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

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.9K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
11.9K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

4.2K
4.2K
Phase Transitions02:31

Phase Transitions

23.3K
Whether solid, liquid, or gas, a substance's state depends on the order and arrangement of its particles (atoms, molecules, or ions). Particles in the solid pack closely together, generally in a pattern. The particles vibrate about their fixed positions but do not move or squeeze past their neighbors. In liquids, although the particles are closely spaced, they are randomly arranged. The position of the particles are not fixed—that is, they are free to move past their neighbors to...
23.3K
Phase Transitions: Vaporization and Condensation02:39

Phase Transitions: Vaporization and Condensation

21.5K
The physical form of a substance changes on changing its temperature. For example, raising the temperature of a liquid causes the liquid to vaporize (convert into vapor). The process is called vaporization—a surface phenomenon. Vaporization occurs when the thermal motion of the molecules overcome the intermolecular forces, and the molecules (at the surface) escape into the gaseous state. When a liquid vaporizes in a closed container, gas molecules cannot escape. As these gas phase molecules...
21.5K
Properties of Transition Metals02:58

Properties of Transition Metals

30.0K
Transition metals are defined as those elements that have partially filled d orbitals. As shown in Figure 1, the d-block elements in groups 3–12 are transition elements. The f-block elements, also called inner transition metals (the lanthanides and actinides), also meet this criterion because the d orbital is partially occupied before the f orbitals.
30.0K
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

8.9K
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
8.9K

You might also read

Related Articles

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

Sort by
Same author

PARROT: Phase-Altering Regulatory Rewiring Over Time.

bioRxiv : the preprint server for biology·2026
Same author

LOESS and DE-SWAN can induce artifactual "waves" of molecular aging.

bioRxiv : the preprint server for biology·2026
Same author

Genomic, Transcriptomic, and Regulomic Analyses Do Not Support Profound Autism as a Distinct Biological Category.

bioRxiv : the preprint server for biology·2026
Same author

Deploying a JupyterHub Server for Academic Research Using Netbooks as an Example.

Current protocols·2026
Same author

Leveraging Artificial Intelligence in Allergy, Asthma, and Immunology With Environmental Exposures.

Allergy·2026
Same author

Gene regulatory network analysis identifies dysregulation of hypoxia pathways as contributing to glioblastoma treatment resistance in females.

Biology of sex differences·2026

Related Experiment Video

Updated: Feb 11, 2026

Developing Neuroimaging Phenotypes of the Default Mode Network in PTSD: Integrating the Resting State, Working Memory, and Structural Connectivity
10:43

Developing Neuroimaging Phenotypes of the Default Mode Network in PTSD: Integrating the Resting State, Working Memory, and Structural Connectivity

Published on: July 1, 2014

15.8K

Detecting phenotype-driven transitions in regulatory network structure.

Megha Padi1, John Quackenbush2,3

  • 11Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ USA.

NPJ Systems Biology and Applications
|May 1, 2018
PubMed
Summary
This summary is machine-generated.

We developed ALPACA (ALtered Partitions Across Community Architectures) to compare biological networks and find condition-specific gene modules. This method enhances the discovery of network changes relevant to complex traits and diseases.

More Related Videos

Author Spotlight: Emerging Technologies and Advanced Tools for Decoding Metabolomics Data Analysis
07:11

Author Spotlight: Emerging Technologies and Advanced Tools for Decoding Metabolomics Data Analysis

Published on: November 10, 2023

3.3K
Detection of Alternative Splicing During Epithelial-Mesenchymal Transition
11:48

Detection of Alternative Splicing During Epithelial-Mesenchymal Transition

Published on: October 9, 2014

13.4K

Related Experiment Videos

Last Updated: Feb 11, 2026

Developing Neuroimaging Phenotypes of the Default Mode Network in PTSD: Integrating the Resting State, Working Memory, and Structural Connectivity
10:43

Developing Neuroimaging Phenotypes of the Default Mode Network in PTSD: Integrating the Resting State, Working Memory, and Structural Connectivity

Published on: July 1, 2014

15.8K
Author Spotlight: Emerging Technologies and Advanced Tools for Decoding Metabolomics Data Analysis
07:11

Author Spotlight: Emerging Technologies and Advanced Tools for Decoding Metabolomics Data Analysis

Published on: November 10, 2023

3.3K
Detection of Alternative Splicing During Epithelial-Mesenchymal Transition
11:48

Detection of Alternative Splicing During Epithelial-Mesenchymal Transition

Published on: October 9, 2014

13.4K

Area of Science:

  • Genomics
  • Systems Biology
  • Bioinformatics

Background:

  • Complex traits and diseases often result from alterations in molecular networks, not single genetic variants.
  • Biological networks exhibit modular structures that vary across tissues, developmental stages, and disease states.
  • Existing methods lack robust approaches for quantifying differences in biological network structures.

Purpose of the Study:

  • To introduce ALPACA (ALtered Partitions Across Community Architectures), a novel method for comparing genome-scale networks.
  • To identify condition-specific gene modules by analyzing differences in network structure between distinct phenotypic states.
  • To provide a robust tool for discovering structural changes in biological networks.

Main Methods:

  • Developed ALPACA for comparing two genome-scale networks derived from different phenotypic states.
  • Utilized simulations to evaluate ALPACA's performance against existing network comparison methods.
  • Applied ALPACA to compare transcriptional networks in ovarian cancer subtypes, viral oncogene-expressing fibroblasts, and human breast tissue sexual dimorphism.

Main Results:

  • ALPACA demonstrated more nuanced, sensitive, and robust module discovery compared to current methods in simulations.
  • The method successfully identified condition-specific modules enriched for phenotype-relevant processes in all tested applications.
  • Specific examples include modules for angiogenic ovarian tumors (blood vessel development) and female breast tissue (estrogen receptor and ERK signaling).

Conclusions:

  • ALPACA effectively identifies structural changes in complex biological networks.
  • The identified network alterations are functionally relevant and can characterize biological phenotypes.
  • This method offers a powerful approach for understanding the molecular basis of complex traits and diseases.