PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2006-12

AUTHORS

Björn Usadel, Axel Nagel, Dirk Steinhauser, Yves Gibon, Oliver E Bläsing, Henning Redestig, Nese Sreenivasulu, Leonard Krall, Matthew A Hannah, Fabien Poree, Alisdair R Fernie, Mark Stitt

ABSTRACT

BACKGROUND: Microarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as microarray experiments have become more routine, large scale experiments have become more common, which investigate multiple time points or sets of mutants or transgenics. To extract biological information from such high-throughput expression data, it is necessary to develop efficient analytical platforms, which combine manually curated gene ontologies with efficient visualization and navigation tools. Currently, most tools focus on a few limited biological aspects, rather than offering a holistic, integrated analysis. RESULTS: Here we introduce PageMan, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies. It includes a GUI tool to transform different ontologies into a suitable format, enabling the user to compare and choose between different ontologies. It is equipped with several statistical modules for data analysis, including over-representation analysis and Wilcoxon statistical testing. Results are exported in a graphical format for direct use, or for further editing in graphics programs.PageMan provides a fast overview of single treatments, allows genome-level responses to be compared across several microarray experiments covering, for example, stress responses at multiple time points. This aids in searching for trait-specific changes in pathways using mutants or transgenics, analyzing development time-courses, and comparison between species. In a case study, we analyze the results of publicly available microarrays of multiple cold stress experiments using PageMan, and compare the results to a previously published meta-analysis.PageMan offers a complete user's guide, a web-based over-representation analysis as well as a tutorial, and is freely available at http://mapman.mpimp-golm.mpg.de/pageman/. CONCLUSION: PageMan allows multiple microarray experiments to be efficiently condensed into a single page graphical display. The flexible interface allows data to be quickly and easily visualized, facilitating comparisons within experiments and to published experiments, thus enabling researchers to gain a rapid overview of the biological responses in the experiments. More... »

