Cancer Reduces Transcriptome Specialization
Publication Date
May 03, 2010
Journal
PLOS ONE
Authors
Octavio Martínez, M. Humberto Reyes Valdés & Luis Herrera Estrella
Volume
5
Issue
5
Pages
e10398
DOI
https://dx.plos.org/10.1371/journal.pone.0010398
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0010398
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/20454660
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862708
Europe PMC
http://europepmc.org/abstract/MED/20454660
Web of Science
000277240300003
Scopus
77956403250
Mendeley
http://www.mendeley.com/research/cancer-reduces-transcriptome-specialization
Events
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/851071"], "description"=>"<p>Frequency <i>p<sub>ij</sub></i> – Relative average frequency of expression in cancer tissues. P-value for the Fisher's Exact Test for the frequency of expression of the gene in the normal vs. cancer tissues</p>", "links"=>[], "tags"=>["genes", "cancer", "dataset"], "article_id"=>521528, "categories"=>["Genetics", "Cell Biology", "Mathematics", "Molecular Biology", "Cancer", "Biological Sciences"], "users"=>["Octavio Martínez", "M. Humberto Reyes-Valdés", "Luis Herrera-Estrella"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010398.t002", "stats"=>{"downloads"=>10, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_genes_highly_expressed_in_only_one_type_of_cancer_in_dataset_A_/521528", "title"=>"Examples of genes highly expressed in only one type of cancer in dataset <i>A.</i>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-05-03 00:25:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/851106"], "description"=>"<p>Frequency <i>p<sub>ij</sub></i> – Relative average frequency of expression in cancer tissues. Tissues <b>–</b> Number of cancerous tissues where the gene was expressed in the 12 tissues studied in dataset <b><i>A</i></b>. P-value for the Fisher's Exact Test for the frequency of expression of the gene in normal vs. cancer tissues; significant at an α≈0.05 experiment-wise confidence level by Bonferroni correction.</p>", "links"=>[], "tags"=>["grouped", "cancer", "tissues", "dataset"], "article_id"=>521562, "categories"=>["Genetics", "Cell Biology", "Mathematics", "Molecular Biology", "Cancer", "Biological Sciences"], "users"=>["Octavio Martínez", "M. Humberto Reyes-Valdés", "Luis Herrera-Estrella"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010398.t001", "stats"=>{"downloads"=>4, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_exclusively_detected_by_the_fully_grouped_analysis_in_cancer_tissues_in_dataset_A_human_data_at_high_expression_frequency_0_0001_/521562", "title"=>"Genes exclusively detected by the fully grouped analysis in cancer tissues in dataset <i>A</i> (human data) at high expression frequency (>0.0001).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-05-03 00:26:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/850965"], "description"=>"<p>Human expression data are from the “Human Transcriptome Map” project (<a href=\"http://bioinfo.amc.uva.nl/HTMseq/controller\" target=\"_blank\">http://bioinfo.amc.uva.nl/HTMseq/controller</a>), datasets “All tissues normal” and “All tissues tumor”. Data consist of 18,609,073 tags for a total of 62,916 loci by chromosome. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010398#pone.0010398.s008\" target=\"_blank\">Figure S7</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010398#pone.0010398.s009\" target=\"_blank\">Figure S8</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010398#pone.0010398.s010\" target=\"_blank\">Figure S9</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010398#pone.0010398.s011\" target=\"_blank\">Figure S10</a> that amplify the boxes of this figure presenting the 95% confidence intervals for the estimates.</p>", "links"=>[], "tags"=>["transcriptomes", "tissues", "dataset"], "article_id"=>521420, "categories"=>["Genetics", "Cell Biology", "Mathematics", "Molecular Biology", "Cancer", "Biological Sciences"], "users"=>["Octavio Martínez", "M. Humberto Reyes-Valdés", "Luis Herrera-Estrella"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010398.