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

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

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

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

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

organism estimate averag chromosom estimate d e gene e d size gene density number number 2900 million bases 2.600 1 gene per 9.750 million bases 2500 million bases 180 million bases 125 million bases ~30.000 42 1 gene per ~30. .8 million bases 19. influenzae (bacteria) 4.000 100.500 10 Caenorhabdit 97 million is elegans bases (roundworm) Saccharomyc 12 million es cerevisiae bases (yeast) Escherichia coli (bacteria) H.000 1 gene per 100.100 12 6300 32 3200 1 1700 1 *Information extracted from genome publication papers below.000 bases 13.000 bases 1 gene per 100. Genome size does not correlate with evolutionary status.000 bases 46 Homo sapiens (human) Rattus norvegicus (rat) Mus musculus (mouse) Drosophila melanogaster (fruit fly) Arabidopsis thaliana (plant) ~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 25.7 million bases 1.

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

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

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

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