Figures and Tables
From the following article:
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium Eric S. Lander, Lauren M. Linton, Bruce Birren, Chad Nusbaum, Michael C. Zody, Jennifer Baldwin, Keri Devon, Ken Dewar, Michael Doyle, William FitzHugh, Roel Funke, Diane Gage, Katrina Harris, Andrew Heaford, John Howland, Lisa Kann, Jessica Lehoczky, Rosie LeVine, Paul McEwan, Kevin McKernan, James Meldrim, Jill P. Mesirov, Cher Miranda, William Morris, Jerome Naylor, Christina Raymond, Mark Rosetti, Ralph Santos, Andrew Sheridan, Carrie Sougnez, Nicole Stange-Thomann, Nikola Stojanovic, Aravind Subramanian & Dudley Wyman for Whitehead Institute for Biomedical Research, Center for Genome Research:, Jane Rogers, John Sulston, Rachael Ainscough, Stephan Beck, David Bentley, John Burton, Christopher Clee, Nigel Carter, Alan Coulson, Rebecca Deadman, Panos Deloukas, Andrew Dunham, Ian Dunham, Richard Durbin, Lisa French, Darren Grafham, Simon Gregory, Tim Hubbard, Sean Humphray, Adrienne Hunt, Matthew Jones, Christine Lloyd, Amanda McMurray, Lucy Matthews, Simon Mercer, Sarah Milne, James C. Mullikin, Andrew Mungall, Robert Plumb, Mark Ross, Ratna Shownkeen & Sarah Sims for The Sanger Centre:, Robert H. Waterston, Richard K. Wilson, LaDeana W. Hillier, John D. McPherson, Marco A. Marra, Elaine R. Mardis, Lucinda A. Fulton, Asif T. Chinwalla, Kymberlie H. Pepin, Warren R. Gish, Stephanie L. Chissoe, Michael C. Wendl, Kim D. Delehaunty, Tracie L. Miner, Andrew Delehaunty, Jason B. Kramer, Lisa L. Cook, Robert S. Fulton, Douglas L. Johnson, Patrick J. Minx & Sandra W. Clifton for Washington University Genome Sequencing Center, Trevor Hawkins, Elbert Branscomb, Paul Predki, Paul Richardson, Sarah Wenning, Tom Slezak, Norman Doggett, Jan-Fang Cheng, Anne Olsen, Susan Lucas, Christopher Elkin, Edward Uberbacher & Marvin Frazier for US DOE Joint Genome Institute:, Richard A. Gibbs, Donna M. Muzny, Steven E. Scherer, John B. Bouck, Erica J. Sodergren, Kim C. Worley, Catherine M. Rives, James H. Gorrell, Michael L. Metzker, Susan L. Naylor, Raju S. Kucherlapati, David L. Nelson & George M. Weinstock for Baylor College of Medicine Human Genome Sequencing Center:, Yoshiyuki Sakaki, Asao Fujiyama, Masahira Hattori, Tetsushi Yada, Atsushi Toyoda, Takehiko Itoh, Chiharu Kawagoe, Hidemi Watanabe, Yasushi Totoki & Todd Taylor for RIKEN Genomic Sciences Center:, Jean Weissenbach, Roland Heilig, William Saurin, Francois Artiguenave, Philippe Brottier, Thomas Bruls, Eric Pelletier, Catherine Robert & Patrick Wincker for Genoscope and CNRS UMR-8030:, André Rosenthal, Matthias Platzer, Gerald Nyakatura, Stefan Taudien & Andreas Rump for Department of Genome Analysis, Institute of Molecular Biotechnology:, Douglas R. Smith, Lynn Doucette-Stamm, Marc Rubenfield, Keith Weinstock, Hong Mei Lee & JoAnn Dubois for GTC Sequencing Center:, Huanming Yang, Jun Yu, Jian Wang, Guyang Huang & Jun Gu for Beijing Genomics Institute/Human Genome Center:, Leroy Hood, Lee Rowen, Anup Madan & Shizen Qin for Multimegabase Sequencing Center, The Institute for Systems Biology:, Ronald W. Davis, Nancy A. Federspiel, A. Pia Abola & Michael J. Proctor for Stanford Genome Technology Center:, Bruce A. Roe, Feng Chen & Huaqin Pan for University of Oklahoma's Advanced Center for Genome Technology:, Juliane Ramser, Hans Lehrach & Richard Reinhardt for Max Planck Institute for Molecular Genetics:, W. Richard McCombie, Melissa de la Bastide & Neilay Dedhia for Cold Spring Harbor Laboratory, Lita Annenberg Hazen Genome Center:, Helmut Blöcker, Klaus Hornischer & Gabriele Nordsiek for GBF—German Research Centre for Biotechnology:, Richa Agarwala, L. Aravind, Jeffrey A. Bailey, Alex Bateman, Serafim Batzoglou, Ewan Birney, Peer Bork, Daniel G. Brown, Christopher B. Burge, Lorenzo Cerutti, Hsiu-Chuan Chen, Deanna Church, Michele Clamp, Richard R. Copley, Tobias Doerks, Sean R. Eddy, Evan E. Eichler, Terrence S. Furey, James Galagan, James G. R. Gilbert, Cyrus Harmon, Yoshihide Hayashizaki, David Haussler, Henning Hermjakob, Karsten Hokamp, Wonhee Jang, L. Steven Johnson, Thomas A. Jones, Simon Kasif, Arek Kaspryzk, Scot Kennedy, W. James Kent, Paul Kitts, Eugene V. Koonin, Ian Korf, David Kulp, Doron Lancet, Todd M. Lowe, Aoife McLysaght, Tarjei Mikkelsen, John V. Moran, Nicola Mulder, Victor J. Pollara, Chris P. Ponting, Greg Schuler, Jörg Schultz, Guy Slater, Arian F. A. Smit, Elia Stupka, Joseph Szustakowki, Danielle Thierry-Mieg, Jean Thierry-Mieg, Lukas Wagner, John Wallis, Raymond Wheeler, Alan Williams, Yuri I. Wolf, Kenneth H. Wolfe, Shiaw-Pyng Yang & Ru-Fang Yeh for *Genome Analysis Group (listed in alphabetical order, also includes individuals listed under other headings):, Francis Collins, Mark S. Guyer, Jane Peterson, Adam Felsenfeld & Kris A. Wetterstrand for Scientific management: National Human Genome Research Institute, US National Institutes of Health:, Richard M. Myers, Jeremy Schmutz, Mark Dickson, Jane Grimwood & David R. Cox for Stanford Human Genome Center:, Maynard V. Olson, Rajinder Kaul & Christopher Raymond for University of Washington Genome Center:, Nobuyoshi Shimizu, Kazuhiko Kawasaki & Shinsei Minoshima for Department of Molecular Biology, Keio University School of Medicine:, Glen A. Evans, Maria Athanasiou & Roger Schultz for University of Texas Southwestern Medical Center at Dallas:, Aristides Patrinos for Office of Science, US Department of Energy: & Michael J. Morgan for The Wellcome Trust:
Nature 409, 860-921(15 February 2001)
doi:10.1038/35057062
Figure 2
Idealized representation of the hierarchical shotgun sequencing strategy.