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Scatter_plot_of_H_j_Diversity_and_j_Specialization_in_transcriptomes_of_normal_blue_and_tumor_red_tissues_in_dataset_C_/521420", "title"=>"Scatter plot of <i>H<sub>j</sub></i> (Diversity) and <i>δ<sub>j</sub></i> (Specialization) in transcriptomes of normal (blue) and tumor (red) tissues in dataset <i>C</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-03 00:23:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/850898"], "description"=>"<p>Comparable data sets are linked by a discontinuous line. <b><i>A</i></b> - Human data from 53 libraries of 13 distinct tissues with a total of 671,197 tags for 28,087 genes; grouped analyses. <b><i>B</i></b> - Mouse data from 29 libraries of 5 distinct tissues and with a total of 541,453 expressed tags for 25,044 distinct genes; grouped analyses. Data for <b><i>A</i></b> and <b><i>B</i></b> are from the “Cancer Genome Anatomy Project” (<a href=\"http://cgap.nci.nih.gov/\" target=\"_blank\">http://cgap.nci.nih.gov/</a>). Approximate 95% confidence intervals for diversity and specialization are plotted as continuous colored lines. See Supporting <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010398#pone.0010398.s001\" target=\"_blank\">Text S1</a> as well as <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010398#pone.0010398.s002\" target=\"_blank\">Figure S1</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010398#pone.0010398.s003\" target=\"_blank\">Figure S2</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010398#pone.0010398.s004\" target=\"_blank\">Figure S3</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010398#pone.0010398.s005\" target=\"_blank\">Figure S4</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010398#pone.0010398.s006\" target=\"_blank\">Figure S5</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010398#pone.0010398.s007\" target=\"_blank\">Figure S6</a> that illustrate individual comparisons and details.</p>", "links"=>[], "tags"=>["transcriptomes", "tissues", "cancerous", "cells"], "article_id"=>521349, "categories"=>["Genetics", "Cell Biology", "Mathematics", "Molecular Biology", "Cancer", "Biological Sciences"], "users"=>["Octavio Martínez", "M. Humberto Reyes-Valdés", "Luis Herrera-Estrella"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010398.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Scatter_plot_of_H_j_Diversity_and_j_Specialization_in_transcriptomes_of_normal_tissues_blue_cancerous_tissues_red_and_stem_cells_black_/521349", "title"=>"Scatter plot of <i>H<sub>j</sub></i> (Diversity) and <i>δ<sub>j</sub></i> (Specialization) in transcriptomes of normal tissues (blue), cancerous tissues (red), and stem cells (black).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-03 00:22:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/423561", "https://ndownloader.figshare.com/files/423570", "https://ndownloader.figshare.com/files/423574", "https://ndownloader.figshare.com/files/423584", "https://ndownloader.figshare.com/files/423588", "https://ndownloader.figshare.com/files/423595", "https://ndownloader.figshare.com/files/423604", "https://ndownloader.figshare.com/files/423613", "https://ndownloader.figshare.com/files/423617", "https://ndownloader.figshare.com/files/423622", "https://ndownloader.figshare.com/files/423630", "https://ndownloader.figshare.com/files/423639", "https://ndownloader.figshare.com/files/423643", "https://ndownloader.figshare.com/files/423648", "https://ndownloader.figshare.com/files/423650", "https://ndownloader.figshare.com/files/423655", "https://ndownloader.figshare.com/files/423663", "https://ndownloader.figshare.com/files/423674", "https://ndownloader.figshare.com/files/423682", "https://ndownloader.figshare.com/files/423690", "https://ndownloader.figshare.com/files/423697", "https://ndownloader.figshare.com/files/423703", "https://ndownloader.figshare.com/files/423708", "https://ndownloader.figshare.com/files/423718", "https://ndownloader.figshare.com/files/423727", "https://ndownloader.figshare.com/files/423737", "https://ndownloader.figshare.com/files/423742", "https://ndownloader.figshare.com/files/423751", "https://ndownloader.figshare.com/files/423763", "https://ndownloader.figshare.com/files/423777", "https://ndownloader.figshare.com/files/423783", "https://ndownloader.figshare.com/files/423790"], "description"=>"<div><p>A