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Related Concept Videos

Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
What is Gene Expression?01:36

What is Gene Expression?

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...
What is Gene Expression?01:42

What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
Master Transcription Regulators02:23

Master Transcription Regulators

Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...

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Related Experiment Video

Updated: May 27, 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

Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers.

Edward Y Chen1, Huilei Xu, Simon Gordonov

  • 1Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, New York, NY, USA.

Bioinformatics (Oxford, England)
|November 15, 2011
PubMed
Summary
This summary is machine-generated.

Expression2Kinases (X2K) identifies upstream regulators of gene expression by integrating multiple data types. This approach advances understanding of cell signaling and drug mechanisms by revealing regulatory networks.

Related Experiment Videos

Last Updated: May 27, 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

Area of Science:

  • * Molecular biology
  • * Systems biology
  • * Bioinformatics

Background:

  • * Genome-wide mRNA profiling offers insights into cellular states but doesn't directly reveal upstream regulatory mechanisms.
  • * Identifying these upstream regulators is crucial for understanding cellular responses and disease.
  • * Existing methods lack a comprehensive approach to infer regulatory networks from expression data.

Purpose of the Study:

  • * To introduce Expression2Kinases (X2K), a novel computational approach to identify upstream regulators of gene expression.
  • * To integrate diverse biological data, including ChIP-seq, PWMs, protein-protein interactions, and kinase-substrate data.
  • * To provide a robust tool for dissecting regulatory mechanisms underlying observed gene expression patterns.

Main Methods:

  • * Developed the Expression2Kinases (X2K) computational framework.
  • * Integrated chromatin immunoprecipitation sequencing (ChIP-seq)/chip data and position weight matrices (PWMs).
  • * Incorporated protein-protein interaction networks and kinase-substrate phosphorylation data.

Main Results:

  • * Validated X2K by successfully identifying drug targets of FDA-approved drugs.
  • * Mapped the regulatory landscape of stem cell differentiation.
  • * Characterized upstream regulatory mechanisms in breast cancer tumors.
  • * Detected key signaling pathways in various cell types.

Conclusions:

  • * X2K effectively identifies upstream regulators controlling genome-wide gene expression.
  • * The approach enhances understanding of cell signaling pathways and kinase activities.
  • * X2K provides a powerful tool for unraveling drug mechanisms of action and disease-related regulatory networks.