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{"title"=>"Genomic Analysis of Stress Response against Arsenic in Caenorhabditis elegans", "type"=>"journal", "authors"=>[{"first_name"=>"Surasri N.", "last_name"=>"Sahu", "scopus_author_id"=>"54890989300"}, {"first_name"=>"Jada", "last_name"=>"Lewis", "scopus_author_id"=>"37666720900"}, {"first_name"=>"Isha", "last_name"=>"Patel", "scopus_author_id"=>"7006093602"}, {"first_name"=>"Serdar", "last_name"=>"Bozdag", "scopus_author_id"=>"24472576200"}, {"first_name"=>"Jeong H.", "last_name"=>"Lee", "scopus_author_id"=>"57196135700"}, {"first_name"=>"Robert", "last_name"=>"Sprando", "scopus_author_id"=>"7004005561"}, {"first_name"=>"Hediye Nese", "last_name"=>"Cinar", "scopus_author_id"=>"6602268520"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"3900051070", "sgr"=>"84880800525", "pui"=>"369437968", "pmid"=>"23894281", "issn"=>"19326203", "scopus"=>"2-s2.0-84880800525", "doi"=>"10.1371/journal.pone.0066431"}, "id"=>"dd8fe350-e491-314d-bbab-839a1976b5a4", "abstract"=>"Arsenic, a known human carcinogen, is widely distributed around the world and found in particularly high concentrations in certain regions including Southwestern US, Eastern Europe, India, China, Taiwan and Mexico. Chronic arsenic poisoning affects millions of people worldwide and is associated with increased risk of many diseases including arthrosclerosis, diabetes and cancer. In this study, we explored genome level global responses to high and low levels of arsenic exposure in Caenorhabditis elegans using Affymetrix expression microarrays. This experimental design allows us to do microarray analysis of dose-response relationships of global gene expression patterns. High dose (0.03%) exposure caused stronger global gene expression changes in comparison with low dose (0.003%) exposure, suggesting a positive dose-response correlation. Biological processes such as oxidative stress, and iron metabolism, which were previously reported to be involved in arsenic toxicity studies using cultured cells, experimental animals, and humans, were found to be affected in C. elegans. We performed genome-wide gene expression comparisons between our microarray data and publicly available C. elegans microarray datasets of cadmium, and sediment exposure samples of German rivers Rhine and Elbe. Bioinformatics analysis of arsenic-responsive regulatory networks were done using FastMEDUSA program. FastMEDUSA analysis identified cancer-related genes, particularly genes associated with leukemia, such as dnj-11, which encodes a protein orthologous to the mammalian ZRF1/MIDA1/MPP11/DNAJC2 family of ribosome-associated molecular chaperones. We analyzed the protective functions of several of the identified genes using RNAi. Our study indicates that C. elegans could be a substitute model to study the mechanism of metal toxicity using high-throughput expression data and bioinformatics tools such as FastMEDUSA.", "link"=>"http://www.mendeley.com/research/genomic-analysis-stress-response-against-arsenic-caenorhabditis-elegans-1", "reader_count"=>32, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>20, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>20}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>3}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"United Kingdom"=>1, "Portugal"=>1}, "group_count"=>1}

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• http://doi.org/10.1016/j.chemosphere.2016.01.004
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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/1129793"], "description"=>"<p>(A) A Venn diagram illustrating number of genes expressed at low and high dose arsenic exposure, 4-hour cadmium exposure, and overlap among these data. (B) A Venn diagram illustrating number of genes expressed at low and high dose arsenic exposure, 24-hour cadmium exposure, and overlap among these data. (C) Enrichment of gene ontology categories for genes differentially expressed at high dose arsenic exposure.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome expression analysis", "Molecular genetics", "Gene regulation", "microarrays", "genetics", "Cancer genetics", "Model organisms", "Animal models", "Caenorhabditis elegans", "Molecular cell biology", "gene expression", "systems biology", "toxicology", "Toxic agents", "hematology", "Hematologic cancers and related disorders", "leukemias", "oncology", "Cancer risk factors", "comparisons", "genes", "regulated", "arsenic"], "article_id"=>754228, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Surasri N. Sahu", "Jada Lewis", "Isha Patel", "Serdar Bozdag", "Jeong H. Lee", "Robert Sprando", "Hediye Nese Cinar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0066431.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_wide_expression_profile_comparisons_of_C_elegans_genes_regulated_by_arsenic_and_cadmium_/754228", "title"=>"Genome-wide expression profile comparisons of <i>C. elegans</i> genes regulated by arsenic and cadmium.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-24 06:25:58"}
