Amplified Genes May Be Overexpressed, Unchanged, or Downregulated in Cervical Cancer Cell Lines
Publication Date
March 07, 2012
Journal
PLOS ONE
Authors
Oscar Vazquez Mena, Ingrid Medina Martinez, Eligia Juárez Torres, Valeria Barrón, et al
Volume
7
Issue
3
Pages
e32667
DOI
https://dx.plos.org/10.1371/journal.pone.0032667
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0032667
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22412903
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296745
Europe PMC
http://europepmc.org/abstract/MED/22412903
Web of Science
000303060800039
Scopus
84857856392
Mendeley
http://www.mendeley.com/research/amplified-genes-overexpressed-unchanged-downregulated-cervical-cancer-cell-lines
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Mendeley | Further Information

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However, the contribution of copy-number alterations to cervical carcinogenesis is unresolved because genome-wide there exists a lack of correlation between copy-number alterations and gene expression. In this study, we investigated whether CNAs in the cell lines CaLo, CaSki, HeLa, and SiHa were associated with changes in gene expression. On average, 19.2% of the cell-line genomes had CNAs. However, only 2.4% comprised minimal recurrent regions (MRRs) common to all the cell lines. Whereas 3q had limited common gains (13%), 5p was entirely duplicated recurrently. Genome-wide, only 15.6% of genes located in CNAs changed gene expression; in contrast, the rate in MRRs was up to 3 times this. Chr 5p was confirmed entirely amplified by FISH; however, maximum 33.5% of the explored genes in 5p were deregulated. In 3q, this rate was 13.4%. Even in 3q26, which had 5 MRRs and 38.7% recurrently gained SNPs, the rate was only 15.1%. Interestingly, up to 19% of deregulated genes in 5p and 73% in 3q26 were downregulated, suggesting additional factors were involved in gene repression. The deregulated genes in 3q and 5p occurred in clusters, suggesting local chromatin factors may also influence gene expression. In regions amplified discontinuously, downregulated genes increased steadily as the number of amplified SNPs increased (p<0.01, Spearman's correlation). Therefore, partial gene amplification may function in silencing gene expression. Additional genes in 1q, 3q and 5p could be involved in cervical carcinogenesis, specifically in apoptosis. These include PARP1 in 1q, TNFSF10 and ECT2 in 3q and CLPTM1L, AHRR, PDCD6, and DAP in 5p. Overall, gene expression and copy-number profiles reveal factors other than gene dosage, like epigenetic or chromatin domains, may influence gene expression within the entirely amplified genome segments.", "link"=>"http://www.mendeley.com/research/amplified-genes-overexpressed-unchanged-downregulated-cervical-cancer-cell-lines", "reader_count"=>35, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Master"=>8, "Other"=>1, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Master"=>8, "Other"=>1, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>21, "Medicine and Dentistry"=>4, "Business, Management and Accounting"=>1, "Physics and Astronomy"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>21}, "Computer Science"=>{"Computer Science"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"United States"=>2, "Mexico"=>2, "Australia"=>1}, "group_count"=>0}

Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/344428", "https://ndownloader.figshare.com/files/344453", "https://ndownloader.figshare.com/files/344502", "https://ndownloader.figshare.com/files/344517", "https://ndownloader.figshare.com/files/344536", "https://ndownloader.figshare.com/files/344571"], "description"=>"<div><p>Several copy number-altered regions (CNAs) have been identified in the genome of cervical cancer, notably, amplifications of 3q and 5p. However, the contribution of copy-number alterations to cervical carcinogenesis is unresolved because genome-wide there exists a lack of correlation between copy-number alterations and gene expression. In this study, we investigated whether CNAs in the cell lines CaLo, CaSki, HeLa, and SiHa were associated with changes