Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-12

AUTHORS

Samira Jaeger, Christine T Sers, Ulf Leser

ABSTRACT

BACKGROUND: While the number of newly sequenced genomes and genes is constantly increasing, elucidation of their function still is a laborious and time-consuming task. This has led to the development of a wide range of methods for predicting protein functions in silico. We report on a new method that predicts function based on a combination of information about protein interactions, orthology, and the conservation of protein networks in different species. RESULTS: We show that aggregation of these independent sources of evidence leads to a drastic increase in number and quality of predictions when compared to baselines and other methods reported in the literature. For instance, our method generates more than 12,000 novel protein functions for human with an estimated precision of ~76%, among which are 7,500 new functional annotations for 1,973 human proteins that previously had zero or only one function annotated. We also verified our predictions on a set of genes that play an important role in colorectal cancer (MLH1, PMS2, EPHB4 ) and could confirm more than 73% of them based on evidence in the literature. CONCLUSIONS: The combination of different methods into a single, comprehensive prediction method infers thousands of protein functions for every species included in the analysis at varying, yet always high levels of precision and very good coverage. More... »

PAGES

717

References to SciGraph publications

  • 2000-05. Gene Ontology: tool for the unification of biology in NATURE GENETICS
  • 2000-12. A network of protein–protein interactions in yeast in NATURE BIOTECHNOLOGY
  • 2005-06. Developmental cell biology: Eph receptor signalling casts a wide net on cell behaviour in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2009-02. Protein function annotation by homology-based inference in GENOME BIOLOGY
  • 2006-11. How complete are current yeast and human protein-interaction networks? in GENOME BIOLOGY
  • 1996-07. Involvement of mouse Mlh1 in DNA mismatch repair and meiotic crossing over in NATURE GENETICS
  • 2000-06. Protein function in the post-genomic era in NATURE
  • 2009-11. Evolution of biomolecular networks — lessons from metabolic and protein interactions in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2004-02. Network biology: understanding the cell's functional organization in NATURE REVIEWS GENETICS
  • 1999-12. From molecular to modular cell biology in NATURE
  • 2003-12. An automated method for finding molecular complexes in large protein interaction networks in BMC BIOINFORMATICS
  • 2008-01. Mechanisms and functions of DNA mismatch repair in CELL RESEARCH
  • 2007-05. Using indirect protein interactions for the prediction of Gene Ontology functions in BMC BIOINFORMATICS
  • 2007-12. Predicting protein function from sequence and structure in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2000-01. Mediating mismatch repair in NATURE GENETICS
  • 2003-06. Global protein function prediction from protein-protein interaction networks in NATURE BIOTECHNOLOGY
  • 2002-05. Comparative assessment of large-scale data sets of protein–protein interactions in NATURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1471-2164-11-717