• {"files"=>["https://ndownloader.figshare.com/files/1129795"], "description"=>"<p>(A) <i>aip-1, p<0.0001</i>, (B) <i>gst-37, p = 0.0085</i>, (C) <i>gcs-1, p<0.0001</i> and (D) <i>hsp-70, p = 0.04</i>, RNAi results in lethality in <i>C. elegans</i> exposed to sodium arsenite.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome expression analysis", "Molecular genetics", "Gene regulation", "microarrays", "genetics", "Cancer genetics", "Model organisms", "Animal models", "Caenorhabditis elegans", "Molecular cell biology", "gene expression", "systems biology", "toxicology", "Toxic agents", "hematology", "Hematologic cancers and related disorders", "leukemias", "oncology", "Cancer risk factors", "induced", "genes", "mediate"], "article_id"=>754230, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Surasri N. Sahu", "Jada Lewis", "Isha Patel", "Serdar Bozdag", "Jeong H. Lee", "Robert Sprando", "Hediye Nese Cinar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0066431.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Arsenic_induced_genes_mediate_stress_response_/754230", "title"=>"Arsenic induced genes mediate stress response.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-24 06:25:58"}
• {"files"=>["https://ndownloader.figshare.com/files/1129796"], "description"=>"<p>(A) A Venn diagram illustrating number of genes expressed at high dose arsenic exposure, paraquat exposure, and overlap among these data. (B) A Venn diagram illustrating number of genes expressed at high dose arsenic exposure, hyperbaric oxygen exposure, and overlap among these data. (C) Enrichment of gene ontology categories for genes differentially expressed at paraquat exposure. (D) Enrichment of gene ontology categories for genes differentially expressed at hyperbaric oxygen exposure.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome expression analysis", "Molecular genetics", "Gene regulation", "microarrays", "genetics", "Cancer genetics", "Model organisms", "Animal models", "Caenorhabditis elegans", "Molecular cell biology", "gene expression", "systems biology", "toxicology", "Toxic agents", "hematology", "Hematologic cancers and related disorders", "leukemias", "oncology", "Cancer risk factors", "comparisons", "genes", "regulated", "arsenic", "oxidative"], "article_id"=>754231, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Surasri N. Sahu", "Jada Lewis", "Isha Patel", "Serdar Bozdag", "Jeong H. Lee", "Robert Sprando", "Hediye Nese Cinar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0066431.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_wide_expression_profile_comparisons_of_C_elegans_genes_regulated_by_arsenic_and_oxidative_stress_/754231", "title"=>"Genome-wide expression profile comparisons of <i>C. elegans</i> genes regulated by arsenic and oxidative stress.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-24 06:25:58"}
• {"files"=>["https://ndownloader.figshare.com/files/1129797"], "description"=>"<p>(A) A Venn diagram illustrating number of genes expressed at low and high dose arsenic exposure, Elbe River sediment exposure, and overlap among these data. (B) A Venn diagram illustrating number of genes expressed at low and high dose arsenic exposure, Rhine River sediment exposure, and overlap among these data. (C) Enrichment of gene ontology categories for genes differentially expressed at Elbe River sediment exposure. (D) Enrichment of gene ontology categories for genes differentially expressed at Rhine River sediment exposure.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome expression analysis", "Molecular genetics", "Gene regulation", "microarrays", "genetics", "Cancer genetics", "Model organisms", "Animal models", "Caenorhabditis elegans", "Molecular cell biology", "gene expression", "systems biology", "toxicology", "Toxic agents", "hematology", "Hematologic cancers and related disorders", "leukemias", "oncology", "Cancer risk factors", "comparisons", "genes", "regulated", "arsenic", "sediment"], "article_id"=>754232, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Surasri N. Sahu", "Jada Lewis", "Isha Patel", "Serdar Bozdag", "Jeong H. Lee", "Robert Sprando", "Hediye Nese Cinar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0066431.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_wide_expression_profile_comparisons_of_C_elegans_genes_regulated_by_arsenic_and_river_sediment_toxicants_/754232", "title"=>"Genome-wide expression profile comparisons of <i>C. elegans</i> genes regulated by arsenic and river sediment toxicants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-24 06:25:58"}
