Related Experiment Video

Updated: Jun 29, 2026

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

ExPlain: finding upstream drug targets in disease gene regulatory networks

A Kel1, N Voss, T Valeev

  • 1BIOBASE GmbH, Wolfenbüttel, Germany. Alexander.kel@biobase-international.com

SAR and QSAR in Environmental Research
|October 15, 2008
PubMed

Insights

A new computational system, ExPlain, aids in analyzing gene expression data to find key signaling molecules involved in diseases. This tool helps identify crucial nodes in cellular networks, offering insights into pathological gene dysregulation.

Area of Science:

  • Computational biology
  • Systems biology
  • Genomics

Background:

  • Signal transduction pathways converge at key regulatory molecules.
  • Dysregulation of these signaling networks can lead to diseases.
  • Analyzing gene expression in this context requires advanced computational tools.

Purpose of the Study:

  • To develop an integrated computational system, ExPlain, for causal interpretation of gene expression data.
  • To identify key signaling molecules and regulatory nodes in biological networks.
  • To apply ExPlain to microarray data for understanding disease mechanisms.

Main Methods:

  • ExPlain integrates TRANSFAC and TRANSPATH databases.
  • Composite Module Analyst (CMA) identifies transcription factor binding sites and composite elements in gene regulatory regions.
  • ArrayAnalyzer searches signal transduction networks to find key molecules controlling gene activation.

Main Results:

  • ExPlain was applied to gene expression data from inflammatory bowel diseases (IBD).
  • The system identified potential key signaling molecules and regulatory pathways involved in IBD.
  • Analysis suggested novel hypotheses regarding molecular mechanisms of pathological genetic disregulation in IBD.

Conclusions:

  • The ExPlain system provides a novel approach for analyzing gene expression data in the context of signaling and regulatory pathways.
  • It facilitates the identification of critical molecular players in disease pathogenesis.
  • This computational tool can generate biologically relevant hypotheses for further investigation.

Related Concept Videos

Pharmacogenomics: Identification of New Drug Targets01:29

Pharmacogenomics: Identification of New Drug Targets

Advances in genomics have profoundly influenced drug discovery by increasing both the speed and accuracy of pharmaceutical development. Pharmacogenomics, which examines how genetic variation influences drug response, facilitates the identification of novel therapeutic targets and enables patient stratification for personalized treatment. These strategies contribute to improved drug efficacy, minimized adverse effects, and more efficient clinical trial design.Mapping genetic differences...
Targets for Drug Action: Overview01:26

Targets for Drug Action: Overview

Drugs target macromolecules to modify ongoing cellular processes. Primary drug targets include receptors, ion channels, transporters, and enzymes.
Receptors are either membrane-spanning or intracellular proteins, which upon binding a ligand, get activated and transmit the signal downstream to elicit a response. Drugs bind receptors, either mimicking the action of endogenous ligands or blocking the receptor activity to bring about a modified response. Nearly 35% of approved drugs target the G...
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,...
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
Pharmacogenetic Phenotypes: Alterations in Pharmacokinetics, Drug Targets and Biologic Milieu01:29

Pharmacogenetic Phenotypes: Alterations in Pharmacokinetics, Drug Targets and Biologic Milieu

Genetic variations significantly influence drug response through pharmacokinetics, receptor interactions, and biologic milieu modifications. Pharmacokinetic alterations impact drug metabolism and clearance, affecting efficacy and toxicity. Variants in drug-metabolizing enzymes, such as CYP2C9 and CYP2C19, alter drug activation and elimination. For example, CYP2C9 loss-of-function variants require lower warfarin doses to prevent excessive bleeding, while CYP2C19 variants reduce clopidogrel...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...