Hidden Chromosome Symmetry: In Silico Transformation Reveals Symmetry in 2D DNA Walk Trajectories of 671 Chromosomes
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{"title"=>"Hidden chromosome symmetry: In silico transformation reveals symmetry in 2D DNA walk trajectories of 671 chromosomes", "type"=>"journal", "authors"=>[{"first_name"=>"Maria S.", "last_name"=>"Poptsova", "scopus_author_id"=>"16177766600"}, {"first_name"=>"Sergei A.", "last_name"=>"Larionov", "scopus_author_id"=>"57198203778"}, {"first_name"=>"Eugeny V.", "last_name"=>"Ryadchenko", "scopus_author_id"=>"23991590600"}, {"first_name"=>"Sergei D.", "last_name"=>"Rybalko", "scopus_author_id"=>"7003684958"}, {"first_name"=>"Ilya A.", "last_name"=>"Zakharov", "scopus_author_id"=>"57197898696"}, {"first_name"=>"Alexander", "last_name"=>"Loskutov", "scopus_author_id"=>"7004818052"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203", "pui"=>"355036153", "doi"=>"10.1371/journal.pone.0006396", "scopus"=>"2-s2.0-68149159883", "sgr"=>"68149159883", "issn"=>"19326203", "pmid"=>"19636424"}, "id"=>"4bcdb344-4a40-35d8-8a75-93d23598bd7f", "abstract"=>"Maps of 2D DNA walk of 671 examined chromosomes show composition complexity change from symmetrical half-turn in bacteria to pseudo-random trajectories in archaea, fungi and humans. In silico transformation of gene order and strand position returns most of the analyzed chromosomes to a symmetrical bacterial-like state with one transition point. The transformed chromosomal sequences also reveal remarkable segmental compositional symmetry between regions from different strands located equidistantly from the transition point. Despite extensive chromosome rearrangement the relation of gene numbers on opposite strands for chromosomes of different taxa varies in narrow limits around unity with Pearson coefficient r = 0.98. Similar relation is observed for total genes' length (r = 0.86) and cumulative GC (r = 0.95) and AT (r = 0.97) skews. This is also true for human coding sequences (CDS), which comprise only several percent of the entire chromosome length. We found that frequency distributions of the length of gene clusters, continuously located on the same strand, have close values for both strands. Eukaryotic gene distribution is believed to be non-random. Contribution of different subsystems to the noted symmetries and distributions, and evolutionary aspects of symmetry are discussed.", "link"=>"http://www.mendeley.com/research/hidden-chromosome-symmetry-silico-transformation-reveals-symmetry-2d-dna-walk-trajectories-671-chrom", "reader_count"=>16, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Student > Master"=>2, "Other"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Student > Master"=>2, "Other"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>2, "Mathematics"=>1, "Agricultural and Biological Sciences"=>12, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>12}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Mathematics"=>{"Mathematics"=>1}}, "reader_count_by_country"=>{"Netherlands"=>1, "Egypt"=>1, "Denmark"=>1, "Germany"=>1, "India"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/890883"], "description"=>"<p>Illustration of how genes from different strands are included in to the sequence: (a) piece of DNA with genes and intergenic areas; (b) sequence, made up of genes only.</p>", "links"=>[], "tags"=>["genes"], "article_id"=>561344, "categories"=>["Biological Sciences", "Infectious Diseases", "Computational Biology"], "users"=>["Maria S. Poptsova", "Sergei A. Larionov", "Eugeny V. Ryadchenko", "Sergei D. Rybalko", "Ilya A. Zakharov", "Alexander Loskutov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006396.g009", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequences_made_up_of_genes_only_/561344", "title"=>"Sequences made up of genes only.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-28 00:22:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/890954"], "description"=>"1<p>The values of g-pos (G−C>0), g-neg (G−C<0), a-pos (A−T>0), a–neg (A−T<0) were calculated for the entire gene sequences.