• {"files"=>["https://ndownloader.figshare.com/files/1129798"], "description"=>"<p>(Assays are performed on arsenic exposure conditions.) (A) <i>dnj-11(gk1025)</i>, <i>p</i><0.0001, (B) and <i>dac-1(gk211)</i>, <i>p</i><0.0001.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome expression analysis", "Molecular genetics", "Gene regulation", "microarrays", "genetics", "Cancer genetics", "Model organisms", "Animal models", "Caenorhabditis elegans", "Molecular cell biology", "gene expression", "systems biology", "toxicology", "Toxic agents", "hematology", "Hematologic cancers and related disorders", "leukemias", "oncology", "Cancer risk factors", "assays", "knock-downs", "fastmedusa", "arsenic", "responsive"], "article_id"=>754233, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Surasri N. Sahu", "Jada Lewis", "Isha Patel", "Serdar Bozdag", "Jeong H. Lee", "Robert Sprando", "Hediye Nese Cinar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0066431.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lethality_assays_of_knock_downs_of_the_FastMedusa_identified_arsenic_responsive_regulatory_genes_/754233", "title"=>"Lethality assays of knock-downs of the FastMedusa identified arsenic responsive regulatory genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-24 06:25:58"}
• {"files"=>["https://ndownloader.figshare.com/files/1129799"], "description"=>"<p>List of genes up-regulated (>4 times) in both high and low dose arsenic exposure.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome expression analysis", "Molecular genetics", "Gene regulation", "microarrays", "genetics", "Cancer genetics", "Model organisms", "Animal models", "Caenorhabditis elegans", "Molecular cell biology", "gene expression", "systems biology", "toxicology", "Toxic agents", "hematology", "Hematologic cancers and related disorders", "leukemias", "oncology", "Cancer risk factors", "genes", "up-regulated", "arsenic"], "article_id"=>754234, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Surasri N. Sahu", "Jada Lewis", "Isha Patel", "Serdar Bozdag", "Jeong H. Lee", "Robert Sprando", "Hediye Nese Cinar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0066431.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_genes_up_regulated_gt_4_times_in_both_high_and_low_dose_arsenic_exposure_/754234", "title"=>"List of genes up-regulated (>4 times) in both high and low dose arsenic exposure.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-24 06:25:58"}
• {"files"=>["https://ndownloader.figshare.com/files/1129800"], "description"=>"<p>Oxidative stress and iron metabolism related gene expression is altered upon arsenic exposure in <i>C. elegans</i>.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome expression analysis", "Molecular genetics", "Gene regulation", "microarrays", "genetics", "Cancer genetics", "Model organisms", "Animal models", "Caenorhabditis elegans", "Molecular cell biology", "gene expression", "systems biology", "toxicology", "Toxic agents", "hematology", "Hematologic cancers and related disorders", "leukemias", "oncology", "Cancer risk factors", "metabolism", "altered", "arsenic"], "article_id"=>754235, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Surasri N. Sahu", "Jada Lewis", "Isha Patel", "Serdar Bozdag", "Jeong H. Lee", "Robert Sprando", "Hediye Nese Cinar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0066431.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Oxidative_stress_and_iron_metabolism_related_gene_expression_is_altered_upon_arsenic_exposure_in_C_elegans_/754235", "title"=>"Oxidative stress and iron metabolism related gene expression is altered upon arsenic exposure in <i>C. elegans</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-24 06:25:58"}
• {"files"=>["https://ndownloader.figshare.com/files/1129801"], "description"=>"<p>Transcription factors that are predicted to be involving in the response to arsenic exposure by FastMEDUSA.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome expression analysis", "Molecular genetics", "Gene regulation", "microarrays", "genetics", "Cancer genetics", "Model organisms", "Animal models", "Caenorhabditis elegans", "Molecular cell biology", "gene expression", "systems biology", "toxicology", "Toxic agents", "hematology", "Hematologic cancers and related disorders", "leukemias", "oncology", "Cancer risk factors", "involving", "arsenic"], "article_id"=>754236, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Surasri N. Sahu", "Jada Lewis", "Isha Patel", "Serdar Bozdag", "Jeong H. Lee", "Robert Sprando", "Hediye Nese Cinar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0066431.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transcription_factors_that_are_predicted_to_be_involving_in_the_response_to_arsenic_exposure_by_FastMEDUSA_/754236", "title"=>"Transcription factors that are predicted to be involving in the response to arsenic exposure by FastMEDUSA.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-24 06:25:58"}
