Analysis of NGS and other sequencing data, gene variants, gene expression, proteomics, and other high-throughput (OMICs) data is challenging because of its biological complexity and high level of technical and biological noise. One way to deal with both problems is to perform analysis with a high fidelity annotated knowledgebase of protein interactions, pathways, and functional ontologies. This knowledgebase has to be structured in a computer-readable format and must include software tools for managing experimental data, analysis, and reporting. Here, we present MetaCore™ and Key Pathway Advisor (KPA), an integrated platform for functional data analysis. On the content side, MetaCore and KPA encompass a comprehensive database of molecular interactions of different types, pathways, network models, and ten functional ontologies covering human, mouse, and rat genes. The analytical toolkit includes tools for gene/protein list enrichment analysis, statistical "interactome" tool for the identification of over- and under-connected proteins in the dataset, and a biological network analysis module made up of network generation algorithms and filters. The suite also features Advanced Search, an application for combinatorial search of the database content, as well as a Java-based tool called Pathway Map Creator for drawing and editing custom pathway maps. Applications of MetaCore and KPA include molecular mode of action of disease research, identification of potential biomarkers and drug targets, pathway hypothesis generation, analysis of biological effects for novel small molecule compounds and clinical applications (analysis of large cohorts of patients, and translational and personalized medicine).
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http://dx.doi.org/10.1007/978-1-4939-7027-8_6 | DOI Listing |
Mach Learn
October 2024
Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, 55455, MN, USA.
Data for several applications in diverse fields can be represented as multiple matrices that are linked across rows or columns. This is particularly common in molecular biomedical research, in which multiple molecular "omics" technologies may capture different feature sets (e.g.
View Article and Find Full Text PDFRep Pract Oncol Radiother
December 2024
Department of Biosciences Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan, India.
Multi-omics approaches are revolutionizing cancer research and treatment by integrating single-modality omics methods, such as the transcriptome, genome, epigenome, epi-transcriptome, proteome, metabolome, and developing omics (single-cell omics). These technologies enable a deeper understanding of cancer and provide personalized treatment strategies. However, challenges such as standardization and appropriate methods for funneling complex information into clinical consequences remain.
View Article and Find Full Text PDFFront Immunol
December 2024
Department of Urology, The Second People's Hospital of Meishan City, Meishan, Sichuan, China.
Background: Prostate cancer (PCa) is a multifactorial and heterogeneous disease, ranking among the most prevalent malignancies in men. In 2020, there were 1,414,259 new cases of PCa worldwide, accounting for 7.3% of all malignant tumors.
View Article and Find Full Text PDFZhonghua Jie He He Hu Xi Za Zhi
January 2025
College of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing100091, China.
This review outlines significant clinical research developments in the field of critical care respiratory medicine from October 2023 to September 2024. In the post-pandemic era, the new global definition of acute respiratory distress syndrome (ARDS) has improved practicality and early warning capabilities, although further refinement through respiratory mechanics and multi-omics approaches is required. Novel patterns of pulmonary microbiota distribution in ARDS patients have emerged, with microbiota-host immune interactions significantly influencing clinical outcomes.
View Article and Find Full Text PDFJ Crohns Colitis
January 2025
Enveda., 5700 Flatiron Parkway, Boulder, CO, 80301, USA.
Background: Inflammatory Bowel Disease (IBD), comprising Crohn's Disease (CD) and Ulcerative Colitis (UC), is a complex condition with diverse manifestations; recent advances in multi-omics technologies are helping researchers unravel its molecular characteristics to develop targeted treatments.
Objective: In this work, we explored one of the largest multi-omics cohorts in Inflammatory Bowel Disease, the Study of a Prospective Adult Research Cohort (SPARC IBD), with the goal of identifying predictive biomarkers for CD and UC and elucidating patient subtypes.
Design: We analyzed genomics, transcriptomics (gut biopsy samples), and proteomics (blood plasma) from hundreds of patients from SPARC IBD.
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