in gene expression. On average, 19.2% of the cell-line genomes had CNAs. However, only 2.4% comprised minimal recurrent regions (MRRs) common to all the cell lines. Whereas 3q had limited common gains (13%), 5p was entirely duplicated recurrently. Genome-wide, only 15.6% of genes located in CNAs changed gene expression; in contrast, the rate in MRRs was up to 3 times this. Chr 5p was confirmed entirely amplified by FISH; however, maximum 33.5% of the explored genes in 5p were deregulated. In 3q, this rate was 13.4%. Even in 3q26, which had 5 MRRs and 38.7% recurrently gained SNPs, the rate was only 15.1%. Interestingly, up to 19% of deregulated genes in 5p and 73% in 3q26 were downregulated, suggesting additional factors were involved in gene repression. The deregulated genes in 3q and 5p occurred in clusters, suggesting local chromatin factors may also influence gene expression. In regions amplified discontinuously, downregulated genes increased steadily as the number of amplified SNPs increased (p<0.01, Spearman's correlation). Therefore, partial gene amplification may function in silencing gene expression. Additional genes in 1q, 3q and 5p could be involved in cervical carcinogenesis, specifically in apoptosis. These include <em>PARP1</em> in 1q, <em>TNFSF10</em> and <em>ECT2</em> in 3q <em>and CLPTM1L</em>, <em>AHRR</em>, <em>PDCD6</em>, and <em>DAP</em> in 5p. Overall, gene expression and copy-number profiles reveal factors other than gene dosage, like epigenetic or chromatin domains, may influence gene expression within the entirely amplified genome segments.</p> </div>", "links"=>[], "tags"=>["amplified", "genes", "downregulated", "cervical", "cancer", "lines"], "article_id"=>128077, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Oscar Vazquez-Mena", "Ingrid Medina-Martinez", "Eligia Juárez-Torres", "Valeria Barrón", "Ana Espinosa", "Nicolás Villegas-Sepúlveda", "Laura Gómez-Laguna", "Karem Nieto-Martínez", "Lorena Orozco", "Edgar Roman-Basaure", "Sergio Muñoz Cortez", "Manuel Borges Ibañez", "Carlos Venegas-Vega", "Mariano Guardado-Estrada", "Angélica Rangel-López", "Susana Kofman", "Jaime Berumen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032667.s001", "https://dx.doi.org/10.1371/journal.pone.0032667.s002", "https://dx.doi.org/10.1371/journal.pone.0032667.s003", "https://dx.doi.org/10.1371/journal.pone.0032667.s004", "https://dx.doi.org/10.1371/journal.pone.0032667.s005", "https://dx.doi.org/10.1371/journal.pone.0032667.s006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Amplified_Genes_May_Be_Overexpressed_Unchanged_or_Downregulated_in_Cervical_Cancer_Cell_Lines/128077", "title"=>"Amplified Genes May Be Overexpressed, Unchanged, or Downregulated in Cervical Cancer Cell Lines", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-03-07 02:14:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/670840"], "description"=>"<p>On the left side, the number of SNPs located in each chromosomal arm is indicated, which were explored by the 100 K microarray. On the right side, the number of genes located in each arm is indicated, which were explored for changes in gene expression by the ST1.0 expression microarray. Each bar represents the percentage of recurrent altered SNPs (left) or deregulated genes (right) common to the 4 cell lines. The chromosomal arms are indicated in the middle column. Arms labeled with asterisks had a mean number of CN-altered SNPs higher and statistically significant (p<0.05, chi-square test) compared with the whole genome means. Arms with a statistically significant deregulated gene enrichment were labeled with “a” (identified with both chi-square test and PAGE), “b” (identified only with chi-square test, p<0.05) or “c” (identified only with PAGE).</p>", "links"=>[], "tags"=>["changes", "chromosomal"], "article_id"=>341306, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Oscar Vazquez-Mena", "Ingrid Medina-Martinez", "Eligia Juárez-Torres", "Valeria Barrón", "Ana Espinosa", "Nicolás Villegas-Sepúlveda", "Laura Gómez-Laguna", "Karem Nieto-Martínez", "Lorena Orozco", "Edgar Roman-Basaure", "Sergio Muñoz Cortez", "Manuel Borges Ibañez", "Carlos Venegas-Vega", "Mariano Guardado-Estrada", "Angélica Rangel-López", "Susana Kofman", "Jaime Berumen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032667.