• {"files"=>["https://ndownloader.figshare.com/files/1129813", "https://ndownloader.figshare.com/files/1129814", "https://ndownloader.figshare.com/files/1129815", "https://ndownloader.figshare.com/files/1129816", "https://ndownloader.figshare.com/files/1129817", "https://ndownloader.figshare.com/files/1129818", "https://ndownloader.figshare.com/files/1129819", "https://ndownloader.figshare.com/files/1129820", "https://ndownloader.figshare.com/files/1129821", "https://ndownloader.figshare.com/files/1129822", "https://ndownloader.figshare.com/files/1129823", "https://ndownloader.figshare.com/files/1129824"], "description"=>"<div><p>Arsenic, a known human carcinogen, is widely distributed around the world and found in particularly high concentrations in certain regions including Southwestern US, Eastern Europe, India, China, Taiwan and Mexico. Chronic arsenic poisoning affects millions of people worldwide and is associated with increased risk of many diseases including arthrosclerosis, diabetes and cancer. In this study, we explored genome level global responses to high and low levels of arsenic exposure in <i>Caenorhabditis elegans</i> using Affymetrix expression microarrays. This experimental design allows us to do microarray analysis of dose-response relationships of global gene expression patterns. High dose (0.03%) exposure caused stronger global gene expression changes in comparison with low dose (0.003%) exposure, suggesting a positive dose-response correlation. Biological processes such as oxidative stress, and iron metabolism, which were previously reported to be involved in arsenic toxicity studies using cultured cells, experimental animals, and humans, were found to be affected in <i>C. elegans</i>. We performed genome-wide gene expression comparisons between our microarray data and publicly available <i>C. elegans</i> microarray datasets of cadmium, and sediment exposure samples of German rivers Rhine and Elbe. Bioinformatics analysis of arsenic-responsive regulatory networks were done using FastMEDUSA program. FastMEDUSA analysis identified cancer-related genes, particularly genes associated with leukemia, such as <i>dnj-11</i>, which encodes a protein orthologous to the mammalian ZRF1/MIDA1/MPP11/DNAJC2 family of ribosome-associated molecular chaperones. We analyzed the protective functions of several of the identified genes using RNAi. Our study indicates that <i>C. elegans</i> could be a substitute model to study the mechanism of metal toxicity using high-throughput expression data and bioinformatics tools such as FastMEDUSA.</p></div>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome expression analysis", "Molecular genetics", "Gene regulation", "microarrays", "genetics", "Cancer genetics", "Model organisms", "Animal models", "Caenorhabditis elegans", "Molecular cell biology", "gene expression", "systems biology", "toxicology", "Toxic agents", "hematology", "Hematologic cancers and related disorders", "leukemias", "oncology", "Cancer risk factors", "genomic", "arsenic"], "article_id"=>754248, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Surasri N. Sahu", "Jada Lewis", "Isha Patel", "Serdar Bozdag", "Jeong H. Lee", "Robert Sprando", "Hediye Nese Cinar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0066431.s001", "https://dx.doi.org/10.1371/journal.pone.0066431.s002", "https://dx.doi.org/10.1371/journal.pone.0066431.s003", "https://dx.doi.org/10.1371/journal.pone.0066431.s004", "https://dx.doi.org/10.1371/journal.pone.0066431.s005", "https://dx.doi.org/10.1371/journal.pone.0066431.s006", "https://dx.doi.org/10.1371/journal.pone.0066431.s007", "https://dx.doi.org/10.1371/journal.pone.0066431.s008", "https://dx.doi.org/10.1371/journal.pone.0066431.s009", "https://dx.doi.org/10.1371/journal.pone.0066431.s010", "https://dx.doi.org/10.1371/journal.pone.0066431.s011", "https://dx.doi.org/10.1371/journal.pone.0066431.s012"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genomic_Analysis_of_Stress_Response_against_Arsenic_in_Caenorhabditis_elegans_/754248", "title"=>"Genomic Analysis of Stress Response against Arsenic in <i>Caenorhabditis elegans</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-07-24 06:25:58"}

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Relative Metric

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F1000Prime