Preservation of Ranking Order in the Expression of Human Housekeeping Genes
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{"title"=>"Preservation of ranking order in the expression of human housekeeping genes", "type"=>"journal", "authors"=>[{"first_name"=>"Grace T.W.", "last_name"=>"Shaw", "scopus_author_id"=>"57192101329"}, {"first_name"=>"Edward S.C.", "last_name"=>"Shih", "scopus_author_id"=>"6603934436"}, {"first_name"=>"Chun Houh", "last_name"=>"Chen", "scopus_author_id"=>"35308604900"}, {"first_name"=>"Ming Jing", "last_name"=>"Hwang", "scopus_author_id"=>"7203023462"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "sgr"=>"84055216973", "scopus"=>"2-s2.0-84055216973", "pui"=>"363132814", "doi"=>"10.1371/journal.pone.0029314", "pmid"=>"22216246"}, "id"=>"c11b51f9-8e4c-3c7c-988c-5ffd22b4145c", "abstract"=>"Housekeeping (HK) genes fulfill the basic needs for a cell to survive and function properly. Their ubiquitous expression, originally thought to be constant, can vary from tissue to tissue, but this variation remains largely uncharacterized and it could not be explained by previously identified properties of HK genes such as short gene length and high GC content. By analyzing microarray expression data for human genes, we uncovered a previously unnoted characteristic of HK gene expression, namely that the ranking order of their expression levels tends to be preserved from one tissue to another. Further analysis by tensor product decomposition and pathway stratification identified three main factors of the observed ranking preservation, namely that, compared to those of non-HK (NHK) genes, the expression levels of HK genes show a greater degree of dispersion (less overlap), stableness (a smaller variation in expression between tissues), and correlation of expression. Our results shed light on regulatory mechanisms of HK gene expression that are probably different for different HK genes or pathways, but are consistent and coordinated in different tissues.", "link"=>"http://www.mendeley.com/research/preservation-ranking-order-expression-human-housekeeping-genes", "reader_count"=>19, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>6, "Student > Ph. D. Student"=>3, "Student > Master"=>1, "Other"=>1, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>2, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>6, "Student > Ph. D. Student"=>3, "Student > Master"=>1, "Other"=>1, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>2, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>15, "Computer Science"=>1, "Unspecified"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Sweden"=>1, "Korea (South)"=>1, "Germany"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/355290", "https://ndownloader.figshare.com/files/355331", "https://ndownloader.figshare.com/files/355379", "https://ndownloader.figshare.com/files/355436", "https://ndownloader.figshare.com/files/355476"], "description"=>"<div><p>Housekeeping (HK) genes fulfill the basic needs for a cell to survive and function properly. Their ubiquitous expression, originally thought to be constant, can vary from tissue to tissue, but this variation remains largely uncharacterized and it could not be explained by previously identified properties of HK genes such as short gene length and high GC content. By analyzing microarray expression data for human genes, we uncovered a previously unnoted characteristic of HK gene expression, namely that the ranking order of their expression levels tends to be preserved from one tissue to another. Further analysis by tensor product decomposition and pathway stratification identified three main factors of the observed ranking preservation, namely that, compared to those of non-HK (NHK) genes, the expression levels of HK genes show a greater degree of dispersion (less overlap), stableness (a smaller variation in expression between tissues), and correlation of expression. Our results shed light on regulatory mechanisms of HK gene expression that are probably different for different HK genes or pathways, but are consistent and coordinated in different tissues.</p> </div>", "links"=>[], "tags"=>["preservation", "ranking", "housekeeping", "genes"], "article_id"=>130208, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Grace T. W. Shaw", "Edward S. C. Shih", "Chun-Houh Chen", "Ming-Jing Hwang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029314.s001", "https://dx.doi.org/10.1371/journal.pone.0029314.s002", "https://dx.doi.org/10.1371/journal.pone.0029314.s003", "https://dx.doi.org/10.1371/journal.pone.0029314.s004", "https://dx.doi.org/10.1371/journal.pone.0029314.s005"], "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Preservation_of_Ranking_Order_in_the_Expression_of_Human_Housekeeping_Genes/130208", "title"=>"Preservation of Ranking Order in the Expression of Human Housekeeping Genes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-12-22 00:03:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/700242"], "description"=>"<p>The four-circle Venn diagram is used to illustrate the intertwined relationships between gene expression ranking () and the three contributing factors of co-expression (, <i>Equation (5</i><i>)</i>), stableness (, <i>Equation (7</i><i>)</i>), and dispersion (, <i>Equation (8</i><i>)</i>). The rectangular box represents the universal set, its 16 components can be deduced from tensor computations (<i>Equation (9</i><i>)</i>), e.g., A8 = , A10 = , and A16 = . The equations for computing these components are described in the <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029314#s4\" target=\"_blank\">Methods</a> (<i>Equation (11</i><i>–</i><i>13</i><i>)</i>). Note that each of the four elements (,,, and ) is a composite of eight components.</p>", "links"=>[], "tags"=>["relationships", "contributing", "components"], "article_id"=>370622, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Grace T. W. Shaw", "Edward S. C. Shih", "Chun-Houh Chen", "Ming-Jing Hwang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029314.g009", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_relationships_of_the_contributing_components_of_gene_expression_rankings_/370622", "title"=>"The relationships of the contributing components of gene expression rankings.