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Related Concept Videos

Genome Annotation and Assembly03:36

Genome 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.
Protein Networks02:26

Protein 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,...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Ribosome Profiling02:24

Ribosome 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
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Proteomics01:33

Proteomics

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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Epistasis Analysis01:09

Epistasis Analysis

Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...

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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Annotating genes of known and unknown function by large-scale coexpression analysis.

Kevin Horan1, Charles Jang, Julia Bailey-Serres

  • 1Department of Botany and Plant Sciences , University of California, Riverside, CA 92521, USA.

Plant Physiology
|March 21, 2008
PubMed
Summary
This summary is machine-generated.

Researchers identified thousands of plant proteins of unknown function (PUFs) and linked them to biological processes and stress responses using gene expression data. This work aids in understanding plant biology and developing new crop traits.

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Area of Science:

  • Plant molecular biology
  • Genomics
  • Bioinformatics

Background:

  • Approximately 40% of eukaryotic proteins, termed proteins of unknown function (PUFs), lack defined roles, posing a significant challenge in biological research.
  • Functional characterization of PUFs is crucial for advancing our understanding of cellular mechanisms and biological processes.

Purpose of the Study:

  • To identify PUF genes in Arabidopsis thaliana.
  • To functionally annotate PUF genes by associating them with known biological processes and regulatory networks using large-scale gene expression data.
  • To identify PUF genes involved in abiotic stress responses.

Main Methods:

  • Identification of PUF genes through sequence similarity, domain-based, and empirical approaches.
  • Genome-wide coexpression analysis of 1,310 Affymetrix expression chips to link PUF genes with proteins of known function (PKFs).
  • Differential gene expression analysis to identify PUF and PKF genes responsive to various abiotic stresses.

Main Results:

  • 1,541 PUF genes were associated with tightly coexpressed PKFs, with over 70% receiving refined biological process annotations.
  • Highly overrepresented functional categories for PUFs included ribosome assembly, photosynthesis, and cell wall pathways.
  • A significant number of PUF genes were identified as responsive to abiotic stresses, with some showing broad responses and others specific ones.

Conclusions:

  • The study provides a comprehensive resource of coexpressed and differentially expressed PUF genes in Arabidopsis.
  • The findings facilitate targeted functional characterization of PUFs and their roles in plant biology.
  • A public database, the Plant Gene Expression Database, was developed to provide access to the generated gene expression data.