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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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Determining Genome-wide Transcript Decay Rates in Proliferating and Quiescent Human Fibroblasts
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Measuring gene expression divergence: the distance to keep.

Galina Glazko1, Arcady Mushegian

  • 1Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA. galina_glazko@urmc.rochester.edu

Biology Direct
|August 10, 2010
PubMed
Summary
This summary is machine-generated.

Choosing the right gene expression distance measure is key. Different methods reveal distinct evolutionary and regulatory patterns, impacting how we understand gene conservation across species and tissues.

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Area of Science:

  • Genomics and Evolutionary Biology
  • Bioinformatics and Computational Biology

Background:

  • Gene expression divergence is a key phenotypic trait reflecting evolutionary changes in gene regulation.
  • It quantifies dissimilarities between species, and between cells or tissues within a species.
  • Existing methods for measuring expression divergence include Euclidean and correlation-based distances.

Purpose of the Study:

  • To investigate how different distance measures impact the interpretation of gene expression patterns.
  • To compare the effectiveness of various distance metrics in identifying conserved gene expression trends.
  • To guide the selection of appropriate distance measures based on research objectives.

Main Methods:

  • Comparative analysis of gene expression patterns using multiple distance metrics.
  • Application of Euclidean, correlation-based, and generalized-average distances.
  • Examination of orthologous genes across eight rat and human tissue types.

Main Results:

  • Different distance measures highlight distinct trends in gene expression patterns.
  • Euclidean distance identifies uniformly expressed genes as most conserved.
  • Correlation-based and generalized-average distances identify concerted changes in homologous tissues as conserved.
  • All tested distances effectively show higher similarity in homologous tissues between species compared to non-homologous tissues within species.

Conclusions:

  • The choice of distance measure is critical for revealing specific trends in high-dimensional gene expression data.
  • Selecting an appropriate measure depends on the specific expression patterns of interest for a given study.
  • This highlights the importance of method selection in evolutionary and comparative genomics research.