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Related Concept Videos

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.
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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.
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ER Retrieval Pathway01:45

ER Retrieval Pathway

In the secretory pathway, vesicles transport proteins from one cellular compartment to another in forward transport to deliver the protein to its correct location. Occasionally, misfolded proteins and incorrect proteins escape their original compartments, and a retrieval pathway is used to return the escaped proteins to their original compartment.
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Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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Diversity in Cell Signaling Responses01:22

Diversity in Cell Signaling Responses

The physiological function of a cell and cellular communication are outcomes of a range of extrinsic signals, intracellular signaling pathways, and cellular responses. No two cell types express the same repertoire of signaling components. Receptors are highly selective for their cognate ligands, but once activated, they can alter multiple cellular processes such as DNA transcription, protein synthesis, and metabolic activity. 
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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

Consistency, comprehensiveness, and compatibility of pathway databases.

Donny Soh1, Difeng Dong, Yike Guo

  • 1School of Computing, National University of Singapore, Building COM1, 117417 Singapore. donnysoh@gmail.com

BMC Bioinformatics
|September 8, 2010
PubMed
Summary

Analyzing biological pathway databases reveals significant inconsistencies. A unified pathway API is crucial for researchers to access comprehensive and consistent biological information from diverse sources like KEGG, Ingenuity, and Wikipathways.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Genomics

Background:

  • Microarray analysis requires integration with biological information for robust inferences.
  • Current biological pathway databases may not adequately meet this need.

Purpose of the Study:

  • To investigate the adequacy of existing biological databases for analyzing microarray experiments.
  • To assess the consistency, comprehensiveness, and compatibility of popular pathway databases.

Main Methods:

  • Comparative analysis of three major pathway databases: KEGG, Ingenuity, and Wikipathways.
  • Evaluation of gene and interacting gene pair consistency across databases.

Main Results:

  • Low consistency observed for genes in similar pathways (0%-88%) and interacting gene pairs (0%-61%) across databases.
  • Despite curated data, significant discordance suggests each database misses substantial information.

Conclusions:

  • Inconsistent pathway information across diverse data sources presents challenges for researchers.
  • A unified pathway API is critical for accessing consistent, comprehensive biological data.
  • An aggregated resource with an API is available at http://www.pathwayapi.com.