PAGES

535

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-7-535

DOI

http://dx.doi.org/10.1186/1471-2105-7-535

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1010456073

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/17176458


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0806", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information Systems", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/08", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information and Computing Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Database Management Systems", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Databases, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Profiling", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Oligonucleotide Array Sequence Analysis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "User-Computer Interface", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Max Planck Institute for Molecular Plant Physiology", 
          "id": "https://www.grid.ac/institutes/grid.418390.7", 
          "name": [
            "Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476, Potsdam, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Usadel", 
        "givenName": "Bj\u00f6rn", 
        "id": "sg:person.01031034727.50", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01031034727.50"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "RZPD: Deutsches Ressourcenzentrum f\u00fcr Genomforschung GmbH, Heubnerweg 6, 14059, Berlin, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Nagel", 
        "givenName": "Axel", 
        "id": "sg:person.01073003567.65", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01073003567.65"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Max Planck Institute for Molecular Plant Physiology", 
          "id": "https://www.grid.ac/institutes/grid.418390.7", 
          "name": [
            "Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476, Potsdam, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Steinhauser", 
        "givenName": "Dirk", 
        "id": "sg:person.01225321457.76", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01225321457.76"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Max Planck Institute for Molecular Plant Physiology", 
          "id": "https://www.grid.ac/institutes/grid.418390.7", 
          "name": [
            "Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476, Potsdam, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gibon", 
        "givenName": "Yves", 
        "id": "sg:person.01122240627.91", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01122240627.91"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Max Planck Institute for Molecular Plant Physiology", 
          "id": "https://www.grid.ac/institutes/grid.418390.7", 
          "name": [
            "Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476, Potsdam, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bl\u00e4sing", 
        "givenName": "Oliver E", 
        "id": "sg:person.0717015423.45", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717015423.45"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Max Planck Institute for Molecular Plant Physiology", 
          "id": "https://www.grid.ac/institutes/grid.418390.7", 
          "name": [
            "Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476, Potsdam, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Redestig", 
        "givenName": "Henning", 
        "id": "sg:person.01040454710.55", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01040454710.55"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Institute of Plant Genetics and Crop Plant Research", 
          "id": "https://www.grid.ac/institutes/grid.418934.3", 
          "name": [
            "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Gatersleben, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Sreenivasulu", 
        "givenName": "Nese", 
        "id": "sg:person.01035551603.11", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01035551603.11"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Max Planck Institute for Molecular Plant Physiology", 
          "id": "https://www.grid.ac/institutes/grid.418390.7", 
          "name": [
            "Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476, Potsdam, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Krall", 
        "givenName": "Leonard", 
        "id": "sg:person.01210035624.07", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01210035624.07"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Max Planck Institute for Molecular Plant Physiology", 
          "id": "https://www.grid.ac/institutes/grid.418390.7", 
          "name": [
            "Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476, Potsdam, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hannah", 
        "givenName": "Matthew A", 
        "id": "sg:person.01327054426.18", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01327054426.18"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Max Planck Institute for Molecular Plant Physiology", 
          "id": "https://www.grid.ac/institutes/grid.418390.7", 
          "name": [
            "Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476, Potsdam, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Poree", 
        "givenName": "Fabien", 
        "id": "sg:person.01333312060.34", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01333312060.34"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Max Planck Institute for Molecular Plant Physiology", 
          "id": "https://www.grid.ac/institutes/grid.418390.7", 
          "name": [
            "Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476, Potsdam, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Fernie", 
        "givenName": "Alisdair R", 
        "id": "sg:person.01021163534.25", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021163534.25"
        ], 
        "type": "Person"
      }, 
      {
        "familyName": "Stitt", 
        "givenName": "Mark", 
        "id": "sg:person.01021103304.09", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021103304.09"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1186/1471-2105-7-335", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008316735", 
          "https://doi.org/10.1186/1471-2105-7-335"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2004-5-10-r80", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018457673", 
          "https://doi.org/10.1186/gb-2004-5-10-r80"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btl424", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019754441"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1104/pp.105.060459", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023916068"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gki056", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024241091"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1104/pp.106.090985", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025078200"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/0-387-29362-0_23", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025432622", 
