Meta-Analysis Using a Novel Database, miRStress, Reveals miRNAs That Are Frequently Associated with the Radiation and Hypoxia Stress-Responses
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{"title"=>"Meta-analysis using a novel database, miRStress, reveals miRNAs that are frequently associated with the radiation and hypoxia stress-responses", "type"=>"journal", "authors"=>[{"first_name"=>"Laura Ann", "last_name"=>"Jacobs", "scopus_author_id"=>"57190135333"}, {"first_name"=>"Findlay", "last_name"=>"Bewicke-Copley", "scopus_author_id"=>"55694654600"}, {"first_name"=>"Mark Graham", "last_name"=>"Poolman", "scopus_author_id"=>"6603365027"}, {"first_name"=>"Ryan Charles", "last_name"=>"Pink", "scopus_author_id"=>"35732105800"}, {"first_name"=>"Laura Ann", "last_name"=>"Mulcahy", "scopus_author_id"=>"55928674500"}, {"first_name"=>"Isabel", "last_name"=>"Baker", "scopus_author_id"=>"56028186400"}, {"first_name"=>"Ellie May", "last_name"=>"Beaman", "scopus_author_id"=>"56026782500"}, {"first_name"=>"Travis", "last_name"=>"Brooks", "scopus_author_id"=>"56027919800"}, {"first_name"=>"Daniel Paul", "last_name"=>"Caley", "scopus_author_id"=>"35730826400"}, {"first_name"=>"William", "last_name"=>"Cowling", "scopus_author_id"=>"56028769800"}, {"first_name"=>"James Michael Stevenson", "last_name"=>"Currie", "scopus_author_id"=>"55628323300"}, {"first_name"=>"Jessica", "last_name"=>"Horsburgh", "scopus_author_id"=>"56027823100"}, {"first_name"=>"Lottie", "last_name"=>"Kenehan", "scopus_author_id"=>"56028531500"}, {"first_name"=>"Emma", "last_name"=>"Keyes", "scopus_author_id"=>"56027363900"}, {"first_name"=>"Daniel", "last_name"=>"Leite", "scopus_author_id"=>"56985625800"}, {"first_name"=>"Davide", "last_name"=>"Massa", "scopus_author_id"=>"56028583200"}, {"first_name"=>"Adam", "last_name"=>"McDermott-Rouse", "scopus_author_id"=>"56028531600"}, {"first_name"=>"Priya", "last_name"=>"Samuel", "scopus_author_id"=>"56027651300"}, {"first_name"=>"Hannah", "last_name"=>"Wood", "scopus_author_id"=>"56027939400"}, {"first_name"=>"Munira", "last_name"=>"Kadhim", "scopus_author_id"=>"6701504722"}, {"first_name"=>"David Raul Francisco", "last_name"=>"Carter", "scopus_author_id"=>"55660203000"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84893550430", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pui"=>"372325219", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0080844", "scopus"=>"2-s2.0-84893550430", "pmid"=>"24244721"}, "id"=>"623ff131-7ca3-3ffd-9ca2-56aca90da15d", "abstract"=>"Organisms are often exposed to environmental pressures that affect homeostasis, so it is important to understand the biological basis of stress-response. Various biological mechanisms have evolved to help cells cope with potentially cytotoxic changes in their environment. miRNAs are small non-coding RNAs which are able to regulate mRNA stability. It has been suggested that miRNAs may tip the balance between continued cytorepair and induction of apoptosis in response to stress. There is a wealth of data in the literature showing the effect of environmental stress on miRNAs, but it is scattered in a large number of disparate publications. Meta-analyses of this data would produce added insight into the molecular mechanisms of stress-response. To facilitate this we created and manually curated the miRStress database, which describes the changes in miRNA levels following an array of stress types in eukaryotic cells. Here we describe this database and validate the miRStress tool for analysing miRNAs that are regulated by stress. To validate the database we performed a cross-species analysis to identify miRNAs that respond to radiation. The analysis tool confirms miR-21 and miR-34a as frequently deregulated in response to radiation, but also identifies novel candidates as potentially important players in this stress response, including miR-15b, miR-19b, and miR-106a. Similarly, we used the miRStress tool to analyse hypoxia-responsive miRNAs. The most frequently deregulated miRNAs were miR-210 and miR-21, as expected. Several other miRNAs were also found to be associated with hypoxia, including miR-181b, miR-26a/b, miR-106a, miR-213 and miR-192. Therefore the miRStress tool has identified miRNAs with hitherto unknown or under-appreciated roles in the response to specific stress types. The miRStress tool, which can be used to uncover new insight into the biological roles of miRNAs, and also has the potential to unearth potential biomarkers for therapeutic response, is freely available at http://mudshark.brookes.ac.uk/MirStress.", "link"=>"http://www.mendeley.com/research/metaanalysis-using-novel-database-mirstress-reveals-mirnas-frequently-associated-radiation-hypoxia-s", "reader_count"=>35, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>12, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>1, "Other"=>3, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>12, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>1, "Other"=>3, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>19, "Medicine and Dentistry"=>6, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>19}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Luxembourg"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1281719"], "description"=>"<p>A: The miRNAs which are most frequently deregulated following radiation stress, as reported by miRStress, were used to ‘predict’ radiation-responsive pathways, as described in the methods. Control pathways were selected by using a list of control miRNAs. These