PhysioSpace: Relating Gene Expression Experiments from Heterogeneous Sources Using Shared Physiological Processes
Events
Loading … Spinner

Mendeley | Further Information

{"title"=>"PhysioSpace: Relating Gene Expression Experiments from Heterogeneous Sources Using Shared Physiological Processes", "type"=>"journal", "authors"=>[{"first_name"=>"Michael", "last_name"=>"Lenz", "scopus_author_id"=>"55368892100"}, {"first_name"=>"Bernhard M.", "last_name"=>"Schuldt", "scopus_author_id"=>"46661458400"}, {"first_name"=>"Franz Josef", "last_name"=>"Müller", "scopus_author_id"=>"35725892100"}, {"first_name"=>"Andreas", "last_name"=>"Schuppert", "scopus_author_id"=>"24345112100"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84885764376", "sgr"=>"84885764376", "pui"=>"370046595", "pmid"=>"24147039", "doi"=>"10.1371/journal.pone.0077627"}, "id"=>"53ca16bd-c49a-3f05-9d50-009e0b89c078", "abstract"=>"Relating expression signatures from different sources such as cell lines, in vitro cultures from primary cells and biopsy material is an important task in drug development and translational medicine as well as for tracking of cell fate and disease progression. Especially the comparison of large scale gene expression changes to tissue or cell type specific signatures is of high interest for the tracking of cell fate in (trans-) differentiation experiments and for cancer research, which increasingly focuses on shared processes and the involvement of the microenvironment. These signature relation approaches require robust statistical methods to account for the high biological heterogeneity in clinical data and must cope with small sample sizes in lab experiments and common patterns of co-expression in ubiquitous cellular processes. We describe a novel method, called PhysioSpace, to position dynamics of time series data derived from cellular differentiation and disease progression in a genome-wide expression space. The PhysioSpace is defined by a compendium of publicly available gene expression signatures representing a large set of biological phenotypes. The mapping of gene expression changes onto the PhysioSpace leads to a robust ranking of physiologically relevant signatures, as rigorously evaluated via sample-label permutations. A spherical transformation of the data improves the performance, leading to stable results even in case of small sample sizes. Using PhysioSpace with clinical cancer datasets reveals that such data exhibits large heterogeneity in the number of significant signature associations. This behavior was closely associated with the classification endpoint and cancer type under consideration, indicating shared biological functionalities in disease associated processes. Even though the time series data of cell line differentiation exhibited responses in larger clusters covering several biologically related patterns, top scoring patterns were highly consistent with a priory known biological information and separated from the rest of response patterns.", "link"=>"http://www.mendeley.com/research/physiospace-relating-gene-expression-experiments-heterogeneous-sources-using-shared-physiological-pr", "reader_count"=>23, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>2, "Researcher"=>10, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>3, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>2, "Researcher"=>10, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>3, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>9, "Medicine and Dentistry"=>2, "Chemistry"=>2, "Computer Science"=>5}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Computer Science"=>{"Computer Science"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}}, "reader_count_by_country"=>{"United Kingdom"=>1, "Germany"=>1}, "group_count"=>1}