</p>", "links"=>[], "tags"=>["g-rich", "a-rich", "genes", "671"], "article_id"=>561402, "categories"=>["Biological Sciences", "Infectious Diseases", "Computational Biology"], "users"=>["Maria S. Poptsova", "Sergei A. Larionov", "Eugeny V. Ryadchenko", "Sergei D. Rybalko", "Ilya A. Zakharov", "Alexander Loskutov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006396.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percent_distribution_of_G_rich_and_A_rich_genes_in_671_chromosomes_1_/561402", "title"=>"Percent distribution of G-rich and A-rich genes in 671 chromosomes<sup>1</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-07-28 00:23:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/890164"], "description"=>"<p>Relation between (a) number (Pearson coefficient r = 0.98), (b) cumulative gene length (r = 0.86), (c) cumulative GC (r = 0.95) and (d) AT (r = 0.97) skews of genes from different strands for 671 chromosomes: 524 bacteria, 36 archaea, 87 fungi and 24 humans.</p>", "links"=>[], "tags"=>["cumulative", "gc", "skews", "genes"], "article_id"=>560615, "categories"=>["Biological Sciences", "Infectious Diseases", "Computational Biology"], "users"=>["Maria S. Poptsova", "Sergei A. Larionov", "Eugeny V. Ryadchenko", "Sergei D. Rybalko", "Ilya A. Zakharov", "Alexander Loskutov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006396.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relations_between_number_cumulative_gene_length_GC_and_AT_skews_of_genes_from_different_strands_/560615", "title"=>"Relations between number, cumulative gene length, GC and AT skews of genes from different strands.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-28 00:10:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/440983", "https://ndownloader.figshare.com/files/441122", "https://ndownloader.figshare.com/files/441167", "https://ndownloader.figshare.com/files/441200", "https://ndownloader.figshare.com/files/441242", "https://ndownloader.figshare.com/files/441321", "https://ndownloader.figshare.com/files/441355", "https://ndownloader.figshare.com/files/441483", "https://ndownloader.figshare.com/files/441498"], "description"=>"<div><p>Maps of 2D DNA walk of 671 examined chromosomes show composition complexity change from symmetrical half-turn in bacteria to pseudo-random trajectories in archaea, fungi and humans. In silico transformation of gene order and strand position returns most of the analyzed chromosomes to a symmetrical bacterial-like state with one transition point. The transformed chromosomal sequences also reveal remarkable segmental compositional symmetry between regions from different strands located equidistantly from the transition point. Despite extensive chromosome rearrangement the relation of gene numbers on opposite strands for chromosomes of different taxa varies in narrow limits around unity with Pearson coefficient r = 0.98. Similar relation is observed for total genes' length (r = 0.86) and cumulative GC (r = 0.95) and AT (r = 0.97) skews. This is also true for human coding sequences (CDS), which comprise only several percent of the entire chromosome length. We found that frequency distributions of the length of gene clusters, continuously located on the same strand, have close values for both strands. Eukaryotic gene distribution is believed to be non-random. Contribution of different subsystems to the noted symmetries and distributions, and evolutionary aspects of symmetry are discussed.</p></div>", "links"=>[], "tags"=>["chromosome", "reveals", "symmetry", "2d", "dna", "trajectories", "671", "chromosomes"], "article_id"=>146920, "categories"=>["Biological Sciences", "Cancer"], "users"=>["Maria S. Poptsova", "Sergei A. Larionov", "Eugeny V. Ryadchenko", "Sergei D. Rybalko", "Ilya A. Zakharov", "Alexander Loskutov"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0006396.s001", "https://dx.doi.org/10.1371/journal.pone.0006396.s002", "https://dx.doi.org/10.1371/journal.pone.0006396.s003", "https://dx.doi.org/10.1371/journal.pone.0006396.s004", "https://dx.doi.org/10.1371/journal.pone.0006396.s005", "https://dx.doi.org/10.1371/journal.pone.0006396.s006", "https://dx.doi.org/10.1371/journal.pone.0006396.s007", "https://dx.doi.org/10.1371/journal.pone.0006396.s008", "https://dx.doi.org/10.1371/journal.pone.0006396.s009"], "stats"=>{"downloads"=>11, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Hidden_Chromosome_Symmetry_In_Silico_Transformation_Reveals_Symmetry_in_2D_DNA_Walk_Trajectories_of_671_Chromosomes/146920", "title"=>"Hidden