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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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The Synapse02:47

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Neurons communicate with one another by passing on their electrical signals to other neurons. A synapse is the location where two neurons meet to exchange signals. At the synapse, the neuron that sends the signal is called the presynaptic cell, while the neuron that receives the message is called the postsynaptic cell. Note that most neurons can be both presynaptic and postsynaptic, as they both transmit and receive information.
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Protein Networks02:26

Protein Networks

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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.
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Integration of Synaptic Events01:28

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Synaptic integration mainly includes the summation of graded potentials. Graded potentials, regardless of their type, cause subtle alterations in membrane voltage, resulting in either depolarization or hyperpolarization. These incremental changes, when combined or summed, can propel the neuron toward its threshold. Consider, for example, a membrane experiencing a +15 mV shift, causing it to depolarize from -70 mV to -55 mV. In this scenario, graded potentials govern the membrane's ability to...
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Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
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High Resolution Quantitative Synaptic Proteome Profiling of Mouse Brain Regions After Auditory Discrimination Learning
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Synaptome.db: a bioconductor package for synaptic proteomics data.

Oksana Sorokina1, Anatoly Sorokin2,3, J Douglas Armstrong1,4

  • 1School of informatics, University of Edinburgh, Edinburgh EH8 9AB, UK.

Bioinformatics Advances
|January 26, 2023
PubMed
Summary
This summary is machine-generated.

Researchers developed Synaptome.db, an R/Bioconductor package providing access to a curated dataset of mammalian synapse proteins. This tool facilitates in-depth analysis of synaptic proteomes, enabling network modeling and exploration of gene functions and disease associations.

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Area of Science:

  • Neuroscience
  • Bioinformatics
  • Computational Biology

Background:

  • The mammalian synapse proteome is vast and distributed across numerous datasets.
  • A unified dataset now catalogs approximately 8000 proteins identified in mammalian synapse studies.
  • Analyzing this complex proteomic data requires integrated computational tools.

Purpose of the Study:

  • To introduce Synaptome.db, an R/Bioconductor package for programmatic access to a curated mammalian synapse proteome dataset.
  • To enable convenient and in-depth analysis of synaptic proteins within the Bioconductor environment.
  • To facilitate the construction of custom protein-protein interaction network models.

Main Methods:

  • Development of the Synaptome.db R/Bioconductor package.
  • Curation of a comprehensive dataset of mammalian synapse proteins.
  • Implementation of functions for retrieving gene information (localization, ontology, disease association) and building network models.

Main Results:

  • Synaptome.db provides programmatic access to a curated mammalian synapse proteome dataset.
  • The package allows users to retrieve detailed gene information, including subcellular localization, brain region specificity, gene ontology, and disease associations.
  • Users can construct custom protein-protein interaction networks for specific gene sets or subcellular compartments.

Conclusions:

  • Synaptome.db offers a valuable resource for researchers studying the synaptic proteome.
  • The package simplifies complex data analysis, enabling novel insights into synaptic function and disease mechanisms.
  • Synaptome.db promotes integrated analysis of synaptic protein data within a widely used bioinformatics framework.