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_between_copy_number_changes_and_gene_expression_by_chromosomal_arms_/341306", "title"=>"Comparison between copy number changes and gene expression by chromosomal arms.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-07 00:21:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/670929"], "description"=>"<p>Panel A shows the copy number log<sub>2</sub> ratio of SNPs investigated in Chr 5 by the 100 K SNP microarray in HeLa, CaSki, SiHa, and CaLo. Panels B to D show the fold change of gene expression of genes evaluated by the ST1.0 expression microarray located in MRR 5-1 (n = 64), MRR 5-4 (n = 44), and MRR 5-5 (n = 37) at 5p. The bars represent upregulated genes, downregulated genes, and genes without change in gene expression. The genes are ordered according to position in the genome. The SAM method was used for the analysis, using cut-off values of fold change of ≥1.5 or ≤0.66 for up- or downregulated genes and fold discovery rate (FDR) of 0%. Genes previously reported associated with cervical cancer are labeled with asterisks (IPA system) or circles (PubMed).</p>", "links"=>[], "tags"=>["amplification", "deregulation", "chr"], "article_id"=>341401, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Oscar Vazquez-Mena", "Ingrid Medina-Martinez", "Eligia Juárez-Torres", "Valeria Barrón", "Ana Espinosa", "Nicolás Villegas-Sepúlveda", "Laura Gómez-Laguna", "Karem Nieto-Martínez", "Lorena Orozco", "Edgar Roman-Basaure", "Sergio Muñoz Cortez", "Manuel Borges Ibañez", "Carlos Venegas-Vega", "Mariano Guardado-Estrada", "Angélica Rangel-López", "Susana Kofman", "Jaime Berumen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032667.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_amplification_and_deregulation_of_gene_expression_in_Chr_5p_/341401", "title"=>"Genome amplification and deregulation of gene expression in Chr 5p.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-07 00:23:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/671064"], "description"=>"<p>Panel A shows the experiments of microarrays and panel B the qRT-PCR experiments. Panels show the mean ± standard error of expression intensity of 9 CN-altered genes located at 1q (<i>PARP1</i>), 3q (<i>MCM2</i>, <i>ECT2</i>, <i>NAALADL2</i>, <i>NLGN1</i>, <i>TNSF10</i> and <i>RFC4</i>) and 5p (<i>TRIO and CLPTM1L</i>). For both methods intensities are expressed in relative units (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032667#s4\" target=\"_blank\">Materials and Methods</a>).</p>", "links"=>[], "tags"=>["lines"], "article_id"=>341534, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Oscar Vazquez-Mena", "Ingrid Medina-Martinez", "Eligia Juárez-Torres", "Valeria Barrón", "Ana Espinosa", "Nicolás Villegas-Sepúlveda", "Laura Gómez-Laguna", "Karem Nieto-Martínez", "Lorena Orozco", "Edgar Roman-Basaure", "Sergio Muñoz Cortez", "Manuel Borges Ibañez", "Carlos Venegas-Vega", "Mariano Guardado-Estrada", "Angélica Rangel-López", "Susana Kofman", "Jaime Berumen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032667.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_gene_expression_of_PARP1_MCM2_ECT2_NAALADL2_NLGN1_TNSF10_RFC4_TRIO_and_CLPTM1L_between_cell_lines_and_controls_/341534", "title"=>"Comparison of gene expression of <i>PARP1</i>, <i>MCM2</i>, <i>ECT2</i>, <i>NAALADL2</i>, <i>NLGN1</i>, <i>TNSF10</i>, <i>RFC4</i>, <i>TRIO</i> and <i>CLPTM1L</i> between cell lines and controls.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-07 00:25:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/671163"], "description"=>"<p>The figure shows the percentage trends of deregulated genes as the number of CN-altered SNPs per region (panel A) or gene (panel B) increased. MRR includes the genes harbored by the minimal recurrent regions common to the 4 cell lines. The linear association between the variables in all but one plot (CNAs, panel A) was statistically significant, p<0.01, Mantel–Haenszel linear-by-linear association chi-squared test.