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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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Food Behavioral Genetics Minorities. Genome researchers look at many different features when comparing genomes: sequence similarity. which is available from the National Center for Biotechnology Information. For instructions on how to use BLAST. roundworm Caenorhabditis elegans. Research Sites Funding Publications Human Genome News Chromosome Poster Primer Molecular Genetics To Know Ourselves Your Genes. Researchers also don't know the role of single nucleotide polymorphisms (SNPs) --single DNA base changes within the genome-. fruit fly Drosophila melanogaster. proteins. Some of these sequencesimilarity tools are accessible to the public over the Internet. Genetics Genetics in Courtroom human genes. Researchers have learned a great deal about the function of human genes by examining their counterparts in simpler model organisms such as the mouse. One of the most widely used is BLAST. the amount of noncoding DNA in each genome. BLAST is a set of programs designed to perform similarity searches on all available sequence data. and laboratory . Research Home Sequencing Instrumentation Mapping Bioinformatics Functional Genomics ELSI Research Recent Abstracts US. the length and number of coding regions (called exons) within 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.or the role of noncoding regions and repeats in the genome. and genetic disorders. see the tutorial Sequence similarity searching using NCBI BLAST available through Gene Gateway.Intl. Race. 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. yeast Saccharomyces cerevisiae. 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. 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. Comparative genomics involves the use of computer programs that can line up multiple genomes and look for regions of similarity among them. Some model organisms studied in the HGP were the bacterium Escherichia coli. an online guide for learning about genes. and highly conserved regions maintained in organisms as simple as bacteria and as complex as humans. gene location.

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

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

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

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

influenzae (bacteria) 4.000 bases 46 Homo sapiens (human) Rattus norvegicus (rat) Mus musculus (mouse) Drosophila melanogaster (fruit fly) Arabidopsis thaliana (plant) ~30.organism estimate averag chromosom estimate d e gene e d size gene density number number 2900 million bases 2.000 bases 1 gene per 100.100 12 6300 32 3200 1 1700 1 *Information extracted from genome publication papers below. Genome size does not correlate with evolutionary status.750 million bases 2500 million bases 180 million bases 125 million bases ~30.000 1 gene per 100. .600 1 gene per 9.8 million bases 19.000 bases 13.000 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 25.7 million bases 1.000 42 1 gene per ~30.000 100.500 10 Caenorhabdit 97 million is elegans bases (roundworm) Saccharomyc 12 million es cerevisiae bases (yeast) Escherichia coli (bacteria) H.

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

Fleischmann. 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. Microbial Genome Program . Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.U.Consortium of U.S. • • • • • • 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. Virtual Library of Genetics . (28 July 1995) 269: 496-512. • • • . D. Science.More technical information Of mice and men (36k GIF) on HGP involvement with comparative and functional genomics.Links to genetic and genomic information organized by organism. NCBI Entrez Genomes Browse the genomes of model organisms with MapViewer and other genome resources from the National Center for Biotechnology Information (NCBI). et al.S.to be Sequenced R. DOE Joint Genome Institute . Department of Energy researchers developing and exploiting new technologies as a means for discovering and characterizing the basic principles and relationships underlying living systems.

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

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

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