ArticlePloS one2015
FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Trial
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- Associations between gut microbiota and incident fractures in the FINRISK cohort.NPJ biofilms and microbiomes · 2024Article
- Inter-individual variations in circadian misalignment-induced NAFLD pathophysiology in mice.iScience · 2024Article
- The Proteome and Lipidome of Extracellular Vesicles fromInternational journal of molecular sciences · 2023Article
- Proteomic analysis of Sarcoptes scabiei reveals that proteins differentially expressed between eggs and female adult stages are involved predominantly in genetic information processing, metabolism and/or host-parasite interactions.PLoS neglected tropical diseases · 2022Article
- Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies.Gut pathogens · 2022Article
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- C10orf99/GPR15L Regulates Proinflammatory Response of Keratinocytes and Barrier Formation of the Skin.Frontiers in immunology · 2022Article
- Associations of healthy food choices with gut microbiota profiles.The American journal of clinical nutrition · 2021Article
- Taxonomic signatures of cause-specific mortality risk in human gut microbiome.Nature communications · 2021Article
- Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals.Journal of the American Heart Association · 2020Article
- Gastric mucosal microbiota in a Mongolian population with gastric cancer and precursor conditions.Alimentary pharmacology & therapeutics · 2020Article
- Chronic circadian misalignment accelerates immune senescence and abbreviates lifespan in mice.Scientific reports · 2020Article
- Essential role of theLife science alliance · 2020Article
- Osteoprotegerin-dependent M cell self-regulation balances gut infection and immunity.Nature communications · 2020Article
- Article
- Targeted enzyme gene re-positioning: A computational approach for discovering alternative bacterial enzymes for the synthesis of plant-specific secondary metabolites.Metabolic engineering communications · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Exponential growth of high-throughput data and the increasing complexity of omics information have been making processing and interpreting biological data an extremely difficult and daunting task. Here we developed FuncTree (http://bioviz.tokyo/functree), a web-based application for analyzing and visualizing large-scale omics data, including but not limited to genomic, metagenomic, and transcriptomic data. FuncTree allows user to map their omics data onto the "Functional Tree map", a predefined circular dendrogram, which represents the hierarchical relationship of all known biological functions defined in the KEGG database. This novel visualization method allows user to overview the broad functionality of their data, thus allowing a more accurate and comprehensive understanding of the omics information. FuncTree provides extensive customization and calculation methods to not only allow user to directly map their omics data to identify the functionality of their data, but also to compute statistically enriched functions by comparing it to other predefined omics data. We have validated FuncTree's analysis and visualization capability by mapping pan-genomic data of three different types of bacterial genera, metagenomic data of the human gut, and transcriptomic data of two different types of human cell expression. All three mapping strongly confirms FuncTree's capability to analyze and visually represent key functional feature of the omics data. We believe that FuncTree's capability to conduct various functional calculations and visualizing the result into a holistic overview of biological function, would make it an integral analysis/visualization tool for extensive omics base research.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.