Scopus | Further Information

{"@_fa"=>"true", "link"=>[{"@_fa"=>"true", "@ref"=>"self", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/84885764376"}, {"@_fa"=>"true", "@ref"=>"author-affiliation", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/84885764376?field=author,affiliation"}, {"@_fa"=>"true", "@ref"=>"scopus", "@href"=>"https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84885764376&origin=inward"}, {"@_fa"=>"true", "@ref"=>"scopus-citedby", "@href"=>"https://www.scopus.com/inward/citedby.uri?partnerID=HzOxMe3b&scp=84885764376&origin=inward"}], "prism:url"=>"https://api.elsevier.com/content/abstract/scopus_id/84885764376", "dc:identifier"=>"SCOPUS_ID:84885764376", "eid"=>"2-s2.0-84885764376", "dc:title"=>"PhysioSpace: Relating Gene Expression Experiments from Heterogeneous Sources Using Shared Physiological Processes", "dc:creator"=>"Lenz M.", "prism:publicationName"=>"PLoS ONE", "prism:eIssn"=>"19326203", "prism:volume"=>"8", "prism:issueIdentifier"=>"10", "prism:pageRange"=>nil, "prism:coverDate"=>"2013-10-17", "prism:coverDisplayDate"=>"17 October 2013", "prism:doi"=>"10.1371/journal.pone.0077627", "citedby-count"=>"11", "affiliation"=>[{"@_fa"=>"true", "affilname"=>"Rheinisch-Westfälische Technische Hochschule Aachen", "affiliation-city"=>"Aachen", "affiliation-country"=>"Germany"}], "pubmed-id"=>"24147039", "prism:aggregationType"=>"Journal", "subtype"=>"ar", "subtypeDescription"=>"Article", "article-number"=>"e77627", "source-id"=>"10600153309", "openaccess"=>"1", "openaccessFlag"=>true}

Facebook

  • {"url"=>"http%3A%2F%2Fjournals.plos.org%2Fplosone%2Farticle%3Fid%3D10.1371%252Fjournal.pone.0077627", "share_count"=>0, "like_count"=>0, "comment_count"=>0, "click_count"=>0, "total_count"=>0}