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-22 00:10:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/700348"], "description"=>"a<p>Based on the distribution of the percentage of HK genes for each of the 155 KEGG pathways, the p value for a 34% was calculated to be 0.04, and 0.006 for 100%.</p>b<p>With the exception of the Proteasome pathway, these values are statistically significant (p value<10<sup>−20</sup> by the paired two-sample Student's t test) compared to the value of 0.58±0.00 obtained for the NHK genes mapped to the remaining 148 KEGG pathways. The p value for the Proteasome pathway was 7.67×10<sup>−4</sup>.</p>c<p>All these values are statistically significant (p value<10<sup>−20</sup> by Student's t test) compared to the alternative hypothesis of no correlation.</p>d<p>SE: standard error.</p>", "links"=>[], "tags"=>["tau", "co-expression", "computed", "hk", "genes", "kegg"], "article_id"=>370729, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Grace T. W. Shaw", "Edward S. C. Shih", "Chun-Houh Chen", "Ming-Jing Hwang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029314.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Kendall_s_tau_and_co_expression_computed_for_the_HK_genes_in_KEGG_pathways_/370729", "title"=>"Kendall's tau () and co-expression () computed for the HK genes in KEGG pathways.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-12-22 00:12:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/699606"], "description"=>"<p>The three contributing factors were dispersion (solid line), stableness (dashed line), and co-expression (dotted line). For each factor, its contribution (in parenthesis) was the sum of the individual contributions calculated using tensor product decomposing equations, such as <i>Equation (11</i><i>)–(13)</i>. The contribution of factors other than these three is given in the black box in the upper right corner of each panel.</p>", "links"=>[], "tags"=>["contributions", "ranking", "preservation", "ts"], "article_id"=>369991, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Grace T. W. Shaw", "Edward S. C. Shih", "Chun-Houh Chen", "Ming-Jing Hwang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029314.g004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_contributions_to_the_ranking_preservation_of_the_HK_MR_and_TS_genes_/369991", "title"=>"The contributions to the ranking preservation of the HK, MR, and TS genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-22 02:46:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/700107"], "description"=>"<p>Shown are gene expression rankings () computed for HK genes coding for proteins involved in different subcomplexes of the proteasome. The value is shown in parenthesis at the bottom of the box. * indicates that the value is significantly different from computed from random sampling using the same number of genes.</p>", "links"=>[], "tags"=>["coherently", "regulated", "subcomplex", "reduced", "ranking", "preservation", "proteasomal"], "article_id"=>370487, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Grace T. W. Shaw", "Edward S. C. Shih", "Chun-Houh Chen", "Ming-Jing Hwang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029314.g008", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_less_coherently_regulated_subcomplex_946_reduced_the_overall_expression_ranking_preservation_of_proteasomal_genes_/370487", "title"=>"A less coherently regulated subcomplex (β) reduced the overall expression ranking preservation of proteasomal genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-22 00:08:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/700384"], "description"=>"<p>Kendall's tau computed for the HK, MR, and TS genes, for four datasets.</p>", "links"=>[], "tags"=>["tau", "computed", "ts"], "article_id"=>370769, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Grace T. W. Shaw", "Edward S. C. Shih", "Chun-Houh Chen", "Ming-Jing Hwang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029314.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Kendall_s_tau_computed_for_the_HK_MR_and_TS_genes_for_four_datasets_/370769", "title"=>"Kendall's tau computed for the HK, MR, and TS genes, for four datasets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-12-22 00:12:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/699403"], "description"=>"<p>(A) Kendall's tau computed for the manually partitioned HK and MR genes (circles) compared to those generated from two different random distributions: the triangles show the results when the GSE2361 expression data were randomly divided into two sets containing the same number of HK (<i>N<sub>g</sub></i> = 388) and MR (<i>N<sub>g</sub></i> = 11,953) genes, while the squares show the results when expression levels were ignored and rankings were randomly created (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029314#s4\" target=\"_blank\">Methods</a>). Each data point is a combination of the two computed for the two gene groups (<i>N<sub>g</sub></i> = 388 and <i>N<sub>g</sub></i> = 11,953) for a particular pair of tissues. (B) The expression of all the genes in any two human tissues (heart and thymus are shown as an example) always has an elliptical shape, resulting in a substantially preserved ranking order with a non-zero (>0.4) even for randomly grouped genes (triangles in (A)). In contrast, randomly assigned rankings would yield a value very close to zero (squares in (A)). Gene expression levels were log2 transformed and were denoted by <i>x<sub>gt</sub></i>.</p>", "links"=>[], "tags"=>["preservation", "hk", "genes", "was"], "article_id"=>369788, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Grace T. W. Shaw", "Edward S. C. Shih", "Chun-Houh Chen", "Ming-Jing Hwang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029314.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ranking_preservation_of_HK_genes_was_not_a_random_event_/369788", "title"=>"Ranking preservation of HK genes was not a random event.