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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
Proteogenomics and systems biology: quest for the ultimate missing parts
1CEA, DSV, IBEB, Lab Biochim System Perturb, CEA Marcoule, DSV, iBEB, SBTN, Laboratoire de Biochimie des Systèmes Perturbés, F-30207 Bagnols-sur-Céze, France. jean.armengaud@cea.fr
Expert Review of Proteomics
|February 4, 2010
Summary
Proteogenomics, integrating protein data with genomics, enhances systems biology by creating comprehensive protein databases. This approach aids in discovering new genes and understanding cellular functions for advancements in synthetic biology.
Area of Science:
- Molecular Biology
- Systems Biology
- Genomics
- Proteomics
Background:
- Systems biology relies on quantitative, cell-wide monitoring of cellular processes.
- Comprehensive protein identification and characterization are essential prerequisites for systems biology analysis.
- High-quality genome annotation is crucial for understanding cellular dynamics.
Purpose of the Study:
- To describe the integration of proteogenomics and systems biology.
- To highlight the role of proteogenomics in advancing genome annotation and systems biology.
- To explore the benefits of proteogenomics for comparative genomics and synthetic biology.
Main Methods:
- Proteogenomics involves high-throughput protein identification and characterization using mass spectrometry (MS/MS).
- Integration of proteomic data with genomic information.
- Application of these methods at a full-genomic scale.
Main Results:
- Proteogenomics enables the discovery of unannotated genes, identification of translational start sites, and characterization of post-translational modifications.
- Proteomic datasets can be utilized to define specific metabolic traits of organisms.
- This approach is becoming integral to genome annotation and comparative genomics.
Conclusions:
- Proteogenomics is a crucial component for advancing systems biology and genome annotation.
- The integration of proteomics with genomics offers significant benefits for understanding cellular functions and metabolic traits.
- Future genome projects will likely adopt proteogenomic approaches, benefiting comparative genomics and synthetic biology.
Related Concept Videos
01:33Proteomics
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 proteomics...
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 proteomics...
02:02Genomics
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...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
02:26Protein Networks
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,...
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,...
02:24Ribosome Profiling
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 helps...
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 helps...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...