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Figure 3
The automated production line for sample preparation at the Whitehead Institute, Center for Genome Research.
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Figure 4
Total amount of human sequence in the High Throughput Genome Sequence (HTGS) division of GenBank.
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Figure 5
Positions of markers on previous maps of the genome (the Genethon101 genetic map and Marshfield genetic map (http://research.marshfieldclinic.org/genetics/genotyping_service/mgsver2.htm ), the GeneMap99 radiation hybrid map100, and the Whitehead YAC and radiation hybrid map29) plotted against their derived position on the draft sequence for chromosome 2.
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Figure 6
The key steps (a–d) in assembling individual sequenced clones into the draft genome sequence.
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Figure 8
Cumulative distributions of several measures of clone level contiguity and sequence contiguity.
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Figure 12
Histogram of GC content of 20-kb windows in the draft genome sequence.
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Figure 14
Number of CpG islands per Mb for each chromosome, plotted against the number of genes per Mb (the number of genes was taken from GeneMap98 (ref.100)).
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Figure 15
Distance in cM along the genetic map of chromosome 12 plotted against position in Mb in the draft genome sequence.
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Figure 16
Rate of recombination averaged across the euchromatic portion of each chromosome arm plotted against the length of the chromosome arm in Mb.
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Figure 17
Almost all transposable elements in mammals fall into one of four classes.
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Figure 18
Age distribution of interspersed repeats in the human and mouse genomes.
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Figure 19
Median ages and per cent of the genome covered by subfamilies of DNA transposons.
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Figure 20
Comparison of the age of interspersed repeats in eukaryotic genomes.
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Figure 22
Density of the major repeat classes as a function of local GC content, in windows of 50 kb.
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Figure 23
Alu elements target AT-rich DNA, but accumulate in GC-rich DNA.
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Figure 24
DNA transposon copies in AT-rich DNA tend to be younger than those in more GC-rich DNA.
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Figure 25
Distribution of various LINE cohorts as a function of local GC content.
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Figure 26
Comparison of the Alu density of each chromosome as a function of local GC content.
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Figure 27
Substitution patterns in interspersed repeats differ as a function of GC content.
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Figure 28
Interspersed repeats tend to diminish the differences between GC bins, despite the fact that GC-rich transposable elements (specifically Alu) accumulate in GC-rich DNA, and AT-rich elements (LINE1) in AT-rich DNA.
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Figure 29
Higher substitution rate on chromosome Y than on chromosome X.
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Figure 35
Size distributions of exons, introns and short introns, in sequenced genomes.
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Figure 38
Distribution of the homologues of the predicted human proteins.
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Figure 39
Simplified cladogram (relationship tree) of the 'many-to-many' relationships of classical nuclear receptors.
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Figure 40
Number of distinct domain architectures in the four eukaryotic genomes, predicted using SMART339.
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Figure 41
Number of different Pfam domain types that co-occur in the same protein, for each of the 10 most common domain families in each of the five eukaryotic proteomes.
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Figure 44
Relative expansions of protein families between human and fly.
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Figure 45
Lineage-specific expansions of domains and architectures of transcription factors.
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Figure 47
Distribution of number of genes per conserved segment between human and mouse genomes.
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Figure 48
Distribution of lengths (in 5-Mb bins) of conserved segments between human and mouse genomes, omitting singletons.
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Figure 49
Number of human paralogues of genes having single orthologues in worm and fly.
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Table 2
Total genome sequence from the collection of sequenced clones, by sequence status
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Number of copies and fraction of genome for classes of interspersed repeat
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Fraction of finished sequence in inter- and intrachromosomal duplications
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Fraction of the draft genome sequence in inter- and intrachromosomal duplications
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Cross-species comparison for large, highly homologous segmental duplications
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Properties of genome and proteome in essentially completed eukaryotic proteomes
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The most populous InterPro families in the human proteome and other species
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New paralogues of common drug targets identified by searching the draft human genome sequence
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