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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

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CiteULike 106 May 16:10 UTC

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{"link"=>{"url"=>"http://www.citeulike.org/user/rdiaz/article/7466414"}, "post_time"=>"2010-07-12 18:06:40", "tag"=>["cancer", "evolution"], "linkout"=>{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pone.0010398"}, "username"=>"rdiaz", "article_id"=>"7466414"}

Mendeley 3025 Apr 09:13 UTC

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{"title"=>"Cancer reduces transcriptome specialization", "type"=>"journal", "authors"=>[{"first_name"=>"Octavio", "last_name"=>"Martínez", "scopus_author_id"=>"6507436552"}, {"first_name"=>"M. Humberto", "last_name"=>"Reyes-Valdés", "scopus_author_id"=>"6506486941"}, {"first_name"=>"Luis", "last_name"=>"Herrera-Estrella", "scopus_author_id"=>"7006634303"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"77956403250", "issn"=>"19326203", "scopus"=>"2-s2.0-77956403250", "pmid"=>"20454660", "pui"=>"359494490", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0010398"}, "id"=>"dbcdd1a0-decf-3a23-b2e2-adc3e2f5ddf5", "abstract"=>"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.", "link"=>"http://www.mendeley.com/research/cancer-reduces-transcriptome-specialization", "reader_count"=>29, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>2, "Other"=>2, "Student > Master"=>1, "Student > Bachelor"=>3, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>2, "Other"=>2, "Student > Master"=>1, "Student > Bachelor"=>3, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>22, "Medicine and Dentistry"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>1, "Mexico"=>2, "United Kingdom"=>1}, "group_count"=>1}

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{"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/02ddac7d-20c8-4c78-a44c-051fa75cc564", "title"=>"Author Summary", "body"=>"The transcriptome is the set of all genes that are expressed in a given tissue. In cancer, the number of expressed genes and their frequencies changes dramatically as the tissue morphology changes. By analyzing datasets through information theory, we found that the specialization of cancerous tissues is less than normal tissues. From these analyses, we were able to identify the genes responsible for this change. Our findings represent advancement in the definition and understanding of cancer that could lead to new opportunities for diagnosis and putative intervention through drug development or genomics medicine.", "isRemoved"=>false, "created"=>"2010-05-04T00:02:27Z", "lastModified"=>"2010-05-04T00:02:27Z", "creator"=>{"userId"=>"32343"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0010398", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2010-05-04T00:02:27Z", "replies"=>[]}

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Figshare

{"files"=>["https://ndownloader.figshare.com/files/851071"], "description"=>"Frequency pij – 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", "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 A.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-05-03 00:25:28"}
{"files"=>["https://ndownloader.figshare.com/files/851106"], "description"=>"Frequency pij – Relative average frequency of expression in cancer tissues. Tissues – Number of cancerous tissues where the gene was expressed in the 12 tissues studied in dataset A. 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.", "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 A (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"=>"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.", "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 Hj (Diversity) and δj (Specialization) in transcriptomes of normal (blue) and tumor (red) tissues in dataset C.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-03 00:23:40"}
{"files"=>["https://ndownloader.figshare.com/files/850898"], "description"=>"Comparable data sets are linked by a discontinuous line. A - Human data from 53 libraries of 13 distinct tissues with a total of 671,197 tags for 28,087 genes; grouped analyses. 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 A and 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.", "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 Hj (Diversity) and δj (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>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.</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"}

PMC Usage Stats 75317 Feb 14:50 UTC

PMC Usage Stats | Further Information

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Relative Metric 34470710 May 16:14 UTC

Relative Metric

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F1000Prime19 Feb 11:53 UTC

F1000Prime

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