Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

Diversity of Protists IV

Diversity of Protists IV

Amoebozoa represent a diverse group of terrestrial and aquatic protists that utilize lobe-shaped pseudopodia for locomotion and feeding. This characteristic differentiates them from the Rhizaria, which possess threadlike pseudopodia. The primary classifications within Amoebozoa include gymnamoebas, entamoebas, and the plasmodial and cellular slime molds. Phylogenetic evidence indicates that Amoebozoa diverged from a lineage that ultimately gave rise to fungi and animals.Gymnamoebas and...

Formation of Species

Formation of Species

Speciation describes the formation of one or more new species from one or sometimes multiple original species. The resulting species are discrete from the parent species, and barriers to reproduction will typically exist. There are two primary mechanisms, speciation with and without geographic isolation—allopatric and sympatric speciation, respectively.

Phylogeny

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.

You might also read

Related Articles

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

Sort by

Same author

Comprehensive analysis of the RBP regulome reveals functional modules and drug candidates in liver cancer.

Scientific reports·2026

Same author

GeneSNAKE: a Python package for simulation of gene regulatory networks and perturbation-induced expression data.

Bioinformatics advances·2026

Same author

Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.

Journal of molecular evolution·2025

Same author

iPSC-derived macrophages: An in vitro model to study human disease-relevant macrophage biology.

Journal of immunology (Baltimore, Md. : 1950)·2025

Same author

BiGSM: Bayesian inference of gene regulatory network via sparse modelling.

Bioinformatics (Oxford, England)·2025

Same author

Topology-based metrics for finding the optimal sparsity in gene regulatory network inference.

Bioinformatics (Oxford, England)·2025

Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026

Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026

Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026

Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026

Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026

Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Feb 18, 2026

Visualization and Quantification of High-Dimensional Cytometry Data using Cytofast and the Upstream Clustering Methods FlowSOM and Cytosplore

Visualization and Quantification of High-Dimensional Cytometry Data using Cytofast and the Upstream Clustering Methods FlowSOM and Cytosplore

Published on: December 12, 2019

FunCoup 4: new species, data, and visualization.

Christoph Ogris¹, Dimitri Guala¹, Erik L L Sonnhammer¹

¹Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden.

Nucleic Acids Research

|November 23, 2017

Summary

This summary is machine-generated.

The FunCoup database now includes more species and gene interaction types, enhancing its comprehensive genome-wide functional association networks. This update offers improved data integration and a new network viewer for better analysis.

More Related Videos

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Related Experiment Videos

Last Updated: Feb 18, 2026

Visualization and Quantification of High-Dimensional Cytometry Data using Cytofast and the Upstream Clustering Methods FlowSOM and Cytosplore

Visualization and Quantification of High-Dimensional Cytometry Data using Cytofast and the Upstream Clustering Methods FlowSOM and Cytosplore

Published on: December 12, 2019

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Area of Science:

Bioinformatics
Systems Biology
Genomics

Background:

The FunCoup database provides genome-wide functional association networks.
Functional associations are inferred using a naive Bayesian algorithm and orthology-based information transfer.
Previous versions focused on eukaryotic species.

Purpose of the Study:

To update and expand the FunCoup database with new species and functional association types.
To improve the quality and coverage of inferred gene interactions.
To introduce a new network visualization tool.

Main Methods:

Integration of diverse data types using a naive Bayesian algorithm.
Orthology-based information transfer across species.
Inclusion of new species (e.g., S. pombe, P. falciparum, B. taurus, O. sativa, E. coli, B. subtilis).
Introduction of co-occurrence in operons as a functional association type.
Updated existing association classes (metabolic, signaling, complex, physical protein interaction).
Utilized InParanoid v8 for orthology and phylogenetic profiles.
Incorporated quantitative mass spectrometry data as a new evidence type.
Developed a JavaScript-based network viewer.

Main Results:

Expanded FunCoup database to include four new eukaryotic and two prokaryotic species.
Introduced 'co-occurrence in operon' as a novel functional association.
Integrated updated information for metabolic, signaling, complex, and physical protein interactions.
Added quantitative mass spectrometry data as a new evidence type.
Enhanced network visualization with an intuitive JavaScript-based viewer.

Conclusions:

The updated FunCoup database offers a more comprehensive resource for exploring genome-wide functional associations.
The inclusion of prokaryotic species and new association types broadens the scope of biological inquiry.
The new network viewer facilitates intuitive exploration and analysis of complex interaction data.