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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.

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Related Experiment Video

Updated: Jul 12, 2026

Pattern-based Search of Epigenomic Data Using GeNemo
06:38

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

MondrianMap: Navigating Gene Set Hierarchies with Multi-Resolution Enrichment Maps.

Fuad Al Abir, Zongliang Yue, Ehsan Saghapour

    Biorxiv : the Preprint Server for Biology
    |July 10, 2026
    PubMed
    Summary
    This summary is machine-generated.

    MondrianMap visualizes gene enrichment data in interactive, layered maps, revealing complex biological patterns missed by standard ranked lists. This tool aids discovery by showing process directionality and multi-scale biological narratives across datasets.

    More Related Videos

    Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
    09:37

    Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

    Published on: August 15, 2019

    Related Experiment Videos

    Last Updated: Jul 12, 2026

    Pattern-based Search of Epigenomic Data Using GeNemo
    06:38

    Pattern-based Search of Epigenomic Data Using GeNemo

    Published on: October 8, 2017

    Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
    09:37

    Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

    Published on: August 15, 2019

    Area of Science:

    • Bioinformatics
    • Systems Biology
    • Genomics

    Background:

    • Gene enrichment analysis is crucial for interpreting large-scale gene expression data.
    • Standard enrichment outputs are flat ranked lists, limiting the ability to view biological processes at different abstraction levels or compare directional changes between conditions.
    • Contemporary systems biology requires tools that preserve hierarchical structure and encode directionality for complex comparisons.

    Purpose of the Study:

    • To introduce MondrianMap, an interactive web application for multi-resolution visualization of gene enrichment results.
    • To enable the recognition of complex biological patterns, such as directional oppositions and temporal dynamics, that are obscured in traditional flat outputs.
    • To facilitate hierarchical visual reasoning and complement statistical enrichment reporting for biological discovery.

    Main Methods:

    • MondrianMap organizes Gene Ontology (GO) terms into 13 semantically principled layers based on the GOALS framework.
    • Enrichment results are rendered as color-encoded rectangular maps where block area signifies significance and color indicates effect direction.
    • The application provides an interactive interface for navigating these layers, preserving semantic relations through spatial proximity.

    Main Results:

    • Case studies using LINCS CRISPR, GTEx aging, and MoTrPat exercise data demonstrate MondrianMap's utility.
    • LINCS data revealed opposite enrichment maps for TP53 and KRAS knockouts concerning immune recruitment processes.
    • GTEx data visualized the inflammaging paradox, showing distinct regulation of antimicrobial defense in aging blood versus liver.
    • MoTrPat data captured temporal dynamics in exercise response, illustrating threshold switches and metabolic shifts in different tissues.

    Conclusions:

    • MondrianMap offers multi-resolution enrichment visualization for Gene Ontology, enhancing biological interpretation.
    • Layer-specific views effectively reveal directional oppositions and multi-scale biological narratives difficult to discern in flat term lists.
    • The tool demonstrated utility across cancer, aging, and exercise datasets, supporting hypothesis generation and cross-dataset discovery.