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Functional and Comparative Genomics Fact Sheet
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What is functional genomics? What is comparative genomics? How does it relate to functional genomics?
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Why is model organism research important? Why do we care what diseases mice get? How closely related are mice and humans? How many genes are the same? What are knockout mice? Why are mice used in this research? What genomes have been sequenced completely? What are the comparative genome sizes of humans and other organisms being studied? More Information

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What is functional genomics?

Understanding the function of genes and other parts of the Ethical, Legal, genome is known as functional genomics. The Human Social Issues Genome Project was just the first step in understanding Home Privacy Legislation humans at the molecular level. Though the project is Gene Testing complete, many questions still remain unanswered, Patenting including the function of most of the estimated 30,000 Forensics
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BLAST is a set of programs designed to perform similarity searches on all available sequence data. Genome researchers look at many different features when comparing genomes: sequence similarity. the amount of noncoding DNA in each genome. Education Teachers Careers Students Webcasts Audio/Video Images Videos Chromosome Poster Presentations Genetics 101 Genética Websites en Español What is comparative genomics? How does it relate to functional genomics? Comparative genomics is the analysis and comparison of genomes from different species. see the tutorial Sequence similarity searching using NCBI BLAST available through Gene Gateway.or the role of noncoding regions and repeats in the genome. proteins. Your Choices List of All Publications Search This Site Why is model organism research important? Why do we care what diseases mice get? Contact Us Privacy Statement Site Stats and Credits Functional genomics research is conducted using model organisms such as mice. Race. and laboratory .Intl. Research Sites Funding Publications Human Genome News Chromosome Poster Primer Molecular Genetics To Know Ourselves Your Genes. yeast Saccharomyces cerevisiae. Researchers also don't know the role of single nucleotide polymorphisms (SNPs) --single DNA base changes within the genome-. the length and number of coding regions (called exons) within genes. and highly conserved regions maintained in organisms as simple as bacteria and as complex as humans.Food Behavioral Genetics Minorities. Comparative genomics involves the use of computer programs that can line up multiple genomes and look for regions of similarity among them. Genetics Genetics in Courtroom human genes. Model organisms offer a costeffective way to follow the inheritance of genes (that are very similar to human genes) through many generations in a relatively short time. and genetic disorders. an online guide for learning about genes. Some of these sequencesimilarity tools are accessible to the public over the Internet. For instructions on how to use BLAST. roundworm Caenorhabditis elegans. One of the most widely used is BLAST. gene location. which is available from the National Center for Biotechnology Information. Researchers have learned a great deal about the function of human genes by examining their counterparts in simpler model organisms such as the mouse. Research Home Sequencing Instrumentation Mapping Bioinformatics Functional Genomics ELSI Research Recent Abstracts US. fruit fly Drosophila melanogaster. The purpose is to gain a better understanding of how species have evolved and to determine the function of genes and noncoding regions of the genome. Some model organisms studied in the HGP were the bacterium Escherichia coli.

and indeed our work and the work of many others have provided evidence to confirm that notion. and vice versa.about 3 billion base pairs. However. Livermore. and for the most part we see essentially a one-to-one correspondence between genes in the two species. cats. many duplicated genes remain active and over time may change enough to perform a new function. and HGN 7 (3-4) "Microbial Genomes Sequenced". won't be significantly larger than 1% of the total. Private Sectors Join in Mouse Consortium". we are very similar to mice. Additionally. HGP spinoffs have led to genetic analysis of other environmentally and industrially important organisms in the United States and abroad. sometimes the duplicated copies degenerate to the point where they no longer are capable of encoding a protein. This comparable DNA content implies that all mammals contain more or less the same number of genes. California. rabbits.mouse. However. and vice versa. Mice and humans (indeed. Nevertheless. For more information see HGN 11 (1-2) "Public. and apes) have roughly the same number of nucleotides in their genomes -. Gene for gene. I believe the number of human genes without a clear mouse counterpart. HGN 8 (1) "Third Branch of Life Confirmed". Since gene duplication is an ongoing process. monkeys. These appear to make up a small percentage of the total genes. the most significant differences between mice and humans are not in the number of genes each carries but in the structure of genes and the activities of their protein products. I know of only a few cases in which no mouse counterpart can be found for a particular human gene. How closely related are mice and humans? How many genes are the same? Answer provided by Lisa Stubbs of Lawrence Livermore National Laboratory. most or all mammals including dogs. mice may have active duplicates that humans do not possess. What really matters is that subtle changes accumulated in each of . these novel genes may play an important role in determining species-specific traits and functions. Gene duplication occurs frequently in complex genomes. The exceptions generally appear to be of a particular type --genes that arise when an existing sequence is duplicated.

