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

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
The Proteasome02:18

The Proteasome

Eukaryotic cells can degrade proteins through several pathways. One of the most important amongst these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. A series of enzymes carry out the ubiquitination of the target proteins - E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...
Synthetic Biology02:55

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

You might also read

Related Articles

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

Sort by
Same author

Differential <i>cis</i>-regulatory regions of KS dehydrins of Arctic and temperate <i>Oxytropis</i> spp.

Genome·2026
Same author

Petota (potatoes) evolved from fortuitous hybridization between Tomato and Etuberosum ancestors.

Molecular plant·2025
Same author

Polyploidy in potatoes: challenges and possibilities for climate resilience.

Trends in genetics : TIG·2025
Same author

Pangenome analyses reveal impact of transposable elements and ploidy on the evolution of potato species.

Proceedings of the National Academy of Sciences of the United States of America·2023
Same author

Development of a Quick-Install Rapid Phenotyping System.

Sensors (Basel, Switzerland)·2023
Same author

Genome sequencing of adapted diploid potato clones.

Frontiers in plant science·2022
Same journal

pGWAS-Portal: a comprehensive online platform for integrative post-genome-wide association study analysis.

BMC genomics·2026
Same journal

Physiological and transcriptomic analyses of Rosa persica in response to drought stress and functional validation of the transcription factor RpERF113-like.

BMC genomics·2026
Same journal

Integrated analysis of chromatin accessibility and transcriptome profiles in granulosa cells of sheep with different FecB genotypes.

BMC genomics·2026
Same journal

Correction: TB-DROP: deep learning-based drug resistance prediction of Mycobacterium tuberculosis utilizing whole genome mutations.

BMC genomics·2026
Same journal

Chromosomal scale genome assembly of medicinal plant Sophora tonkinensis.

BMC genomics·2026
Same journal

Variant-specific RNA testing resolves variants of uncertain significance in exome testing.

BMC genomics·2026
See all related articles

Related Experiment Video

Updated: Jul 3, 2026

A Simple Method for Isolation of Soybean Protoplasts and Application to Transient Gene Expression Analyses
09:22

A Simple Method for Isolation of Soybean Protoplasts and Application to Transient Gene Expression Analyses

Published on: January 25, 2018

SoyXpress: a database for exploring the soybean transcriptome.

Kei Chin Christine Cheng1, Martina V Strömvik

  • 1Department of Plant Science, McGill University, 21,111 Lakeshore Rd, Sainte Anne de Bellevue, QC H9X 3V9, Canada. kei.cheng@elf.mcgill.ca

BMC Genomics
|August 2, 2008
PubMed
Summary
This summary is machine-generated.

SoyXpress is a new database for analyzing soybean gene expression. It integrates transcriptome data with functional annotations, aiding research on gene expression differences in various soybean cultivars.

More Related Videos

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Published on: May 9, 2017

Polysome Purification from Soybean Symbiotic Nodules
07:02

Polysome Purification from Soybean Symbiotic Nodules

Published on: July 1, 2022

Related Experiment Videos

Last Updated: Jul 3, 2026

A Simple Method for Isolation of Soybean Protoplasts and Application to Transient Gene Expression Analyses
09:22

A Simple Method for Isolation of Soybean Protoplasts and Application to Transient Gene Expression Analyses

Published on: January 25, 2018

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Published on: May 9, 2017

Polysome Purification from Soybean Symbiotic Nodules
07:02

Polysome Purification from Soybean Symbiotic Nodules

Published on: July 1, 2022

Area of Science:

  • Plant genomics and bioinformatics
  • Transcriptome analysis and data integration

Background:

  • Whole transcriptome microarray experiments generate vast datasets requiring integration with gene function and metabolic pathway information.
  • Bioinformatics tools are crucial for managing and interpreting complex gene expression data.
  • A dedicated database for soybean (Glycine max (L) Merr.) whole transcriptome analysis, integrated with biological functions, was previously unavailable.

Purpose of the Study:

  • To develop SoyXpress, a relational database and web interface for exploring soybean transcriptome data.
  • To facilitate the retrieval and interpretation of microarray experiment results.
  • To enable comparison of gene expression between different soybean cultivars, including transgenic and non-transgenic types.

Main Methods:

  • Development of a relational database (SoyXpress) using MySQL and a Perl CGI interface.
  • Integration of 380,095 soybean Expressed Sequence Tags (ESTs) with metabolic pathways, Gene Ontology (GO) terms, and SwissProt identifiers.
  • Linking Affymetrix gene expression data from microarray experiments with sequence data.

Main Results:

  • SoyXpress houses a comprehensive collection of soybean ESTs and associated functional annotations.
  • The database links microarray data with sequence data for enhanced knowledge extraction.
  • Gene expression data from conventional and genetically engineered soybean cultivars are available.

Conclusions:

  • SoyXpress provides an integrated platform for exploring transcriptome differences in various soybean genotypes.
  • The database facilitates the analysis of gene expression, functional annotations, and pathway data.
  • SoyXpress is publicly accessible, supporting research on soybean genetics and crop improvement.