    DOI

    http://dx.doi.org/10.1186/1471-2164-11-717

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1008666800

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21171995


    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/2008/0601", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biochemistry and Cell Biology", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Animals", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Base Pair Mismatch", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Computational Biology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Conserved Sequence", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA Repair", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Evolution, Molecular", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Humans", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Protein Binding", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Protein Interaction Mapping", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Sequence Homology, Amino Acid", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Species Specificity", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Humboldt University of Berlin", 
              "id": "https://www.grid.ac/institutes/grid.7468.d", 
              "name": [
                "Knowledge Management in Bioinformatics, Humboldt-Universitat zu Berlin Unter den Linden 6, 10099, Berlin, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Jaeger", 
            "givenName": "Samira", 
            "id": "sg:person.01072107703.46", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01072107703.46"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Charit\u00e9", 
              "id": "https://www.grid.ac/institutes/grid.6363.0", 
              "name": [
                "Institute of Pathology, Molecular Tumorpathology, University Medicine Charite, Chariteplatz 1, 10117, Berlin, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Sers", 
            "givenName": "Christine T", 
            "id": "sg:person.0665247717.59", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0665247717.59"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Humboldt University of Berlin", 
              "id": "https://www.grid.ac/institutes/grid.7468.d", 
              "name": [
                "Knowledge Management in Bioinformatics, Humboldt-Universitat zu Berlin Unter den Linden 6, 10099, Berlin, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Leser", 
            "givenName": "Ulf", 
            "id": "sg:person.0656252313.13", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0656252313.13"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "https://doi.org/10.1101/gr.1224503", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000505228"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/bti115", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000935925"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm2787", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001267578", 
              "https://doi.org/10.1038/nrm2787"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm2787", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001267578", 
              "https://doi.org/10.1038/nrm2787"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btm576", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001327568"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.str.2004.10.015", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001335576"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0955-0674(03)00009-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002143112"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0955-0674(03)00009-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002143112"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkh052", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002546052"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.datak.2006.05.003", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004259965"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1072165", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004577893"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35015694", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005971304", 
              "https://doi.org/10.1038/35015694"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35015694", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005971304", 
              "https://doi.org/10.1038/35015694"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btm195", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006143058"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkj109", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007734343"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1158/0008-5472.can-08-3232", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008767384"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1146/annurev.genet.40.110405.090439", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009563788"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkg056", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009644940"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkl1094", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010536783"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/prot.22172", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011291951"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/yea.706", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011830580"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkl988", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012601238"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.pnpbp.2004.05.025", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012702292"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1534/genetics.106.055616", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012788378"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1534/genetics.106.055616", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012788378"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-4-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013256259", 
              "https://doi.org/10.1186/1471-2105-4-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-4-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013256259", 
              "https://doi.org/10.1186/1471-2105-4-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pcbi.1000160", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013373824"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.0809583105", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013847515"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkm1000", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015047250"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2006-7-11-120", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015165657", 
              "https://doi.org/10.1186/gb-2006-7-11-120"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/0471250953.bi0207s21", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015402311"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-8-s4-s8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016062280", 
              "https://doi.org/10.1186/1471-2105-8-s4-s8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.bbrc.2003.11.092", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017182855"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pcbi.1000431", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017687419"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature750", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017837373", 
              "https://doi.org/10.1038/nature750"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature750", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017837373", 
              "https://doi.org/10.1038/nature750"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg1272", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018231980", 
              "https://doi.org/10.1038/nrg1272"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg1272", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018231980", 
              "https://doi.org/10.1038/nrg1272"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.192159399", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018429006"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btp551", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019469116"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35011540", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019498862", 
              "https://doi.org/10.1038/35011540"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35011540", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019498862", 
              "https://doi.org/10.1038/35011540"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt825", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019729549", 
              "https://doi.org/10.1038/nbt825"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt825", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019729549", 
              "https://doi.org/10.1038/nbt825"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0960-9822(06)00337-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019836351"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btm194", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021186259"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.1534710100", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022732383"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/cr.2007.115", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023538498", 