          "https://doi.org/10.1007/0-387-29362-0_23"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1105/tpc.105.035261", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025584953"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gki022", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033237811"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-6-269", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033565357", 
          "https://doi.org/10.1186/1471-2105-6-269"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-6-269", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033565357", 
          "https://doi.org/10.1186/1471-2105-6-269"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1104/pp.105.060525", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034581641"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pgen.0010026", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034858561"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1214/aos/1013699998", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036427477"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/biostatistics/4.2.249", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037543114"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-7-109", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038053078", 
          "https://doi.org/10.1186/1471-2105-7-109"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-7-109", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038053078", 
          "https://doi.org/10.1186/1471-2105-7-109"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s11103-005-5772-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038364433", 
          "https://doi.org/10.1007/s11103-005-5772-4"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/75556", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044135237", 
          "https://doi.org/10.1038/75556"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/75556", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044135237", 
          "https://doi.org/10.1038/75556"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkh133", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046446976"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-313x.2004.02016.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046563795"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-6-168", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047729779", 
          "https://doi.org/10.1186/1471-2105-6-168"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkl329", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048036243"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bti565", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050298763"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1104/pp.102.017236", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051961219"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1137/0701008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062850527"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.2517-6161.1995.tb02031.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1110458929"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.2517-6161.1995.tb02031.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1110458929"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2006-12", 
    "datePublishedReg": "2006-12-01", 
    "description": "BACKGROUND: Microarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as microarray experiments have become more routine, large scale experiments have become more common, which investigate multiple time points or sets of mutants or transgenics. To extract biological information from such high-throughput expression data, it is necessary to develop efficient analytical platforms, which combine manually curated gene ontologies with efficient visualization and navigation tools. Currently, most tools focus on a few limited biological aspects, rather than offering a holistic, integrated analysis.\nRESULTS: Here we introduce PageMan, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies. It includes a GUI tool to transform different ontologies into a suitable format, enabling the user to compare and choose between different ontologies. It is equipped with several statistical modules for data analysis, including over-representation analysis and Wilcoxon statistical testing. Results are exported in a graphical format for direct use, or for further editing in graphics programs.PageMan provides a fast overview of single treatments, allows genome-level responses to be compared across several microarray experiments covering, for example, stress responses at multiple time points. This aids in searching for trait-specific changes in pathways using mutants or transgenics, analyzing development time-courses, and comparison between species. In a case study, we analyze the results of publicly available microarrays of multiple cold stress experiments using PageMan, and compare the results to a previously published meta-analysis.PageMan offers a complete user's guide, a web-based over-representation analysis as well as a tutorial, and is freely available at http://mapman.mpimp-golm.mpg.de/pageman/.\nCONCLUSION: PageMan allows multiple microarray experiments to be efficiently condensed into a single page graphical display. The flexible interface allows data to be quickly and easily visualized, facilitating comparisons within experiments and to published experiments, thus enabling researchers to gain a rapid overview of the biological responses in the experiments.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1471-2105-7-535", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1023786", 
        "issn": [
          "1471-2105"
        ], 
        "name": "BMC Bioinformatics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "7"
      }
    ], 
    "name": "PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments", 
    "pagination": "535", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "31cff0c4fc49784864b57324a7eb5ec2a20cf4c7e13acae1ff24e8cfa0187951"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "17176458"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965194"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2105-7-535"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1010456073"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2105-7-535", 
      "https://app.dimensions.ai/details/publication/pub.1010456073"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T09:32", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000346_0000000346/records_99809_00000000.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://link.springer.com/10.1186%2F1471-2105-7-535"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-7-535'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-7-535'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-7-535'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-7-535'


