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Amino Acid Biosynthetic Pathways01:29

Amino Acid Biosynthetic Pathways

Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which provide...
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Related Experiment Video

Updated: May 17, 2026

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

Pathway Distiller - multisource biological pathway consolidation.

Mark S Doderer1, Zachry Anguiano, Uthra Suresh

  • 1Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.

BMC Genomics
|November 9, 2012
PubMed
Summary

Consolidating redundant biological pathways from multiple databases into unified concepts aids in analyzing large gene sets from experiments. This approach provides streamlined, unbiased functional insights for genomic studies.

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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

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Last Updated: May 17, 2026

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

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Gene expression microarray analysis generates large gene sets requiring functional interpretation.
  • Biological pathways provide functional context for gene sets.
  • Publicly available pathway databases often contain redundant or highly related pathways, necessitating consolidation.

Purpose of the Study:

  • To develop and evaluate methods for consolidating biological pathways to facilitate unbiased and comprehensive analysis of large gene sets.
  • To create a user-friendly framework for pathway consolidation.

Main Methods:

  • Exploration of three complementary pathway consolidation methods: Enrichment Consolidation, Weighted Consolidation (using Protein-Protein Interaction networks), and de novo Consolidation.
  • Development of a web-based framework, Pathway Distiller, integrating these methods.

Main Results:

  • Demonstration that the three consolidation methods offer distinct yet unified functional insights into gene sets.
  • Presentation of results showcasing applications in biological studies and comparison with existing pathway frameworks.
  • Establishment of Pathway Distiller for researchers to analyze their own gene lists using the developed methods.

Conclusions:

  • Combining multiple pathway databases and complementary consolidation methods enables extraction of functional explanations from genome-wide experiments.
  • A user-friendly, web-accessible tool (Pathway Distiller) is provided for researchers.