Chromosome Symmetry: <em>In Silico</em> Transformation Reveals Symmetry in 2D DNA Walk Trajectories of 671 Chromosomes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-07-28 01:55:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/890766"], "description"=>"<p>(a)–an example of the 2D DNA walk of chromosome 1 of <i>Saccharomyces cerevisiae</i>; (b) - zoomed in fragment of 2D DNA walk with FLO genes family in the blue circle; (c) - zoomed in fragment of the part of FLO genes in the violet rectangle; (d)–low level representation of the 2D DNA walk method for a short sequence.</p>", "links"=>[], "tags"=>["2d", "dna"], "article_id"=>561222, "categories"=>["Biological Sciences", "Infectious Diseases", "Computational Biology"], "users"=>["Maria S. Poptsova", "Sergei A. Larionov", "Eugeny V. Ryadchenko", "Sergei D. Rybalko", "Ilya A. Zakharov", "Alexander Loskutov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006396.g008", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_the_2D_DNA_walk_method_/561222", "title"=>"Illustration of the 2D DNA walk method.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-28 00:20:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/890242"], "description"=>"<p>See text for explanation. Symmetrically correlated regions are drawn in the same color.</p>", "links"=>[], "tags"=>["gene-vector", "2d", "dna"], "article_id"=>560692, "categories"=>["Biological Sciences", "Infectious Diseases", "Computational Biology"], "users"=>["Maria S. Poptsova", "Sergei A. Larionov", "Eugeny V. Ryadchenko", "Sergei D. Rybalko", "Ilya A. Zakharov", "Alexander Loskutov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006396.g003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_gene_vector_model_on_a_2D_DNA_plane_/560692", "title"=>"Illustration of gene-vector model on a 2D DNA plane.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-28 00:11:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/890586"], "description"=>"<p>(a) - bacteria (<i>Bacillus anthracis Ames</i>), (b) - archaea (<i>Sulfalobus solfataricus</i>), (c) - fungi (<i>Saccharomyces cerevisiae</i>, chromosome 12), (d) - <i>Homo sapiens</i> (chromosome 8). Red arrows point to the positions of the known origins of replications.</p>", "links"=>[], "tags"=>["strands"], "article_id"=>561041, "categories"=>["Biological Sciences", "Infectious Diseases", "Computational Biology"], "users"=>["Maria S. Poptsova", "Sergei A. Larionov", "Eugeny V. Ryadchenko", "Sergei D. Rybalko", "Ilya A. Zakharov", "Alexander Loskutov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006396.g006", "stats"=>{"downloads"=>3, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_distribution_over_strands_in_the_entire_chromosome_/561041", "title"=>"Gene distribution over strands in the entire chromosome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-28 00:17:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/890297"], "description"=>"<p>(a)–chromosome clusters after GSS transformation, (b)–chromosome clusters in the original order.</p>", "links"=>[], "tags"=>["chromosome"], "article_id"=>560753, "categories"=>["Biological Sciences", "Infectious Diseases", "Computational Biology"], "users"=>["Maria S. Poptsova", "Sergei A. Larionov", "Eugeny V. Ryadchenko", "Sergei D. Rybalko", "Ilya A. Zakharov", "Alexander Loskutov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006396.g004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cluster_model_of_chromosome_organization_/560753", "title"=>"Cluster model of chromosome organization.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-28 00:12:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/890010"], "description"=>"<p>(a) - bacteria (<i>Bacillus anthracis Ames</i>), (b) - archaea (<i>Sulfalobus solfataricus</i>), (c)–fungi (<i>Saccharomyces cerevisiae</i>, chromosome 12), (d) - <i>Homo sapiens</i> (chromosome 8). Trajectories of the genes in the original order are shown on the left, GSS transformed trajectories on the right.</p>", "links"=>[], "tags"=>["dna", "graphs", "genes", "chromosome"], "article_id"=>560462, "categories"=>["Biological Sciences", "Infectious Diseases", "Computational Biology"], "users"=>["Maria S. Poptsova", "Sergei A. Larionov", "Eugeny V. Ryadchenko", "Sergei D. Rybalko", "Ilya A. Zakharov", "Alexander Loskutov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006396.