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-22 02:43:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/699710"], "description"=>"<p>Shown is the percentage contribution of the three factors, stableness, co-expression, and dispersion to the expression ranking (Kendall's tau, ) computed for the HK genes found in each of the seven HK-enriched KEGG pathways. The black bars are the contributions of other unknown factors.</p>", "links"=>[], "tags"=>["contributions", "ranking", "preservation", "hk", "genes", "hk-enriched", "kegg"], "article_id"=>370085, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Grace T. W. Shaw", "Edward S. C. Shih", "Chun-Houh Chen", "Ming-Jing Hwang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029314.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_contributions_to_the_ranking_preservation_of_the_HK_genes_in_seven_HK_enriched_KEGG_pathways_/370085", "title"=>"The contributions to the ranking preservation of the HK genes in seven HK-enriched KEGG pathways.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-22 00:01:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/699832"], "description"=>"<p>Shown are boxplots of the tissue-wide expression profiles of the HK genes in each of the 7 HK-enriched KEGG pathways. The results for the whole HK set (388 genes) and for the NHK set (12,687 genes) are presented on the right for comparison. Each box is bounded by the 25<sup>th</sup> and 75<sup>th</sup> percentile of the data, with the solid line within the box marking the median and the dotted line the mean, while the two short horizontal bars indicate the 90<sup>th</sup> and 10<sup>th</sup> percentile of the data and dots beyond these two bars are outliers. Gene expression levels were log2 transformed and are denoted by <i>x<sub>gt</sub></i>.</p>", "links"=>[], "tags"=>["levels", "hk", "genes", "hk-enriched", "kegg"], "article_id"=>370213, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Grace T. W. Shaw", "Edward S. C. Shih", "Chun-Houh Chen", "Ming-Jing Hwang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029314.g006", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Range_of_expression_levels_of_the_HK_genes_in_HK_enriched_KEGG_pathways_/370213", "title"=>"Range of expression levels of the HK genes in HK-enriched KEGG pathways.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-22 00:03:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/699963"], "description"=>"<p>Shown are boxplots of expression levels on a log2 scale (<i>x<sub>gt</sub></i>) for 79 ribosomal HK genes (94.1% of the 84 ribosomal genes, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029314#pone-0029314-t002\" target=\"_blank\">Table 2</a>) in each human tissue. Each box is bounded by the 25<sup>th</sup> and 75<sup>th</sup> percentile of the data, the solid line within the box marking the median. The two short horizontal bars indicate the 90<sup>th</sup> and 10<sup>th</sup> percentile of the data, while the crosses mark the 95<sup>th</sup> and the 5<sup>th</sup> percentile of the data. The tissues are grouped according to their embryonic origin.</p>", "links"=>[], "tags"=>["ribosomal", "hk", "genes", "levels", "tissues", "embryonic"], "article_id"=>370341, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Grace T. W. Shaw", "Edward S. C. Shih", "Chun-Houh Chen", "Ming-Jing Hwang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029314.g007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_ribosomal_HK_genes_are_expressed_at_different_levels_in_tissues_of_different_embryonic_origins_/370341", "title"=>"The ribosomal HK genes are expressed at different levels in tissues of different embryonic origins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-22 00:05:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/699523"], "description"=>"<p>The three factors represent three different types of expression pattern of a pair of genes in different tissues: (A) Co-expression (<i>r<sub>gg′</sub></i>; <i>Equation (5</i><i>)</i>), (B) stableness (<i>S<sub>gg′</sub></i>; <i>Equation (7</i><i>)</i>), and (C) dispersion (<i>D<sub>gg′</sub></i><sub>; </sub><i>Equation (8</i><i>)</i>).</p>", "links"=>[], "tags"=>["factors"], "article_id"=>369910, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Grace T. W. Shaw", "Edward S. C. Shih", "Chun-Houh Chen", "Ming-Jing Hwang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029314.g003", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_illustration_of_the_three_factors_that_contribute_to_preserve_gene_expression_rankings_/369910", "title"=>"Schematic illustration of the three factors that contribute to preserve gene expression rankings.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-22 02:45:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/699329"], "description"=>"<p>Frequency is the percentage of tissue pairs with the indicated Kendall's tau (). Each distribution is a compilation of 630 Kendall's tau (; <i>Equation (3</i><i>)</i>), where each was for a pair of tissues sampled from a 36-tissue pool and the frequency of at a particular value was computed on a histogram using a bin width of 0.1. The average value () of the distribution for the HK, MR, and TS gene sets was 0.77, 0.59, and 0.41, respectively, and the standard errors were all small, mostly less than 0.01.</p>", "links"=>[], "tags"=>["genes", "exhibited", "preserved", "ranking", "mr", "ts"], "article_id"=>369715, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Grace T. W. Shaw", "Edward S. C. Shih", "Chun-Houh Chen", "Ming-Jing Hwang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029314.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_HK_genes_exhibited_a_significantly_more_preserved_expression_ranking_order_than_MR_or_TS_genes_/369715", "title"=>"HK genes exhibited a significantly more preserved expression ranking order than MR or TS genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-22 02:41:55"}

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Relative Metric

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