while others are nearly unrecognizable as close relatives). In addition. but probably only a relatively small percentage. hands can develop structures that look like toes instead of fingers. these events do not always occur in an identical way in the two species. and a mouse's tail can disappear completely. quite a few genes probably are not common to humans and apes. cystic fibrosis. Some nucleotide changes are “neutral” and do not yield a significantly altered protein. and these may influence uniquely human or ape traits. A gene can produce more or less protein in different cells at various times in response to developmental or environmental cues. The often-quoted statement that we share over 98% of our genes with apes (chimpanzees. Put these alterations in the context of known inherited human diseases: a single nucleotide change can lead to inheritance of sickle cell disease. some mouse and human gene products are almost identical. Single-nucleotide changes in the same genes but in different positions in the coding sequence might do nothing harmful at all. or breast cancer. genes and proteins interact in complex ways that multiply the functions of each.000 estimated genes. facial structure. due to single nucleotide changes. Single nucleotide changes have been linked to hereditary differences in height.the approximately 30. and orangutans) actually should be put another way. Thus.) Similarities between mouse and human genes range from about 70% to 90%. would introduce changes that could substantially alter what the protein does. Further.. subtle distinctions are multiplied by the more than 30. and many proteins can express disparate functions in various biological contexts. Evolutionary changes are the same as these sequence differences that are linked to person-toperson variation: many of the average 15% nucleotide . Others. pigmentation.000 genes add together to make quite different organisms. and many other striking morphological differences. a gene can produce more than one protein product through alternative splicing or post-translational modification.g. gorillas. (Just as in the mouse. brain development. A single nucleotide difference can alter protein function in such a way that it causes a terrible tissue malfunction. That is. with an average of 85% similarity but a lot of variation from gene to gene (e. there is more than 95% to 98% similarity between related genes in humans and apes in general.

These include the mouse Mus musculus. but they also aid scientists in testing new drugs and devising novel therapies. When researchers isolate human genes with unknown functions. the worm Caenorhabditis elegans. some lead to subtle changes. as evidenced by the huge range of metabolic. but also the traits coded for by the inserted human DNA. researchers target specific genes --causing them to be expressed or inactivated. Using this technology. What are knockout mice? How will they help us determine human gene function? Knockout mice are transgenic mice whose genetic code has been altered by the insertion of foreign genetic material into their DNA. These mice are then bred --creating a population of offspring with the trait. They not only allow researchers to determine gene function and understand diseases at the molecular level. whereas others are associated with dramatic differences. numerous other genomes have been sequenced. They also reproduce rapidly. This helps researchers understand health and disease by observing how genes work in cells. and they can make quite an impact. and behavioral differences we see among organisms. Instead of creating merely the mouse equivalent of the human gene. Subsequent offspring will inherit not only the instructions coded by their original mouse genome. the . morphological. are inexpensive and easy to handle. and can be genetically manipulated at the molecular level. have short life spans. Knockout mice have many benefits. they can create knockout mice with these genes and observe the results. researchers are able to reproduce and express actual human genes and their corresponding proteins in mice. the bacterium Escherichia coli. Why are mice used in this research? Mice are genetically very similar to humans. the fruitfly Drosophila melanogaster.changes that distinguish humans and mouse genes are neutral. Add them all together. What genomes have been sequenced completely? In addition to the human genome.

yeast Saccharomyces cerevisiae. From The Institute for Genomic Research (TIGR).A tool that allows the researcher to access all of the bacterial genome sequences completed to date. For a complete listing see A Quick Guide to Sequenced Genomes from the Genome News Network. • • What are the comparative genome sizes of humans and other organisms being studied? . and several microbes. Other resources for information on sequenced genomes: • GOLD -.A resource from the National Center for Biotechnology Information (NCBI) for accessing information about completed and in-progress genomes.Genomes Online Database provides comprehensive access to information regarding complete and ongoing genome projects around the world. the plant Arabidopsis thaliana. Entrez Genome -. Comprehensive Microbial Resource -.

influenzae (bacteria) 4.100 12 6300 32 3200 1 1700 1 *Information extracted from genome publication papers below.000 1 gene per 100.000 42 1 gene per ~30.000 bases 1 gene per 4000 bases 1 gene per 5000 bases 1 gene per 2000 bases 1 gene per 1400 bases 1 gene per 1000 bases 40 8 25.8 million bases 19.600 1 gene per 9.750 million bases 2500 million bases 180 million bases 125 million bases ~30.000 bases 13.organism estimate averag chromosom estimate d e gene e d size gene density number number 2900 million bases 2.000 100.000 bases 46 Homo sapiens (human) Rattus norvegicus (rat) Mus musculus (mouse) Drosophila melanogaster (fruit fly) Arabidopsis thaliana (plant) ~30.500 10 Caenorhabdit 97 million is elegans bases (roundworm) Saccharomyc 12 million es cerevisiae bases (yeast) Escherichia coli (bacteria) H. .7 million bases 1.000 bases 1 gene per 100. Genome size does not correlate with evolutionary status.