 

This table displays all metadata directly associated to this object as RDF triples.

256 TRIPLES      21 PREDICATES      60 URIs      27 LITERALS      15 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2105-7-535 schema:about N49717e7fb63b4d008ed66e8f6ac7fd74
2 N856648d7d14d49d4bb8d8ae1e5f3a8dd
3 N98004db3b0534ff18262737c6a3322ed
4 N99e272122b724fcead314297e0086014
5 Nfeb70d6aef144e17ae66929329b8b0f4
6 Nff16a3c6f7864a2fb6add9da8c39b82f
7 anzsrc-for:08
8 anzsrc-for:0806
9 schema:author N7e85d52f4f474c04bb1977ba661c024a
10 schema:citation sg:pub.10.1007/0-387-29362-0_23
11 sg:pub.10.1007/s11103-005-5772-4
12 sg:pub.10.1038/75556
13 sg:pub.10.1186/1471-2105-6-168
14 sg:pub.10.1186/1471-2105-6-269
15 sg:pub.10.1186/1471-2105-7-109
16 sg:pub.10.1186/1471-2105-7-335
17 sg:pub.10.1186/gb-2004-5-10-r80
18 https://doi.org/10.1093/bioinformatics/bti565
19 https://doi.org/10.1093/bioinformatics/btl424
20 https://doi.org/10.1093/biostatistics/4.2.249
21 https://doi.org/10.1093/nar/gkh133
22 https://doi.org/10.1093/nar/gki022
23 https://doi.org/10.1093/nar/gki056
24 https://doi.org/10.1093/nar/gkl329
25 https://doi.org/10.1104/pp.102.017236
26 https://doi.org/10.1104/pp.105.060459
27 https://doi.org/10.1104/pp.105.060525
28 https://doi.org/10.1104/pp.106.090985
29 https://doi.org/10.1105/tpc.105.035261
30 https://doi.org/10.1111/j.1365-313x.2004.02016.x
31 https://doi.org/10.1111/j.2517-6161.1995.tb02031.x
32 https://doi.org/10.1137/0701008
33 https://doi.org/10.1214/aos/1013699998
34 https://doi.org/10.1371/journal.pgen.0010026
35 schema:datePublished 2006-12
36 schema:datePublishedReg 2006-12-01
37 schema:description BACKGROUND: Microarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as microarray experiments have become more routine, large scale experiments have become more common, which investigate multiple time points or sets of mutants or transgenics. To extract biological information from such high-throughput expression data, it is necessary to develop efficient analytical platforms, which combine manually curated gene ontologies with efficient visualization and navigation tools. Currently, most tools focus on a few limited biological aspects, rather than offering a holistic, integrated analysis. RESULTS: Here we introduce PageMan, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies. It includes a GUI tool to transform different ontologies into a suitable format, enabling the user to compare and choose between different ontologies. It is equipped with several statistical modules for data analysis, including over-representation analysis and Wilcoxon statistical testing. Results are exported in a graphical format for direct use, or for further editing in graphics programs.PageMan provides a fast overview of single treatments, allows genome-level responses to be compared across several microarray experiments covering, for example, stress responses at multiple time points. This aids in searching for trait-specific changes in pathways using mutants or transgenics, analyzing development time-courses, and comparison between species. In a case study, we analyze the results of publicly available microarrays of multiple cold stress experiments using PageMan, and compare the results to a previously published meta-analysis.PageMan offers a complete user's guide, a web-based over-representation analysis as well as a tutorial, and is freely available at http://mapman.mpimp-golm.mpg.de/pageman/. CONCLUSION: PageMan allows multiple microarray experiments to be efficiently condensed into a single page graphical display. The flexible interface allows data to be quickly and easily visualized, facilitating comparisons within experiments and to published experiments, thus enabling researchers to gain a rapid overview of the biological responses in the experiments.
38 schema:genre research_article
39 schema:inLanguage en
40 schema:isAccessibleForFree true
41 schema:isPartOf N1a4ef0888887444ba35e0968f1b5d618
42 Nabebb14972354a9897e58454fcd0dd93
43 sg:journal.1023786
44 schema:name PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments
45 schema:pagination 535
46 schema:productId N92159c99718849feb3f8e4eb4282421f
47 Na1893dca14524bd4bbf0a9f0b2ad0bf7
48 Ndd3e1dd3c55948e6a2c85ce60dc54c2f
49 Nf924795fddfb4ae6a9d2ac1965d80bb3
50 Nfa35b891576143fdb1c49e939fdf393b
51 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010456073
52 https://doi.org/10.1186/1471-2105-7-535
53 schema:sdDatePublished 2019-04-11T09:32
54 schema:sdLicense https://scigraph.springernature.com/explorer/license/
55 schema:sdPublisher N3232446afff14350b16b94c6e91e6c8b
56 schema:url https://link.springer.com/10.1186%2F1471-2105-7-535
57 sgo:license sg:explorer/license/
58 sgo:sdDataset articles
59 rdf:type schema:ScholarlyArticle
60 N0a40476851494d3da1325354878df305 rdf:first sg:person.01327054426.18
61 rdf:rest N0b2356d2c41142deb95bad8bb23ed004
62 N0b2356d2c41142deb95bad8bb23ed004 rdf:first sg:person.01333312060.34
63 rdf:rest Nf3bd3d88e3d54c97a56bf4ea118af395
64 N1a4ef0888887444ba35e0968f1b5d618 schema:issueNumber 1
65 rdf:type schema:PublicationIssue
66 N3232446afff14350b16b94c6e91e6c8b schema:name Springer Nature - SN SciGraph project
67 rdf:type schema:Organization
68 N49717e7fb63b4d008ed66e8f6ac7fd74 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