Counter

  • {"month"=>"10", "year"=>"2013", "pdf_views"=>"25", "xml_views"=>"8", "html_views"=>"171"}
  • {"month"=>"11", "year"=>"2013", "pdf_views"=>"14", "xml_views"=>"2", "html_views"=>"83"}
  • {"month"=>"12", "year"=>"2013", "pdf_views"=>"13", "xml_views"=>"0", "html_views"=>"70"}
  • {"month"=>"1", "year"=>"2014", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"57"}
  • {"month"=>"2", "year"=>"2014", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"24"}
  • {"month"=>"3", "year"=>"2014", "pdf_views"=>"12", "xml_views"=>"2", "html_views"=>"67"}
  • {"month"=>"4", "year"=>"2014", "pdf_views"=>"5", "xml_views"=>"2", "html_views"=>"36"}
  • {"month"=>"5", "year"=>"2014", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"35"}
  • {"month"=>"6", "year"=>"2014", "pdf_views"=>"4", "xml_views"=>"1", "html_views"=>"22"}
  • {"month"=>"7", "year"=>"2014", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"30"}
  • {"month"=>"8", "year"=>"2014", "pdf_views"=>"3", "xml_views"=>"2", "html_views"=>"38"}
  • {"month"=>"9", "year"=>"2014", "pdf_views"=>"6", "xml_views"=>"1", "html_views"=>"32"}
  • {"month"=>"10", "year"=>"2014", "pdf_views"=>"9", "xml_views"=>"1", "html_views"=>"35"}
  • {"month"=>"11", "year"=>"2014", "pdf_views"=>"3", "xml_views"=>"2", "html_views"=>"24"}
  • {"month"=>"12", "year"=>"2014", "pdf_views"=>"3", "xml_views"=>"2", "html_views"=>"23"}
  • {"month"=>"1", "year"=>"2015", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"28"}
  • {"month"=>"2", "year"=>"2015", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"37"}
  • {"month"=>"3", "year"=>"2015", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"11"}
  • {"month"=>"4", "year"=>"2015", "pdf_views"=>"5", "xml_views"=>"1", "html_views"=>"16"}
  • {"month"=>"5", "year"=>"2015", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"34"}
  • {"month"=>"6", "year"=>"2015", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"36"}
  • {"month"=>"7", "year"=>"2015", "pdf_views"=>"0", "xml_views"=>"0", "html_views"=>"21"}
  • {"month"=>"8", "year"=>"2015", "pdf_views"=>"5", "xml_views"=>"1", "html_views"=>"38"}
  • {"month"=>"9", "year"=>"2015", "pdf_views"=>"5", "xml_views"=>"1", "html_views"=>"13"}
  • {"month"=>"10", "year"=>"2015", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"38"}
  • {"month"=>"11", "year"=>"2015", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"20"}
  • {"month"=>"12", "year"=>"2015", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"38"}
  • {"month"=>"1", "year"=>"2016", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"26"}
  • {"month"=>"2", "year"=>"2016", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"28"}
  • {"month"=>"3", "year"=>"2016", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"47"}
  • {"month"=>"4", "year"=>"2016", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"21"}
  • {"month"=>"5", "year"=>"2016", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"12"}
  • {"month"=>"6", "year"=>"2016", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"20"}
  • {"month"=>"7", "year"=>"2016", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"15"}
  • {"month"=>"8", "year"=>"2016", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"14"}
  • {"month"=>"9", "year"=>"2016", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"29"}
  • {"month"=>"10", "year"=>"2016", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"29"}
  • {"month"=>"11", "year"=>"2016", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"31"}
  • {"month"=>"12", "year"=>"2016", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"26"}
  • {"month"=>"1", "year"=>"2017", "pdf_views"=>"7", "xml_views"=>"1", "html_views"=>"19"}
  • {"month"=>"2", "year"=>"2017", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"25"}
  • {"month"=>"3", "year"=>"2017", "pdf_views"=>"1", "xml_views"=>"1", "html_views"=>"18"}
  • {"month"=>"4", "year"=>"2017", "pdf_views"=>"5", "xml_views"=>"1", "html_views"=>"35"}
  • {"month"=>"5", "year"=>"2017", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"24"}
  • {"month"=>"6", "year"=>"2017", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"35"}
  • {"month"=>"7", "year"=>"2017", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"18"}
  • {"month"=>"8", "year"=>"2017", "pdf_views"=>"3", "xml_views"=>"1", "html_views"=>"38"}
  • {"month"=>"9", "year"=>"2017", "pdf_views"=>"1", "xml_views"=>"0", "html_views"=>"13"}
  • {"month"=>"10", "year"=>"2017", "pdf_views"=>"7", "xml_views"=>"1", "html_views"=>"23"}
  • {"month"=>"11", "year"=>"2017", "pdf_views"=>"2", "xml_views"=>"1", "html_views"=>"70"}
  • {"month"=>"12", "year"=>"2017", "pdf_views"=>"2", "xml_views"=>"1", "html_views"=>"33"}
  • {"month"=>"1", "year"=>"2018", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"27"}
  • {"month"=>"2", "year"=>"2018", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"7"}
  • {"month"=>"3", "year"=>"2018", "pdf_views"=>"1", "xml_views"=>"0", "html_views"=>"7"}
  • {"month"=>"4", "year"=>"2018", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"19"}
  • {"month"=>"5", "year"=>"2018", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"11"}
  • {"month"=>"6", "year"=>"2018", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"7"}
  • {"month"=>"7", "year"=>"2018", "pdf_views"=>"1", "xml_views"=>"3", "html_views"=>"1"}
  • {"month"=>"8", "year"=>"2018", "pdf_views"=>"3", "xml_views"=>"1", "html_views"=>"3"}
  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"3"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"0", "xml_views"=>"1", "html_views"=>"5"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"4", "xml_views"=>"1", "html_views"=>"4"}
  • {"month"=>"12", "year"=>"2018", "pdf_views"=>"0", "xml_views"=>"0", "html_views"=>"1"}
  • {"month"=>"1", "year"=>"2019", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"4"}
  • {"month"=>"2", "year"=>"2019", "pdf_views"=>"0", "xml_views"=>"0", "html_views"=>"1"}
  • {"month"=>"3", "year"=>"2019", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"6"}
  • {"month"=>"4", "year"=>"2019", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"7"}
  • {"month"=>"5", "year"=>"2019", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"6"}
  • {"month"=>"6", "year"=>"2019", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"11"}
  • {"month"=>"7", "year"=>"2019", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"9"}
  • {"month"=>"8", "year"=>"2019", "pdf_views"=>"6", "xml_views"=>"1", "html_views"=>"11"}
  • {"month"=>"9", "year"=>"2019", "pdf_views"=>"1", "xml_views"=>"0", "html_views"=>"3"}

Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1245730"], "description"=>"<p>(A) In the case of relatively high heterogeneity and comparably low signal strength, the spherical transformation increases sensitivity and specificity of the simulated effect, i.e. results in a strong and specific increase of the ESC score (left part). The results without spherical transformation (right part) are more heterogeneous. (B) The null-distribution obtained from re-sampling without spherical transformation is not meaningful in cases of high signal strength and low heterogeneity, leading to increasing p-values for increasing signal strength in simulated data. This effect does not occur when the spherical transformation is applied. Depicted are permutation p-values for the lung signature with (red dots) and without (black dots) spherical transformation. (C) The mean matching score of 21 simulated mixtures is compared between the implemented PhysioSpace algorithm and a classical GSEA based method. The matching score is defined as the quotient of the respective tissue (or ESC) score and the highest (lowest) score. It is truncated at a minimum of zero, avoiding negative values. While there are some differences between the two methods, especially for very low mixture values, the overall performance does not generally favor one or the other algorithm. (D) The PhysioScores of simulated mixtures of 97% ESCs with 3% of different tissues are visualized as an exemplary case, showing a very nice agreement with biological expectations. Correlations between different signatures are represented by the dendrogram on the left hand side as well as by simultaneous increasing PhysioScores in the columns of the heatmap-like representation. </p>", "links"=>[], "tags"=>["evaluations", "simulated"], "article_id"=>826336, "categories"=>["Biological Sciences"], "users"=>["Michael Lenz", "Bernhard M. Schuldt", "Franz-Josef Müller", "Andreas Schuppert"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077627.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_evaluations_with_simulated_data_/826336", "title"=>"Performance evaluations with simulated data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-17 02:58:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1245727"], "description"=>"<p>Main steps of the PhysioSpace generation and mapping algorithms.</p>", "links"=>[], "tags"=>["steps", "physiospace"], "article_id"=>826334, "categories"=>["Biological Sciences"], "users"=>["Michael Lenz", "Bernhard M. Schuldt", "Franz-Josef Müller", "Andreas Schuppert"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077627.g001", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Main_steps_of_the_PhysioSpace_generation_and_mapping_algorithms_/826334", "title"=>"Main steps of the PhysioSpace generation and mapping algorithms.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-17 02:58:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1245735"], "description"=>"<p>(A) Line plots of most relevant PhysioScores for the three differentiation time series comparing scores from PhysioSpaces 1 and 3. Lines with names ending with “Lukk” correspond to the third PhysioSpace (Lukk et al. 2010 [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077627#B18\" target=\"_blank\">18</a>], E-MTAB-62), other lines correspond to the first PhysioSpace (GSE7307). (B) Heart and ESC increasingly dominate leading PhysioScores in the cardiomyocyte differentiation time series. Depicted are the PhysioScores of the 5 strongest signatures from cardiomyocyte differentiation. Red (blue) colors correspond to positive (negative) PhysioScores. (C) Comparison of pluripotency (ESC) and lineage (fetal brain/placenta/heart) scores for the three differentiation time series exhibit different dynamics in PhysioSpace 1. The lineage score corresponds to the dominant lineage in each differentiation, i.e. fetal brain, placenta, and heart for the neural, trophoblast, and cardiomyocyte differentiation, respectively. (D) The matching score is used to compare the implemented PhysioSpace algorithm to a classical GSEA based algorithm, showing relatively strong differences between the two methods for the trophoblast and cardiomyocyte differentiations. The implemented PhysioSpace algorithm has generally a higher matching score.</p>", "links"=>[], "tags"=>["differentiation"], "article_id"=>826339, "categories"=>["Biological Sciences"], "users"=>["Michael Lenz", "Bernhard M. Schuldt", "Franz-Josef Müller", "Andreas Schuppert"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077627.g006", "stats"=>{"downloads"=>2, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detailed_results_of_the_differentiation_time_series_analyses_/826339", "title"=>"Detailed results of the differentiation time series analyses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-17 02:58:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1245734"], "description"=>"<p>The PhysioScores for all six investigated datasets are visualized in context for selected signatures. In order to evaluate the stability of the method, the signatures were derived from three different physiological databases resulting in PhysioSpaces 1-3. The results are depicted in a heatmap-like representation. The color scheme differs between datasets but is the same for the PhysioSpaces 1-3, ranging from negative values in blue and green to positive values in orange and red. The dendrogram represents a hierarchical clustering of the signatures according to a Pearson-correlation distance. Values within clusters are usually similar, e.g clusters of neural or immune signatures. The results corresponding to PhysioSpaces 1-3 show similar dynamics and consistent dominating signatures, while the absolute values are only approximately comparable.