              "https://doi.org/10.1038/cr.2007.115"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1074/jbc.m106120200", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024622554"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.febslet.2006.02.053", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025225657"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btn161", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025732104"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2006.07.003", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025997887"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.0409522102", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026062100"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.2032324100", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026727582"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkl950", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026903670"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkg095", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027045924"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm2281", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027198313", 
              "https://doi.org/10.1038/nrm2281"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pcbi.0030237", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027342833"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.dnarep.2007.04.013", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028124587"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btp309", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028922385"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/82360", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028970743", 
              "https://doi.org/10.1038/82360"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/82360", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028970743", 
              "https://doi.org/10.1038/82360"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pone.0001562", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029608735"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1090289", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029676590"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1038/msb4100129", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030436057"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1038/msb4100129", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030436057"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.205301", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031531293"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1006/mcne.1995.0001", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032255513"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng0796-336", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032473067", 
              "https://doi.org/10.1038/ng0796-336"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.canlet.2005.12.009", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032533792"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btl145", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033113903"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkm961", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038250419"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.mad.2008.02.012", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039114399"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkh086", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039774953"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2009-10-2-207", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040399255", 
              "https://doi.org/10.1186/gb-2009-10-2-207"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pcbi.0010045", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040557220"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pcbi.0010045", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040557220"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkl818", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1042758114"
            ], 
            "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/10.1016/j.molcel.2006.04.023", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044829373"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btn312", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045432146"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/71698", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045849899", 
              "https://doi.org/10.1038/71698"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/71698", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045849899", 
              "https://doi.org/10.1038/71698"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pone.0000383", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046430504"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/25.17.3389", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047265454"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/emboj/20.19.5521", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047285323"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btl683", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049590204"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.1680803", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051307680"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm1662", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051545057", 
              "https://doi.org/10.1038/nrm1662"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm1662", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051545057", 
              "https://doi.org/10.1038/nrm1662"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm1662", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051545057", 
              "https://doi.org/10.1038/nrm1662"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/bth919", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051576699"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkm909", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051781785"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s1357-2725(02)00096-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051844460"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkg094", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053722790"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1021/cr068303k", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053927079"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1021/cr068303k", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053927079"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1089/106652703322756168", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1059204990"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/hmg/4.11.2033", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1059645233"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://app.dimensions.ai/details/publication/pub.1074873306", 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://app.dimensions.ai/details/publication/pub.1074882107", 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://app.dimensions.ai/details/publication/pub.1075243181", 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2010-12", 
        "datePublishedReg": "2010-12-01", 
        "description": "BACKGROUND: While the number of newly sequenced genomes and genes is constantly increasing, elucidation of their function still is a laborious and time-consuming task. This has led to the development of a wide range of methods for predicting protein functions in silico. We report on a new method that predicts function based on a combination of information about protein interactions, orthology, and the conservation of protein networks in different species.\nRESULTS: We show that aggregation of these independent sources of evidence leads to a drastic increase in number and quality of predictions when compared to baselines and other methods reported in the literature. For instance, our method generates more than 12,000 novel protein functions for human with an estimated precision of ~76%, among which are 7,500 new functional annotations for 1,973 human proteins that previously had zero or only one function annotated. We also verified our predictions on a set of genes that play an important role in colorectal cancer (MLH1, PMS2, EPHB4 ) and could confirm more than 73% of them based on evidence in the literature.\nCONCLUSIONS: The combination of different methods into a single, comprehensive prediction method infers thousands of protein functions for every species included in the analysis at varying, yet always high levels of precision and very good coverage.", 
        "genre": "research_article", 
        "id": "sg:pub.10.1186/1471-2164-11-717", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": true, 
        "isPartOf": [
          {
            "id": "sg:journal.1023790", 
            "issn": [
              "1471-2164"
            ], 
            "name": "BMC Genomics", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "11"
          }
        ], 
        "name": "Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction", 
        "pagination": "717", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "294a62de7fb4f73bd7b062a9855bb295d16edc8e078b1a1d396e6c0e22c3ffc5"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "21171995"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "100965258"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/1471-2164-11-717"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1008666800"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/1471-2164-11-717", 
          "https://app.dimensions.ai/details/publication/pub.1008666800"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-10T16:40", 
        "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/v90/0000000001_0000000264/records_8669_00000503.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "http://link.springer.com/10.1186%2F1471-2164-11-717"
      }
    ]
     