elegans: A platform for investigating biology. Nature. R. Initial sequencing and analysis of the human genome. D. coli F. influenzae . (11 December 1998) 282: 2012-8.First Plant Sequenced The Arabidopsis Genome Initiative. Nature. (14 December 2000) Roundworm . (5 September 1997) Bacteria . (5 December 2002) [Full Text] Fruit Fly M. Science.H. Genome Sequence of the Brown Norway Rat Yields Insights into Mammalian Evolution. Nature. Adams. Science. The genome sequence of Drosophila melanogaster. 420: 520 -562.nor is the number of genes proportionate with genome size.Genome sequence of the nematode C. Life with 6000 genes. Science. Bacteria . Nature 408: 796-815. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. (25 October 1996) 274: 546. Blattner. elegans Sequencing Consortium. (15 February 2001) [ Full Text] Rat Rat Genome Sequencing Project Consortium. (1 April 2004) [Full Text Mouse Mouse Genome Sequencing Consortium. Arabidopsis . Genome Publication Papers Human International Human Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. The complete genome sequence of Escherichia coli K-12. (24 March 2000) 287: 2185-95. 563-7.First Free-living Organism . 409: 860-921. et al. et al. Goffeau. 428: 493-521.E. et al. Science. Yeast A. 277: 1453-1474.First Mutlicellular Eukaryote Sequenced The C.

DOE Joint Genome Institute . Microbial Genome Program . • • • .to be Sequenced R. Department of Energy researchers developing and exploiting new technologies as a means for discovering and characterizing the basic principles and relationships underlying living systems. D. Science.S.U. Fleischmann. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Virtual Library of Genetics . NCBI Entrez Genomes Browse the genomes of model organisms with MapViewer and other genome resources from the National Center for Biotechnology Information (NCBI). For a step-by-step tutorial on how to use NCBI MapViwer to view the human genome see Finding a gene on a chromosome map. (28 July 1995) 269: 496-512.Links to genetic and genomic information organized by organism.Consortium of U. • • • • • • Homo sapiens Genome View (human) Mus musculus Genome View (mouse) Drosophila melanogaster Genome View (fruit fly) Arabidopsis thaliana Genome View (plant) Caenorhabditis elegans Genome View (roundworm) Saccharomyces cerevisiae Genome View (baker's yeast) More Information Related Web Sites • Functional and Comparative Genomics Research . Department of Energy program to study the genetic material of microbes that may be useful in helping DOE fulfill its missions.More technical information Of mice and men (36k GIF) on HGP involvement with comparative and functional genomics.S.

• • • • • • Other Resources • Genomics: The Human Genome and Beyond .Illustrated index of organisms that have had their genomes sequenced. Why You Can Read This — And Why the Chimp Can't-from USA Today (April 14. a publication of the American Chemical Society. Monitors. 2002.Gateway to functional genomics sources from Science.• A Quick Guide to Sequenced Genomes . Of Mice.Gateway to mouse resources in and beyond National Center for Biotechnology Information (NCBI) resources. • • • • Articles • Comparative Genomics: The Mouse That Roared Article from the December 5.Narrative from To Know Ourselves (1996). 1999). Interactive Mouse Genetics from Explore Learning . Mysteries of Life: From Molecules to Mice .Article from the ORNL Review (1999). 2002). The Mighty Mouse . Mouse Genome Resources . issue of Nature. From the Genome News Network.Learn about mouse genetics and the statistics behind the inheritance of red eyes • .Article from the Physiological Genomics (July 15. Ecce homology: A primer on comparative genomics From Modern Drug Discovery. and Medicine .Article from the ORNL Review (1999). Functional Genomics Articles from Human Genome News Functional Genomics: Technological Challenges and Opportunities . Functional Genomics . Model Organisms for Biomedical Research Information on model organisms from the National Institutes of Health.Poster available from the DOE Joint Genome Institute.

Mouse-human homology.S.M. November 18.ornl. Requires free Shockwave plug-in. Campbell and L. From the HGP Image Gallery.J. Office of Biological and Environmental Research. Last modified: Friday. Discovering Genomics. Human Genome Program . Department of Energy Office of Science. download the free Acrobat Reader software.Researcher and mouse. Graphic . and Bioinformatics by A. Proteomics. Cold Spring Harbor Laboratory Press (2003). 252 pp.Using Mice to Understand Human Gene Function. • Graphic .gov/hgmis Site sponsored by the U. Heyer. Graphic . Send the url of this page to a friend • • • To read pdf files.and black fur. 2005 Home * Contacts * Disclaimer Base URL: www.