</p>", "links"=>[], "tags"=>["physioscores", "combining", "signatures"], "article_id"=>826338, "categories"=>["Biological Sciences"], "users"=>["Michael Lenz", "Bernhard M. Schuldt", "Franz-Josef Müller", "Andreas Schuppert"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077627.g005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heatmap_of_PhysioScores_combining_selected_signatures_from_three_PhysioSpaces_/826338", "title"=>"Heatmap of PhysioScores combining selected signatures from three PhysioSpaces.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-17 02:58:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1245738", "https://ndownloader.figshare.com/files/1245739", "https://ndownloader.figshare.com/files/1245740"], "description"=>"<div><p>Relating expression signatures from different sources such as cell lines, in vitro cultures from primary cells and biopsy material is an important task in drug development and translational medicine as well as for tracking of cell fate and disease progression. Especially the comparison of large scale gene expression changes to tissue or cell type specific signatures is of high interest for the tracking of cell fate in (trans-) differentiation experiments and for cancer research, which increasingly focuses on shared processes and the involvement of the microenvironment. These signature relation approaches require robust statistical methods to account for the high biological heterogeneity in clinical data and must cope with small sample sizes in lab experiments and common patterns of co-expression in ubiquitous cellular processes. We describe a novel method, called PhysioSpace, to position dynamics of time series data derived from cellular differentiation and disease progression in a genome-wide expression space. The PhysioSpace is defined by a compendium of publicly available gene expression signatures representing a large set of biological phenotypes. The mapping of gene expression changes onto the PhysioSpace leads to a robust ranking of physiologically relevant signatures, as rigorously evaluated via sample-label permutations. A spherical transformation of the data improves the performance, leading to stable results even in case of small sample sizes. Using PhysioSpace with clinical cancer datasets reveals that such data exhibits large heterogeneity in the number of significant signature associations. This behavior was closely associated with the classification endpoint and cancer type under consideration, indicating shared biological functionalities in disease associated processes. Even though the time series data of cell line differentiation exhibited responses in larger clusters covering several biologically related patterns, top scoring patterns were highly consistent with a priory known biological information and separated from the rest of response patterns. </p> </div>", "links"=>[], "tags"=>["relating", "experiments", "heterogeneous", "sources", "physiological", "processes"], "article_id"=>826340, "categories"=>["Biological Sciences"], "users"=>["Michael Lenz", "Bernhard M. Schuldt", "Franz-Josef Müller", "Andreas Schuppert"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0077627.s001", "https://dx.doi.org/10.1371/journal.pone.0077627.s002", "https://dx.doi.org/10.1371/journal.pone.0077627.s003"], "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PhysioSpace_Relating_Gene_Expression_Experiments_from_Heterogeneous_Sources_Using_Shared_Physiological_Processes_/826340", "title"=>"PhysioSpace: Relating Gene Expression Experiments from Heterogeneous Sources Using Shared Physiological Processes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-10-17 02:58:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1245732"], "description"=>"<p>Ranking of PhysioScores comparing breast cancer samples of grade 1 to grade 2 or 3 (A) and lung samples from never smokers to former or current smokers (B). Apparently, grading differences in breast cancer are associated with more signatures from the PhysioSpace than differences in gene expression of smokers and non-smokers. Blue (red) colors depict negative (positive) PhysioScores. Filled bars indicate significant scores according to a sample-permutation FDR (Benjamini-Hochberg) cutoff of 0.1. </p>", "links"=>[], "tags"=>["cancer"], "article_id"=>826337, "categories"=>["Biological Sciences"], "users"=>["Michael Lenz", "Bernhard M. Schuldt", "Franz-Josef Müller", "Andreas Schuppert"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077627.g004", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Details_of_results_from_cancer_progression_/826337", "title"=>"Details of results from cancer progression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-17 02:58:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1245728"], "description"=>"<p>(A) Data from a new experiment is transformed to remove ellipticity and the resulting fold-change vector is compared to a compendium of signatures from prior experiments using a robust, rank-based scoring method. Graphical displays and the statistical validation allow to evaluate the position of the new experiment in the global PhysioSpace. (B, C) Illustration of the influence of non-sphericity on sample permutations. (B) In the presence of a strong ellipticity, sample permutation does not randomize directions in contrast to more spherically distributed samples as obtained through the spherical transformation approach (C).</p>", "links"=>[], "tags"=>["physiospace"], "article_id"=>826335, "categories"=>["Biological Sciences"], "users"=>["Michael Lenz", "Bernhard M. Schuldt", "Franz-Josef Müller", "Andreas Schuppert"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077627.g002", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_over_the_PhysioSpace_algorithm_/826335", "title"=>"Overview over the PhysioSpace algorithm.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-17 02:58:11"}