</p>", "links"=>[], "tags"=>["deregulated", "genes", "cn-altered", "snps"], "article_id"=>341629, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Oscar Vazquez-Mena", "Ingrid Medina-Martinez", "Eligia Juárez-Torres", "Valeria Barrón", "Ana Espinosa", "Nicolás Villegas-Sepúlveda", "Laura Gómez-Laguna", "Karem Nieto-Martínez", "Lorena Orozco", "Edgar Roman-Basaure", "Sergio Muñoz Cortez", "Manuel Borges Ibañez", "Carlos Venegas-Vega", "Mariano Guardado-Estrada", "Angélica Rangel-López", "Susana Kofman", "Jaime Berumen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032667.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Trend_of_deregulated_genes_as_CN_altered_SNPs_increased_by_gene_or_region_/341629", "title"=>"Trend of deregulated genes as CN-altered SNPs increased by gene or region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-07 00:27:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/671257"], "description"=>"<p>In panel A, the percentage trend of deregulated genes is compared among the genes located in MRRs having 1–100, 101–500, and >500 SNPs. The trends of up- and downregulated genes are shown in panels B (47 deleted MRRs, <500 SNPs), C (51 amplified MRRs, <500 SNPs), and D (2 amplified MRRs, >500 SNPs). The total number of genes studied for expression and included in the analysis of panels B, C, and D was 390, 267, and 108, respectively. The numbers above the bars indicate the number of deregulated genes.</p>", "links"=>[], "tags"=>["down-", "upregulated", "genes", "cn-altered", "deleted", "amplified"], "article_id"=>341720, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Oscar Vazquez-Mena", "Ingrid Medina-Martinez", "Eligia Juárez-Torres", "Valeria Barrón", "Ana Espinosa", "Nicolás Villegas-Sepúlveda", "Laura Gómez-Laguna", "Karem Nieto-Martínez", "Lorena Orozco", "Edgar Roman-Basaure", "Sergio Muñoz Cortez", "Manuel Borges Ibañez", "Carlos Venegas-Vega", "Mariano Guardado-Estrada", "Angélica Rangel-López", "Susana Kofman", "Jaime Berumen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032667.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Trend_of_down_and_upregulated_genes_as_CN_altered_SNPs_gene_increased_in_deleted_and_amplified_MRRs_/341720", "title"=>"Trend of down- and upregulated genes as CN-altered SNPs/gene increased in deleted and amplified MRRs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-07 00:28:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/671382"], "description"=>"<p>Panel A shows the copy number log<sub>2</sub> ratio of SNPs investigated in Chr 3 by the 100 K SNP microarray in HeLa, CaSki, SiHa, and CaLo. Panels B to D show the fold change of gene expression of genes evaluated by the ST1.0 expression microarray located at 3q26 (n = 73), 3q27 (n = 63), and 3q28–29 (n = 66). The genes are ordered according to the position in the genome. See the legend of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032667#pone-0032667-g002\" target=\"_blank\">Figure 2</a> for further information.</p>", "links"=>[], "tags"=>["amplification", "deregulation"], "article_id"=>341854, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Oscar Vazquez-Mena", "Ingrid Medina-Martinez", "Eligia Juárez-Torres", "Valeria Barrón", "Ana Espinosa", "Nicolás Villegas-Sepúlveda", "Laura Gómez-Laguna", "Karem Nieto-Martínez", "Lorena Orozco", "Edgar Roman-Basaure", "Sergio Muñoz Cortez", "Manuel Borges Ibañez", "Carlos Venegas-Vega", "Mariano Guardado-Estrada", "Angélica Rangel-López", "Susana Kofman", "Jaime Berumen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032667.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_amplification_and_deregulation_of_gene_expression_in_3q_/341854", "title"=>"Genome amplification and deregulation of gene expression in 3q.