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Related Concept Videos

Positive Regulator Molecules02:39

Positive Regulator Molecules

Mitotic cell division results in daughter cells that exactly resemble the parent cell. However, errors in the DNA replication or distribution of genetic material may lead to genetic mutations that may be passed down to every new cell formed from the resulting abnormal cell. Propagation of such mutant cells is restricted through checkpoint mechanisms present at different stages of the cell cycle. These checkpoints involve regulator molecules that either promote or demote cell cycle events.
Global Regulatory Systems01:28

Global Regulatory Systems

Global regulatory systems in bacteria enable rapid and coordinated responses to environmental changes by integrating sensory inputs with gene expression, ensuring efficient adaptation to fluctuating conditions. Key global regulatory mechanisms include regulons, two-component systems, sigma factors, and secondary messengers.Regulons and Global RegulatorsA regulon is a collection of genes and operons controlled by a common global regulator. These regulators enable bacteria to prioritize resource...
IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the  phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and produces two-second...
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...
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.

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A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Regulatory network operations in the Pathway Tools software.

Suzanne M Paley1, Mario Latendresse, Peter D Karp

  • 1Bioinformatics Research Group, SRI International 333 Ravenswood Ave, Menlo Park, CA 94025, USA.

BMC Bioinformatics
|September 25, 2012
PubMed
Summary
This summary is machine-generated.

Pathway Tools software aids biologists in managing complex genetic regulatory data. It offers novel visualizations and analysis methods for understanding gene regulation across organisms.

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Area of Science:

  • Computational Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Biologists are increasingly generating complex genetic regulatory data across various organisms.
  • There is a critical need for specialized software to manage and analyze this regulatory network data effectively.

Purpose of the Study:

  • To introduce and describe the Pathway Tools software for handling genetic regulatory information.
  • To present novel methods for visualizing and analyzing regulatory networks and gene expression data.

Main Methods:

  • The Pathway Tools software utilizes a regulation ontology to capture diverse regulatory interactions.
  • Novel visualization techniques include gene regulatory summaries, transcription-unit diagrams, and interactive network visualizations.
  • New algorithms are presented for regulatory influence ranking and enrichment analysis of gene expression datasets.

Main Results:

  • Pathway Tools supports the storage and manipulation of regulatory data, including transcriptional, translational, and post-translational modifications.
  • Novel visualizations allow for comprehensive summaries of gene regulation and interactive exploration of transcriptional networks.
  • New enrichment analysis identifies over-representation of known regulators in gene expression datasets.
  • Algorithms for ranking regulatory influence and computing net regulatory effects are introduced.

Conclusions:

  • Pathway Tools offers a comprehensive environment for manipulating molecular regulatory interactions.
  • It integrates regulatory data with genomic and metabolic network information.
  • Curated regulatory data collections are available for key model organisms like *Escherichia coli*, *Bacillus subtilis*, and *Shewanella oneidensis*.