PMC Usage Stats | Further Information

  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"10", "cited-by"=>"0", "year"=>"2013", "month"=>"10"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"11"}
  • {"unique-ip"=>"8", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2013", "month"=>"12"}
  • {"unique-ip"=>"11", "full-text"=>"8", "pdf"=>"1", "abstract"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"1"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"2"}
  • {"unique-ip"=>"8", "full-text"=>"4", "pdf"=>"3", "abstract"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"3"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"5"}
  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"4"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"4"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"5"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"6"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"7"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"3"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"2"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"8"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"9"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2015", "month"=>"10"}
  • {"unique-ip"=>"7", "full-text"=>"3", "pdf"=>"2", "abstract"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"7"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"8"}
  • {"unique-ip"=>"4", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2014", "month"=>"9"}
  • {"unique-ip"=>"13", "full-text"=>"6", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2014", "month"=>"10"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
  • {"unique-ip"=>"7", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2014", "month"=>"11"}
  • {"unique-ip"=>"7", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2014", "month"=>"12"}
  • {"unique-ip"=>"12", "full-text"=>"6", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2015", "month"=>"1"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2015", "month"=>"11"}
  • {"unique-ip"=>"7", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"12"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"1"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"3"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"4"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"5"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"6"}
  • {"unique-ip"=>"5", "full-text"=>"2", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"7"}
  • {"unique-ip"=>"1", "full-text"=>"0", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"8"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
  • {"unique-ip"=>"5", "full-text"=>"2", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
  • {"unique-ip"=>"4", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
  • {"unique-ip"=>"5", "full-text"=>"1", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"7"}
  • {"unique-ip"=>"1", "full-text"=>"0", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"5", "full-text"=>"2", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"6", "full-text"=>"4", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"7", "full-text"=>"3", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"7", "full-text"=>"4", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}, {"subject_area"=>"/Physical sciences", "average_usage"=>[254, 431, 547, 651, 748, 842, 932, 1017, 1098, 1178, 1259, 1336, 1404]}, {"subject_area"=>"/Physical sciences/Mathematics", "average_usage"=>[259, 431, 541, 639, 727, 816, 898, 980, 1061, 1136, 1214, 1294, 1356]}]}
Loading … Spinner
There are currently no alerts