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Genome Size and the Evolution of New Genes03:21

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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.
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The functional classification of joints is determined by the amount of mobility between the adjacent bones. Joints are functionally classified as a synarthrosis or immobile joint, an amphiarthrosis or slightly moveable joint, or as a diarthrosis, a freely moveable joint. Fibrous and cartilaginous joints can be functionally classified as either synarthroses  or amphiarthroses, whereas all synovial joints are classified as diarthroses.
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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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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0).

Huaiyu Mi1, Anushya Muruganujan2, Xiaosong Huang2,3

  • 1Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA. huaiyumi@usc.edu.

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The PANTHER classification system provides updated tools for analyzing large-scale genomic data, integrating gene families, pathways, and statistical models. This comprehensive resource aids biologists in understanding gene function and evolutionary relationships.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Systems Biology

Background:

  • The PANTHER classification system integrates genomes, gene function annotations, and pathways for large-scale data analysis.
  • Previous protocols were published in 2013, necessitating an update due to significant system improvements.

Purpose of the Study:

  • To provide updated, detailed instructions for utilizing the PANTHER classification system.
  • To highlight recent advancements in data quality, coverage, statistical algorithms, and user experience.

Main Methods:

  • Utilizes a comprehensive database covering 131 genomes, organized into gene families and subfamilies.
  • Employs phylogenetic trees, multiple sequence alignments, and hidden Markov models (HMMs) for evolutionary analysis.
  • Integrates Gene Ontology (GO) terms and PANTHER pathways for functional annotation.

Main Results:

  • PANTHER v.14.0 offers enhanced data quality and coverage across 131 genomes.
  • Improved statistical algorithms and user interface facilitate efficient genome-wide data analysis.
  • The system supports browsing, querying gene functions, and statistical testing for experimental data.

Conclusions:

  • The updated PANTHER system provides a robust platform for analyzing complex genomic datasets.
  • It empowers researchers across various disciplines, including bench scientists, bioinformaticians, and systems biologists.
  • This protocol update ensures users can leverage the latest features for biological discovery.