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_2D_DNA_graphs_of_all_genes_from_a_chromosome_for_different_organisms_/560462", "title"=>"2D DNA graphs of all genes from a chromosome for different organisms.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-28 00:07:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/890682"], "description"=>"<p>Data are approximated by exponential functions with scale parameter beta = 2.36 for (a) bacteria (<i>Bacillus anthracis Ames</i>), beta = 2.01 (b) for archaea (<i>Sulfalobus solfataricus</i>), beta = 1.33 (c) for fungi (<i>Saccharomyces cerevisiae</i>, chromosome 12), beta = 1.3 (d) for <i>Homo sapiens</i> (chromosome 8).</p>", "links"=>[], "tags"=>["distributions", "clusters", "genes", "continuously", "located"], "article_id"=>561130, "categories"=>["Biological Sciences", "Infectious Diseases", "Computational Biology"], "users"=>["Maria S. Poptsova", "Sergei A. Larionov", "Eugeny V. Ryadchenko", "Sergei D. Rybalko", "Ilya A. Zakharov", "Alexander Loskutov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006396.g007", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Normalized_frequency_distributions_of_clusters_with_genes_continuously_located_on_one_strand_/561130", "title"=>"Normalized frequency distributions of clusters with genes continuously located on one strand.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-28 00:18:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/890422"], "description"=>"<p>(a–b)–<i>Saccharomyces cerevisiae</i>, chromosome 1, - (c–d)–<i>Saccharomyces cerevisiae</i>, chromosome 16, (e–f)–<i>Encephalitozoon cuniculi</i>, chromosome 10. (a,c,e)–2D DNA walk maps of chromosomes made of genes in the original order; genes from «+»-strand are colored in red, genes from «−»-strand are colored in black. (b,d,f)–GSS-transformed trajectories, I–in the original form, II–two arms of GSS-transformed trajectories are detached to show symmetrical correlated regions, which are highlighted and numbered (see blast hits for these regions in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006396#pone.0006396.s008\" target=\"_blank\">Table S2</a>).</p>", "links"=>[], "tags"=>["correlated", "symmetry", "2d", "dna", "trajectories", "gss"], "article_id"=>560870, "categories"=>["Biological Sciences", "Infectious Diseases", "Computational Biology"], "users"=>["Maria S. Poptsova", "Sergei A. Larionov", "Eugeny V. Ryadchenko", "Sergei D. Rybalko", "Ilya A. Zakharov", "Alexander Loskutov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006396.g005", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Emergence_of_correlated_symmetry_of_2D_DNA_walk_trajectories_after_GSS_transformation_/560870", "title"=>"Emergence of correlated symmetry of 2D DNA walk trajectories after GSS transformation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-28 00:14:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/890992"], "description"=>"2<p>The values of g-pos (G−C>0), a-pos (A−T>0) were calculated for the 1<sup>st</sup>, 2<sup>nd</sup>, and 3<sup>rd</sup> codon positions. The values of g-neg and a–neg are calculated as 100% - g-pos and 100% - a-pos.</p>", "links"=>[], "tags"=>["g-rich", "a-rich", "genes", "codon", "positions", "671"], "article_id"=>561439, "categories"=>["Biological Sciences", "Infectious Diseases", "Computational Biology"], "users"=>["Maria S. Poptsova", "Sergei A. Larionov", "Eugeny V. Ryadchenko", "Sergei D. Rybalko", "Ilya A. Zakharov", "Alexander Loskutov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006396.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percent_distribution_of_G_rich_and_A_rich_genes_for_the_1_st_2_nd_and_3_rd_codon_positions_in_671_chromosomes_2_/561439", "title"=>"Percent distribution of G-rich and A-rich genes for the 1<sup>st</sup>, 2<sup>nd</sup>, and 3<sup>rd</sup> codon positions in 671 chromosomes<sup>2</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-07-28 00:23:59"}

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  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

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