    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.10.1186/1471-2164-11-717'

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

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-11-717'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-11-717'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-11-717'


     

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

    408 TRIPLES      21 PREDICATES      128 URIs      33 LITERALS      21 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/1471-2164-11-717 schema:about N1f18eede805a4b23b013df56a694980a
    2 N1f2c1953d78342d88cad93f49c2475b7
    3 N3490e69c3b0d47fab8ab15d475d36eaf
    4 N544aea9a23cb417e9dd20bb8a4b5bb8c
    5 N6f88834a15714ab9ab9a86898a636b6b
    6 N73062bfd7f804e78a9e2995864bd16c5
    7 N94f5f1518375408f847b9dceba34714e
    8 Ncef53df60bd74b249a2e3d4f9dcfaed3
    9 Nd69b1d3c1a6f4c4997ee0063c2f3c4c8
    10 Nd7fba64a9aca4f59acb45027bccd99f5
    11 Nda26f1fa6c0d4918b75d0c89b4ac6e9d
    12 Nef159c39b4e34a48bf5b4f0f2f555955
    13 anzsrc-for:06
    14 anzsrc-for:0601
    15 schema:author N67a2549a7d214e7b801df066e02c1065
    16 schema:citation sg:pub.10.1038/35011540
    17 sg:pub.10.1038/35015694
    18 sg:pub.10.1038/71698
    19 sg:pub.10.1038/75556
    20 sg:pub.10.1038/82360
    21 sg:pub.10.1038/cr.2007.115
    22 sg:pub.10.1038/nature750
    23 sg:pub.10.1038/nbt825
    24 sg:pub.10.1038/ng0796-336
    25 sg:pub.10.1038/nrg1272
    26 sg:pub.10.1038/nrm1662
    27 sg:pub.10.1038/nrm2281
    28 sg:pub.10.1038/nrm2787
    29 sg:pub.10.1186/1471-2105-4-2
    30 sg:pub.10.1186/1471-2105-8-s4-s8
    31 sg:pub.10.1186/gb-2006-7-11-120
    32 sg:pub.10.1186/gb-2009-10-2-207
    33 https://app.dimensions.ai/details/publication/pub.1074873306
    34 https://app.dimensions.ai/details/publication/pub.1074882107
    35 https://app.dimensions.ai/details/publication/pub.1075243181
    36 https://doi.org/10.1002/0471250953.bi0207s21
    37 https://doi.org/10.1002/prot.22172
    38 https://doi.org/10.1002/yea.706
    39 https://doi.org/10.1006/mcne.1995.0001
    40 https://doi.org/10.1016/j.bbrc.2003.11.092
    41 https://doi.org/10.1016/j.canlet.2005.12.009
    42 https://doi.org/10.1016/j.cell.2006.07.003
    43 https://doi.org/10.1016/j.datak.2006.05.003
    44 https://doi.org/10.1016/j.dnarep.2007.04.013
    45 https://doi.org/10.1016/j.febslet.2006.02.053
    46 https://doi.org/10.1016/j.mad.2008.02.012
    47 https://doi.org/10.1016/j.molcel.2006.04.023
    48 https://doi.org/10.1016/j.pnpbp.2004.05.025
    49 https://doi.org/10.1016/j.str.2004.10.015
    50 https://doi.org/10.1016/s0955-0674(03)00009-7
    51 https://doi.org/10.1016/s0960-9822(06)00337-x
    52 https://doi.org/10.1016/s1357-2725(02)00096-1
    53 https://doi.org/10.1021/cr068303k
    54 https://doi.org/10.1038/msb4100129
    55 https://doi.org/10.1073/pnas.0409522102
    56 https://doi.org/10.1073/pnas.0809583105
    57 https://doi.org/10.1073/pnas.1534710100
    58 https://doi.org/10.1073/pnas.192159399
    59 https://doi.org/10.1073/pnas.2032324100
    60 https://doi.org/10.1074/jbc.m106120200
    61 https://doi.org/10.1089/106652703322756168
    62 https://doi.org/10.1093/bioinformatics/bth919
    63 https://doi.org/10.1093/bioinformatics/bti115
    64 https://doi.org/10.1093/bioinformatics/btl145
    65 https://doi.org/10.1093/bioinformatics/btl683
    66 https://doi.org/10.1093/bioinformatics/btm194
    67 https://doi.org/10.1093/bioinformatics/btm195
    68 https://doi.org/10.1093/bioinformatics/btm576
    69 https://doi.org/10.1093/bioinformatics/btn161
    70 https://doi.org/10.1093/bioinformatics/btn312
    71 https://doi.org/10.1093/bioinformatics/btp309
    72 https://doi.org/10.1093/bioinformatics/btp551
    73 https://doi.org/10.1093/emboj/20.19.5521
    74 https://doi.org/10.1093/hmg/4.11.2033
    75 https://doi.org/10.1093/nar/25.17.3389
    76 https://doi.org/10.1093/nar/gkg056
    77 https://doi.org/10.1093/nar/gkg094
    78 https://doi.org/10.1093/nar/gkg095
    79 https://doi.org/10.1093/nar/gkh052
    80 https://doi.org/10.1093/nar/gkh086
    81 https://doi.org/10.1093/nar/gkj109
    82 https://doi.org/10.1093/nar/gkl1094
    83 https://doi.org/10.1093/nar/gkl818
    84 https://doi.org/10.1093/nar/gkl950
    85 https://doi.org/10.1093/nar/gkl988
    86 https://doi.org/10.1093/nar/gkm1000
    87 https://doi.org/10.1093/nar/gkm909
    88 https://doi.org/10.1093/nar/gkm961