69 schema:name Software
70 rdf:type schema:DefinedTerm
71 N5269378134bc4bdcb9025c037a135801 rdf:first sg:person.01225321457.76
72 rdf:rest Needc21801fe84d4b820071cac1adaa2c
73 N5f450b2a293a4ab3aba939df02520e79 rdf:first sg:person.01021103304.09
74 rdf:rest rdf:nil
75 N6f08d1d87ddd4d9e8f64971706e0c09a rdf:first sg:person.0717015423.45
76 rdf:rest N804bcfed9a374e5e9e12ffe4aed3dd5f
77 N7e85d52f4f474c04bb1977ba661c024a rdf:first sg:person.01031034727.50
78 rdf:rest N914a7f4614614255aad0522af578bdb9
79 N804bcfed9a374e5e9e12ffe4aed3dd5f rdf:first sg:person.01040454710.55
80 rdf:rest Na7afd9184a9f4e02b4bb6b95db48f66f
81 N856648d7d14d49d4bb8d8ae1e5f3a8dd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
82 schema:name Databases, Genetic
83 rdf:type schema:DefinedTerm
84 N914a7f4614614255aad0522af578bdb9 rdf:first sg:person.01073003567.65
85 rdf:rest N5269378134bc4bdcb9025c037a135801
86 N92159c99718849feb3f8e4eb4282421f schema:name nlm_unique_id
87 schema:value 100965194
88 rdf:type schema:PropertyValue
89 N98004db3b0534ff18262737c6a3322ed schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
90 schema:name Database Management Systems
91 rdf:type schema:DefinedTerm
92 N99e272122b724fcead314297e0086014 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
93 schema:name User-Computer Interface
94 rdf:type schema:DefinedTerm
95 Na1893dca14524bd4bbf0a9f0b2ad0bf7 schema:name doi
96 schema:value 10.1186/1471-2105-7-535
97 rdf:type schema:PropertyValue
98 Na7afd9184a9f4e02b4bb6b95db48f66f rdf:first sg:person.01035551603.11
99 rdf:rest Nb0aebfaa9473475aaf923fdbd90e60ee
100 Nabebb14972354a9897e58454fcd0dd93 schema:volumeNumber 7
101 rdf:type schema:PublicationVolume
102 Nb0aebfaa9473475aaf923fdbd90e60ee rdf:first sg:person.01210035624.07
103 rdf:rest N0a40476851494d3da1325354878df305
104 Ndd3e1dd3c55948e6a2c85ce60dc54c2f schema:name pubmed_id
105 schema:value 17176458
106 rdf:type schema:PropertyValue
107 Ne40e015cb1ca45df90cdae709459656b schema:name RZPD: Deutsches Ressourcenzentrum für Genomforschung GmbH, Heubnerweg 6, 14059, Berlin, Germany
108 rdf:type schema:Organization
109 Needc21801fe84d4b820071cac1adaa2c rdf:first sg:person.01122240627.91
110 rdf:rest N6f08d1d87ddd4d9e8f64971706e0c09a
111 Nf3bd3d88e3d54c97a56bf4ea118af395 rdf:first sg:person.01021163534.25
112 rdf:rest N5f450b2a293a4ab3aba939df02520e79
113 Nf924795fddfb4ae6a9d2ac1965d80bb3 schema:name dimensions_id
114 schema:value pub.1010456073
115 rdf:type schema:PropertyValue
116 Nfa35b891576143fdb1c49e939fdf393b schema:name readcube_id
117 schema:value 31cff0c4fc49784864b57324a7eb5ec2a20cf4c7e13acae1ff24e8cfa0187951
118 rdf:type schema:PropertyValue
119 Nfeb70d6aef144e17ae66929329b8b0f4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
120 schema:name Gene Expression Profiling
121 rdf:type schema:DefinedTerm
122 Nff16a3c6f7864a2fb6add9da8c39b82f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
123 schema:name Oligonucleotide Array Sequence Analysis
124 rdf:type schema:DefinedTerm
125 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
126 schema:name Information and Computing Sciences
127 rdf:type schema:DefinedTerm
128 anzsrc-for:0806 schema:inDefinedTermSet anzsrc-for:
129 schema:name Information Systems
130 rdf:type schema:DefinedTerm
131 sg:journal.1023786 schema:issn 1471-2105
132 schema:name BMC Bioinformatics
133 rdf:type schema:Periodical
134 sg:person.01021103304.09 schema:familyName Stitt
135 schema:givenName Mark
136 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021103304.09
137 rdf:type schema:Person
138 sg:person.01021163534.25 schema:affiliation https://www.grid.ac/institutes/grid.418390.7
139 schema:familyName Fernie
140 schema:givenName Alisdair R
141 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021163534.25
142 rdf:type schema:Person
143 sg:person.01031034727.50 schema:affiliation https://www.grid.ac/institutes/grid.418390.7
144 schema:familyName Usadel
145 schema:givenName Björn
146 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01031034727.50
147 rdf:type schema:Person
148 sg:person.01035551603.11 schema:affiliation https://www.grid.ac/institutes/grid.418934.3
149 schema:familyName Sreenivasulu
150 schema:givenName Nese
151 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01035551603.11
152 rdf:type schema:Person
153 sg:person.01040454710.55 schema:affiliation https://www.grid.ac/institutes/grid.418390.7
154 schema:familyName Redestig
155 schema:givenName Henning
156 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01040454710.55
157 rdf:type schema:Person
158 sg:person.01073003567.65 schema:affiliation Ne40e015cb1ca45df90cdae709459656b
159 schema:familyName Nagel
160 schema:givenName Axel
161 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01073003567.65
162 rdf:type schema:Person
163 sg:person.01122240627.91 schema:affiliation https://www.grid.ac/institutes/grid.418390.7
164 schema:familyName Gibon
165 schema:givenName Yves
166 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01122240627.91
167 rdf:type schema:Person
168 sg:person.01210035624.07 schema:affiliation https://www.grid.ac/institutes/grid.418390.7
169 schema:familyName Krall
170 schema:givenName Leonard
171 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01210035624.07