were then compared to a list of KEGG pathways which are observed (as opposed to predicted) to actually change following radiation (in a total of 18 datasets). The average frequency with which the predicted control or radiation pathways appears in the observed pathways is shown. On average the radiation predicted-pathways are more frequently present in the observed pathways (t test, p 0.002). In other words, the radiation miRNAs are predicted to target pathways which actually change following radiation. Error bars show standard error of the mean for 20 (for radiation) and 21 (for control) pathways. B: Radiation and control miRNAs used in part A were used to test for correlations between SF5 (surviving fraction of cells following a 5 Gray radiation dose) and miRNA level across the NCI-60 panel. A Pearson correlation was obtained for each radiation and control miRNA (not all were available on the microarray platform). The average Pearson correlation value (see methods) for the control and radiation miRNAs is shown. The radiation miRNAs have a significantly higher correlation with radiosensitivity compared to the control miRNAs (t test, p = 0.02). </p>", "links"=>[], "tags"=>["mirnas", "mirstress", "biologically"], "article_id"=>851389, "categories"=>["Biological Sciences"], "users"=>["Laura Ann Jacobs", "Findlay Bewicke-Copley", "Mark Graham Poolman", "Ryan Charles Pink", "Laura Ann Mulcahy", "Isabel Baker", "Ellie-May Beaman", "Travis Brooks", "Daniel Paul Caley", "William Cowling", "James Michael Stevenson Currie", "Jessica Horsburgh", "Lottie Kenehan", "Emma Keyes", "Daniel Leite", "Davide Massa", "Adam McDermott-Rouse", "Priya Samuel", "Hannah Wood", "Munira Kadhim", "David Raul Francisco Carter"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080844.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Radiation_responsive_miRNAs_predicted_by_miRStress_are_biologically_relevant_/851389", "title"=>"Radiation-responsive miRNAs predicted by miRStress are biologically relevant.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-14 04:20:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1281720"], "description"=>"<div><p>Organisms are often exposed to environmental pressures that affect homeostasis, so it is important to understand the biological basis of stress-response. Various biological mechanisms have evolved to help cells cope with potentially cytotoxic changes in their environment. miRNAs are small non-coding RNAs which are able to regulate mRNA stability. It has been suggested that miRNAs may tip the balance between continued cytorepair and induction of apoptosis in response to stress. There is a wealth of data in the literature showing the effect of environmental stress on miRNAs, but it is scattered in a large number of disparate publications. Meta-analyses of this data would produce added insight into the molecular mechanisms of stress-response. To facilitate this we created and manually curated the miRStress database, which describes the changes in miRNA levels following an array of stress types in eukaryotic cells. Here we describe this database and validate the miRStress tool for analysing miRNAs that are regulated by stress. To validate the database we performed a cross-species analysis to identify miRNAs that respond to radiation. The analysis tool confirms miR-21 and miR-34a as frequently deregulated in response to radiation, but also identifies novel candidates as potentially important players in this stress response, including miR-15b, miR-19b, and miR-106a. Similarly, we used the miRStress tool to analyse hypoxia-responsive miRNAs. The most frequently deregulated miRNAs were miR-210 and miR-21, as expected. Several other miRNAs were also found to be associated with hypoxia, including miR-181b, miR-26a/b, miR-106a, miR-213 and miR-192. Therefore the miRStress tool has identified miRNAs with hitherto unknown or under-appreciated roles in the response to specific stress types. The miRStress tool, which can be used to uncover new insight into the biological roles of miRNAs, and also has the potential to unearth potential biomarkers for therapeutic response, is freely available at <a href=\"http://mudshark.brookes.ac.uk/MirStress\" target=\"_blank\">http://mudshark.brookes.ac.uk/MirStress</a>.</p> </div>", "links"=>[], "tags"=>["reveals", "mirnas", "hypoxia"], "article_id"=>851390, "categories"=>["Biological Sciences"], "users"=>["Laura Ann Jacobs", "Findlay Bewicke-Copley", "Mark Graham Poolman", "Ryan Charles Pink", "Laura Ann Mulcahy", "Isabel Baker", "Ellie-May Beaman", "Travis Brooks", "Daniel Paul Caley", "William Cowling", "James Michael Stevenson Currie", "Jessica Horsburgh", "Lottie Kenehan", "Emma Keyes", "Daniel Leite", "Davide Massa", "Adam McDermott-Rouse", "Priya Samuel", "Hannah Wood", "Munira Kadhim", "David Raul Francisco Carter"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080844", "stats"=>{"downloads"=>5, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Meta_Analysis_Using_a_Novel_Database_miRStress_Reveals_miRNAs_That_Are_Frequently_Associated_with_the_Radiation_and_Hypoxia_Stress_Responses_/851390", "title"=>"Meta-Analysis Using a Novel Database, miRStress, Reveals miRNAs That Are Frequently Associated with the Radiation and Hypoxia Stress-Responses", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-14 04:20:14"}

PMC Usage Stats | Further Information

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Relative Metric

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