central goal of cancer biology is to understand how cells from this family of genetic diseases undergo specific morphological and physiological changes and regress to a de-regulated state of the cell cycle. The fact that tumors are unable to perform most of the specific functions of the original tissue led us to hypothesize that the degree of specialization of the transcriptome of cancerous tissues must be less than their normal counterparts. With the aid of information theory tools, we analyzed four datasets derived from transcriptomes of normal and tumor tissues to quantitatively test the hypothesis that cancer reduces transcriptome specialization. Here, we show that the transcriptional specialization of a tumor is significantly less than the corresponding normal tissue and comparable with the specialization of dedifferentiated embryonic stem cells. Furthermore, we demonstrate that the drop in specialization in cancerous tissues is largely due to a decrease in expression of genes that are highly specific to the normal organ. This approach gives us a better understanding of carcinogenesis and offers new tools for the identification of genes that are highly influential in cancer progression.</p></div>", "links"=>[], "tags"=>["cancer", "reduces", "transcriptome", "specialization"], "article_id"=>143631, "categories"=>["Genetics", "Cell Biology", "Mathematics", "Molecular Biology", "Cancer", "Biological Sciences"], "users"=>["Octavio Martínez", "M. Humberto Reyes-Valdés", "Luis Herrera-Estrella"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0010398.s001", "https://dx.doi.org/10.1371/journal.pone.0010398.s002", "https://dx.doi.org/10.1371/journal.pone.0010398.s003", "https://dx.doi.org/10.1371/journal.pone.0010398.s004", "https://dx.doi.org/10.1371/journal.pone.0010398.s005", "https://dx.doi.org/10.1371/journal.pone.0010398.s006", "https://dx.doi.org/10.1371/journal.pone.0010398.s007", "https://dx.doi.org/10.1371/journal.pone.0010398.s008", "https://dx.doi.org/10.1371/journal.pone.0010398.s009", "https://dx.doi.org/10.1371/journal.pone.0010398.s010", "https://dx.doi.org/10.1371/journal.pone.0010398.s011", "https://dx.doi.org/10.1371/journal.pone.0010398.s012", "https://dx.doi.org/10.1371/journal.pone.0010398.s013", "https://dx.doi.org/10.1371/journal.pone.0010398.s014", "https://dx.doi.org/10.1371/journal.pone.0010398.s015", "https://dx.doi.org/10.1371/journal.pone.0010398.s016", "https://dx.doi.org/10.1371/journal.pone.0010398.s017", "https://dx.doi.org/10.1371/journal.pone.0010398.s018", "https://dx.doi.org/10.1371/journal.pone.0010398.s019", "https://dx.doi.org/10.1371/journal.pone.0010398.s020", "https://dx.doi.org/10.1371/journal.pone.0010398.s021", "https://dx.doi.org/10.1371/journal.pone.0010398.s022", "https://dx.doi.org/10.1371/journal.pone.0010398.s023", "https://dx.doi.org/10.1371/journal.pone.0010398.s024", "https://dx.doi.org/10.1371/journal.pone.0010398.s025", "https://dx.doi.org/10.1371/journal.pone.0010398.s026", "https://dx.doi.org/10.1371/journal.pone.0010398.s027", "https://dx.doi.org/10.1371/journal.pone.0010398.s028", "https://dx.doi.org/10.1371/journal.pone.0010398.s029", "https://dx.doi.org/10.1371/journal.pone.0010398.s030", "https://dx.doi.org/10.1371/journal.pone.0010398.s031", "https://dx.doi.org/10.1371/journal.pone.0010398.s032"], "stats"=>{"downloads"=>41, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Cancer_Reduces_Transcriptome_Specialization/143631", "title"=>"Cancer Reduces Transcriptome Specialization", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-05-03 01:00:31"}

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