Patients with Cardiovascular Risk Factors
Integration of peripheral transcriptomics, genomics, and interactomics following trauma identifies causal genes for symptoms of post-traumatic stress and major depression.
On parallelizing graph theoretical approaches for identifying causal genes and pathways from very large biological networks
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
STING Receptor Agonists
Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.
Chronic Fatigue Syndrome
Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.
Spatio-Temporal Regulation of DNA Repair
DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.
Glut1 deficiency, an autosomal dominant, genetic metabolic disorder associated with a deficiency of GLUT1, the protein that transports glucose across the blood brain barrier, is characterized by mental and motor developmental delays and infantile seizures. Follow the latest research on Glut1 deficiency with this feed.
Hereditary Sensory Autonomic Neuropathy
Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.
Separation anxiety is a type of anxiety disorder that involves excessive distress and anxiety with separation. This may include separation from places or people to which they have a strong emotional connection with. It often affects children more than adults. Here is the latest research on separation anxiety.
Neural Activity: Imaging
Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.
Applications of Molecular Barcoding
The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.