Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

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...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Role of oral bacteria composition and functional gene profiles in respiratory diseases.

BMJ open respiratory research·2026
Same author

Comparative investigation of the potential of glyphosate and glyphosate-based formulations to cause oxidative stress and DNA damage in human skin and liver cell systems.

Toxicological sciences : an official journal of the Society of Toxicology·2026
Same author

Household environmental characteristics influence the house dust metagenome.

Environmental research·2026
Same author

Challenging Additivity: Comparing Predicted and Observed AhR Activity of Polycyclic Aromatic Compound (PAC) Mixtures Containing Active and Inactive Constituents.

Environmental science & technology·2026
Same author

Comparison of overnight trends in relative power for specific frequency bands, sleep stages, and brain regions between patients with depressive disorder and matched control subjects.

Psychiatry research. Neuroimaging·2025
Same author

Age Trajectories of O<sub>2</sub> Saturation and Levels of Serum Bicarbonate or End-Tidal CO<sub>2</sub> Across the Life Course of Women and Men: Insights from EHR and PSG Data.

Biomolecules·2025

Related Experiment Video

Updated: Jun 17, 2026

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
07:35

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

A response to information criterion-based clustering with order-restricted candidate profiles in short time-course

Shyamal D Peddada, David M Umbach, Shawn F Harris

    BMC Bioinformatics
    |December 24, 2009
    PubMed
    Summary

    The ORIOGEN software for gene expression clustering is significantly faster and more accurate than claimed by Liu et al. This study confirms ORIOGEN maintains the desired false positive rate, correcting inaccuracies in prior research.

    More Related Videos

    Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations
    12:27

    Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations

    Published on: February 15, 2017

    Related Experiment Videos

    Last Updated: Jun 17, 2026

    Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
    07:35

    Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

    Published on: October 11, 2018

    Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations
    12:27

    Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations

    Published on: February 15, 2017

    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Statistical Genetics

    Background:

    • Gene expression data analysis from time-course microarray experiments requires robust clustering algorithms.
    • Liu et al. proposed a novel algorithm for gene expression profile clustering, comparing it against existing methods.
    • This work addresses inaccuracies in Liu et al.'s performance evaluation of clustering algorithms.

    Discussion:

    • The order-restricted inference based methodology (ORIOGEN) demonstrates superior computational efficiency compared to Liu et al.'s reported run times.
    • ORIOGEN consistently maintains the nominal Type 1 error level, crucial for statistical decision-making.
    • Discrepancies in reported false positive rates suggest potential programming errors in Liu et al.'s implementation.

    Key Insights:

    • ORIOGEN's Java implementation is substantially faster than reported Matlab and R implementations by Liu et al.
    • ORIOGEN accurately controls the false positive rate, contrary to claims in Liu et al.'s study.
    • The study validates ORIOGEN as a reliable and efficient tool for gene expression clustering.

    Outlook:

    • Further investigation into the discrepancies identified in Liu et al.'s study is warranted.
    • The findings support the continued use and development of ORIOGEN for time-course gene expression data analysis.
    • Accurate performance evaluation is critical for advancing bioinformatics tools.