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-07 00:30:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/671546"], "description"=>"<p>Panel A shows the copy number log2 ratio of SNPs investigated in Chr 1 by the 100 K SNP microarray in HeLa, CaSki, SiHa, and CaLo. Panels B to D show the fold change of gene expression of genes evaluated by the ST1.0 expression microarray located at MRRs 1-8, 1-9, 1-14 and 1-15. The genes are ordered according to position in the genome. For panel F, the mean ± S.D. of the log2 ratio signal of 110 SNPs located in the MRR-15 was plotted. In panel G is shown the copy number of PARP1 gene calculated by qPCR in triplicate experiments. See the legend of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032667#pone-0032667-g002\" target=\"_blank\">Figure 2</a> for further information.</p>", "links"=>[], "tags"=>["amplification", "deregulation", "chr"], "article_id"=>342012, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Oscar Vazquez-Mena", "Ingrid Medina-Martinez", "Eligia Juárez-Torres", "Valeria Barrón", "Ana Espinosa", "Nicolás Villegas-Sepúlveda", "Laura Gómez-Laguna", "Karem Nieto-Martínez", "Lorena Orozco", "Edgar Roman-Basaure", "Sergio Muñoz Cortez", "Manuel Borges Ibañez", "Carlos Venegas-Vega", "Mariano Guardado-Estrada", "Angélica Rangel-López", "Susana Kofman", "Jaime Berumen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032667.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_amplification_and_deregulation_of_gene_expression_in_Chr_1q_/342012", "title"=>"Genome amplification and deregulation of gene expression in Chr 1q.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-07 00:33:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/671773"], "description"=>"<p>Representative experiments of FISH analysis of cytobands 5p15.33, 5p15.2, and 3q26 in 3 cell lines (CaLo, CaSki, and HeLa) are shown. Two sets of probes were used for the analysis of 5p15 and one for the analysis of 3q26 (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032667#s4\" target=\"_blank\">Materials and Methods</a>). The sets for 5p15 included a target probe (green signals) and a control probe (red signals) located at 5q. The set for 3q26 included a target probe (green signals) and a control probe located at the centromere. Nuclei in interphase (first, third, and fourth rows) and Chr in metaphase (second row) were counterstained with DAPI.</p>", "links"=>[], "tags"=>["cytobands", "5p15", "3q26", "fluorescence", "situ", "hybridization"], "article_id"=>342231, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Oscar Vazquez-Mena", "Ingrid Medina-Martinez", "Eligia Juárez-Torres", "Valeria Barrón", "Ana Espinosa", "Nicolás Villegas-Sepúlveda", "Laura Gómez-Laguna", "Karem Nieto-Martínez", "Lorena Orozco", "Edgar Roman-Basaure", "Sergio Muñoz Cortez", "Manuel Borges Ibañez", "Carlos Venegas-Vega", "Mariano Guardado-Estrada", "Angélica Rangel-López", "Susana Kofman", "Jaime Berumen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032667.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Copy_number_analysis_of_cytobands_5p15_and_3q26_with_fluorescence_in_situ_hybridization_FISH_/342231", "title"=>"Copy number analysis of cytobands 5p15 and 3q26 with fluorescence in situ hybridization (FISH).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-07 00:37:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/671929"], "description"=>"<p>Top 25 canonical pathways identified in the set of 3,122 genes deregulated in the four cell lines (A) and in the subset of 147 deregulated and recurrent CN-altered genes (B). The canonical pathways were identified with the Ingenuity Pathway Analysis (IPA) system. The −log (p-value), gray bars, and the ratio, black dots, were calculated comparing the number of genes of the pathways present in the datasets versus the human database. The p-value was calculated with the chi square or Fisher exact tests as appropriate and the values of −log (p-value)>1.3 (dash line) correspond to p<0.05.</p>", "links"=>[], "tags"=>["pathways", "deregulated", "genes"], "article_id"=>342398, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Oscar Vazquez-Mena", "Ingrid Medina-Martinez", "Eligia Juárez-Torres", "Valeria Barrón", "Ana Espinosa", "Nicolás Villegas-Sepúlveda", "Laura Gómez-Laguna", "Karem Nieto-Martínez", "Lorena Orozco", "Edgar Roman-Basaure", "Sergio Muñoz Cortez", "Manuel Borges Ibañez", "Carlos Venegas-Vega", "Mariano Guardado-Estrada", "Angélica Rangel-López", "Susana Kofman", "Jaime Berumen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032667.