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Related Concept Videos

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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Proteomics01:33

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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.
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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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Smoother: on-the-fly processing of interactome data using prefix sums.

Markus R Schmidt1,2, Anna Barcons-Simon1,2, Claudia Rabuffo1,2

  • 1Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.

Nucleic Acids Research
|January 28, 2024
PubMed
Summary

We developed Smoother, a tool for rapid analysis of nucleic acid interactome data. It enables on-the-fly exploration and comparison of chromosome conformation capture and RNA-DNA interactome datasets.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Nucleic acid interactome data analysis relies on pipelines requiring reruns for parameter optimization.
  • This process is time-consuming and inefficient when optimal parameters are unknown.

Purpose of the Study:

  • To develop a dynamic and efficient approach for analyzing nucleic acid interactome data.
  • To create a visualization and analysis tool for interactive exploration of interactome datasets.

Main Methods:

  • Developed a sparse prefix sum index for on-the-fly interactome data processing.
  • Created Smoother, a visualization tool integrating interactive filtering and normalization comparisons.

Main Results:

  • Smoother enables rapid processing of interactome data, including chromosome conformation capture and RNA-DNA interactome data.
  • The tool facilitates interactive filtering, comparison of normalization methods, and virtual 4C analysis.

Conclusions:

  • Smoother offers a novel, flexible, and efficient method for exploring and analyzing nucleic acid interactome data.
  • This approach fosters comprehensive, high-quality data analysis and discovery.