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Related Concept Videos

Proteomics01:33

Proteomics

10.0K
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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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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Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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Methods, Tools and Current Perspectives in Proteogenomics.

Kelly V Ruggles1, Karsten Krug2, Xiaojing Wang3,4

  • 1From the ‡Department of Medicine, New York University School of Medicine, New York, New York 10016.

Molecular & Cellular Proteomics : MCP
|May 1, 2017
PubMed
Summary
This summary is machine-generated.

Proteogenomics, integrating genomic and proteomic data, offers new insights into gene expression and disease. This review systematically classifies methods and tools for analyzing these complex biological datasets.

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Area of Science:

  • Proteogenomics
  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Proteogenomics, the integration of proteomic and genomic data, has rapidly advanced due to high-throughput sequencing and mass spectrometry.
  • Initial research focused on enhancing protein identification using sample-specific genomic and transcriptomic data.
  • Recent studies leverage quantitative proteogenomic data for novel insights into gene expression, cell signaling, and disease mechanisms.

Purpose of the Study:

  • To systematically classify and review existing methods and tools for integrative proteogenomic analysis.
  • To categorize these approaches into four major areas: sequence-centric, relationship analysis, integrative modeling, and data sharing/visualization.
  • To highlight the typical applications of these methods and tools in biological research.

Main Methods:

  • Systematic classification of published proteogenomic methods and tools.
  • Categorization into four key areas: Sequence-centric proteogenomics, Analysis of proteogenomic relationships, Integrative modeling of proteogenomic data, and Data sharing and visualization.
  • Comprehensive review of methods and available tools within each category.

Main Results:

  • Identification and classification of a wide array of proteogenomic methods and tools.
  • Structured overview of approaches for sequence-centric analysis, relationship analysis, data modeling, and data management in proteogenomics.
  • Demonstration of the diverse applications enabled by these integrated analytical strategies.

Conclusions:

  • Proteogenomics is a rapidly evolving field with diverse analytical methodologies.
  • A systematic classification of tools and methods is crucial for advancing proteogenomic research.
  • This review provides a valuable resource for researchers utilizing integrative proteogenomic approaches.