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Canonical_pathways_where_deregulated_genes_are_involved_/342398", "title"=>"Canonical pathways where deregulated genes are involved.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-07 00:39:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/672089"], "description"=>"a<p>20,741 genes were explored for changes in expression with HG-ST1.0 microarray. On average 7,349 of them were CN-altered (CN+) and 13,393 did not have copy number alterations (CN−).</p>b<p>Potentially copy number altered genes according to data obtained with 100 k microarray. On average only 63% of those genes were explored for changes in gene expression (numbers in column n of CN+ subset).</p>c<p>Genes who were copy number altered in the four cell lines.</p>d<p>Genes who were found deregulated when all four cell lines, by triplicate, were compared together against the control sample (n = 10).</p>e<p>In the genome, included genes that were found in MRRs, and in the transcriptome, include genes which were found deregulated uniformly in the four cell lines (described in d).</p><p>EX+ = Genes that were up- or down- regulated in cancer cell lines compared with the control sample.</p>", "links"=>[], "tags"=>["alterations", "deregulation", "cervical", "cancer"], "article_id"=>342554, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Oscar Vazquez-Mena", "Ingrid Medina-Martinez", "Eligia Juárez-Torres", "Valeria Barrón", "Ana Espinosa", "Nicolás Villegas-Sepúlveda", "Laura Gómez-Laguna", "Karem Nieto-Martínez", "Lorena Orozco", "Edgar Roman-Basaure", "Sergio Muñoz Cortez", "Manuel Borges Ibañez", "Carlos Venegas-Vega", "Mariano Guardado-Estrada", "Angélica Rangel-López", "Susana Kofman", "Jaime Berumen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032667.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Influence_of_copy_number_alterations_in_gene_deregulation_in_cervical_cancer_cell_lines_/342554", "title"=>"Influence of copy number alterations in gene deregulation in cervical cancer cell lines.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-07 00:42:34"}

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  • {"unique-ip"=>"16", "full-text"=>"19", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}
  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"18", "supp-data"=>"4", "cited-by"=>"1", "year"=>"2020", "month"=>"6"}
  • {"unique-ip"=>"7", "full-text"=>"9", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
  • {"unique-ip"=>"9", "full-text"=>"10", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"6", "cited-by"=>"1", "year"=>"2020", "month"=>"8"}
  • {"unique-ip"=>"23", "full-text"=>"11", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}
  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"10"}
  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"11"}
  • {"unique-ip"=>"8", "full-text"=>"3", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"12"}
  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2021", "month"=>"1"}

Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[322, 550, 671, 773, 864, 955, 1048, 1135, 1223, 1308, 1387, 1465, 1534, 1602, 1673, 1744, 1813, 1885, 1955, 2026, 2093, 2160, 2228, 2290, 2349]}, {"subject_area"=>"/Biology and life sciences/Cell biology", "average_usage"=>[319, 556, 679, 785, 881, 970, 1062, 1149, 1236, 1323, 1402, 1474, 1545, 1617, 1681, 1754, 1822, 1892, 1963, 2031, 2099, 2165, 2233, 2299, 2359]}, {"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[375, 629, 760, 889, 1000, 1110, 1203, 1298, 1399, 1492, 1603, 1699, 1774, 1855, 1918, 1998, 2062, 2152, 2227, 2312, 2378, 2461, 2528, 2600, 2664]}, {"subject_area"=>"/Physical sciences", "average_usage"=>[304, 506, 616, 712, 799, 879, 968, 1052, 1134, 1212, 1284, 1357, 1427, 1494, 1557, 1621, 1689, 1756, 1823, 1883, 1944, 1997, 2056, 2118, 2171]}, {"subject_area"=>"/Physical sciences/Mathematics", "average_usage"=>[325, 522, 627, 718, 804, 884, 969, 1052, 1131, 1207, 1277, 1346, 1415, 1478, 1542, 1605, 1663, 1723, 1776, 1839, 1895, 1955, 2008, 2066, 2123]}]}
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