172 rdf:type schema:Person
173 sg:person.01225321457.76 schema:affiliation https://www.grid.ac/institutes/grid.418390.7
174 schema:familyName Steinhauser
175 schema:givenName Dirk
176 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01225321457.76
177 rdf:type schema:Person
178 sg:person.01327054426.18 schema:affiliation https://www.grid.ac/institutes/grid.418390.7
179 schema:familyName Hannah
180 schema:givenName Matthew A
181 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01327054426.18
182 rdf:type schema:Person
183 sg:person.01333312060.34 schema:affiliation https://www.grid.ac/institutes/grid.418390.7
184 schema:familyName Poree
185 schema:givenName Fabien
186 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01333312060.34
187 rdf:type schema:Person
188 sg:person.0717015423.45 schema:affiliation https://www.grid.ac/institutes/grid.418390.7
189 schema:familyName Bläsing
190 schema:givenName Oliver E
191 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717015423.45
192 rdf:type schema:Person
193 sg:pub.10.1007/0-387-29362-0_23 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025432622
194 https://doi.org/10.1007/0-387-29362-0_23
195 rdf:type schema:CreativeWork
196 sg:pub.10.1007/s11103-005-5772-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038364433
197 https://doi.org/10.1007/s11103-005-5772-4
198 rdf:type schema:CreativeWork
199 sg:pub.10.1038/75556 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044135237
200 https://doi.org/10.1038/75556
201 rdf:type schema:CreativeWork
202 sg:pub.10.1186/1471-2105-6-168 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047729779
203 https://doi.org/10.1186/1471-2105-6-168
204 rdf:type schema:CreativeWork
205 sg:pub.10.1186/1471-2105-6-269 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033565357
206 https://doi.org/10.1186/1471-2105-6-269
207 rdf:type schema:CreativeWork
208 sg:pub.10.1186/1471-2105-7-109 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038053078
209 https://doi.org/10.1186/1471-2105-7-109
210 rdf:type schema:CreativeWork
211 sg:pub.10.1186/1471-2105-7-335 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008316735
212 https://doi.org/10.1186/1471-2105-7-335
213 rdf:type schema:CreativeWork
214 sg:pub.10.1186/gb-2004-5-10-r80 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018457673
215 https://doi.org/10.1186/gb-2004-5-10-r80
216 rdf:type schema:CreativeWork
217 https://doi.org/10.1093/bioinformatics/bti565 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050298763
218 rdf:type schema:CreativeWork
219 https://doi.org/10.1093/bioinformatics/btl424 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019754441
220 rdf:type schema:CreativeWork
221 https://doi.org/10.1093/biostatistics/4.2.249 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037543114
222 rdf:type schema:CreativeWork
223 https://doi.org/10.1093/nar/gkh133 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046446976
224 rdf:type schema:CreativeWork
225 https://doi.org/10.1093/nar/gki022 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033237811
226 rdf:type schema:CreativeWork
227 https://doi.org/10.1093/nar/gki056 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024241091
228 rdf:type schema:CreativeWork
229 https://doi.org/10.1093/nar/gkl329 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048036243
230 rdf:type schema:CreativeWork
231 https://doi.org/10.1104/pp.102.017236 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051961219
232 rdf:type schema:CreativeWork
233 https://doi.org/10.1104/pp.105.060459 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023916068
234 rdf:type schema:CreativeWork
235 https://doi.org/10.1104/pp.105.060525 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034581641
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1104/pp.106.090985 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025078200
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1105/tpc.105.035261 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025584953
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1111/j.1365-313x.2004.02016.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1046563795
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1111/j.2517-6161.1995.tb02031.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1110458929
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1137/0701008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062850527
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1214/aos/1013699998 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036427477
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1371/journal.pgen.0010026 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034858561
250 rdf:type schema:CreativeWork
251 https://www.grid.ac/institutes/grid.418390.7 schema:alternateName Max Planck Institute for Molecular Plant Physiology
252 schema:name Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
253 rdf:type schema:Organization
254 https://www.grid.ac/institutes/grid.418934.3 schema:alternateName Institute of Plant Genetics and Crop Plant Research
255 schema:name Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Gatersleben, Germany
256 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...