    89 https://doi.org/10.1101/gr.1224503
    90 https://doi.org/10.1101/gr.1680803
    91 https://doi.org/10.1101/gr.205301
    92 https://doi.org/10.1126/science.1072165
    93 https://doi.org/10.1126/science.1090289
    94 https://doi.org/10.1146/annurev.genet.40.110405.090439
    95 https://doi.org/10.1158/0008-5472.can-08-3232
    96 https://doi.org/10.1371/journal.pcbi.0010045
    97 https://doi.org/10.1371/journal.pcbi.0030237
    98 https://doi.org/10.1371/journal.pcbi.1000160
    99 https://doi.org/10.1371/journal.pcbi.1000431
    100 https://doi.org/10.1371/journal.pone.0000383
    101 https://doi.org/10.1371/journal.pone.0001562
    102 https://doi.org/10.1534/genetics.106.055616
    103 schema:datePublished 2010-12
    104 schema:datePublishedReg 2010-12-01
    105 schema:description BACKGROUND: While the number of newly sequenced genomes and genes is constantly increasing, elucidation of their function still is a laborious and time-consuming task. This has led to the development of a wide range of methods for predicting protein functions in silico. We report on a new method that predicts function based on a combination of information about protein interactions, orthology, and the conservation of protein networks in different species. RESULTS: We show that aggregation of these independent sources of evidence leads to a drastic increase in number and quality of predictions when compared to baselines and other methods reported in the literature. For instance, our method generates more than 12,000 novel protein functions for human with an estimated precision of ~76%, among which are 7,500 new functional annotations for 1,973 human proteins that previously had zero or only one function annotated. We also verified our predictions on a set of genes that play an important role in colorectal cancer (MLH1, PMS2, EPHB4 ) and could confirm more than 73% of them based on evidence in the literature. CONCLUSIONS: The combination of different methods into a single, comprehensive prediction method infers thousands of protein functions for every species included in the analysis at varying, yet always high levels of precision and very good coverage.
    106 schema:genre research_article
    107 schema:inLanguage en
    108 schema:isAccessibleForFree true
    109 schema:isPartOf N9a3bae8ce301436093031e4ac9828012
    110 Nb239d787c119437ebb0b00cfdcd61286
    111 sg:journal.1023790
    112 schema:name Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction
    113 schema:pagination 717
    114 schema:productId N1d9dc1975e734868949365c39ae21e20
    115 N262b96d1a1c84e008379d8eed624cbc0
    116 N2aa20473ec214e09bd0ade8f19cb56d4
    117 N39050d47468a4c83b4d85f8c573665d5
    118 Nf1fb0b9a90d542688b206a598fe31650
    119 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008666800
    120 https://doi.org/10.1186/1471-2164-11-717
    121 schema:sdDatePublished 2019-04-10T16:40
    122 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    123 schema:sdPublisher N7b953510f664414f84d6f4072d122dfe
    124 schema:url http://link.springer.com/10.1186%2F1471-2164-11-717
    125 sgo:license sg:explorer/license/
    126 sgo:sdDataset articles
    127 rdf:type schema:ScholarlyArticle
    128 N1d9dc1975e734868949365c39ae21e20 schema:name nlm_unique_id
    129 schema:value 100965258
    130 rdf:type schema:PropertyValue
    131 N1f18eede805a4b23b013df56a694980a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    132 schema:name Conserved Sequence
    133 rdf:type schema:DefinedTerm
    134 N1f2c1953d78342d88cad93f49c2475b7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    135 schema:name Evolution, Molecular
    136 rdf:type schema:DefinedTerm
    137 N262b96d1a1c84e008379d8eed624cbc0 schema:name doi
    138 schema:value 10.1186/1471-2164-11-717
    139 rdf:type schema:PropertyValue
    140 N2aa20473ec214e09bd0ade8f19cb56d4 schema:name pubmed_id
    141 schema:value 21171995
    142 rdf:type schema:PropertyValue
    143 N3490e69c3b0d47fab8ab15d475d36eaf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    144 schema:name Animals
    145 rdf:type schema:DefinedTerm
    146 N39050d47468a4c83b4d85f8c573665d5 schema:name dimensions_id
    147 schema:value pub.1008666800
    148 rdf:type schema:PropertyValue
    149 N4859f06af66b413f8536b68dd8309057 rdf:first sg:person.0656252313.13
    150 rdf:rest rdf:nil
    151 N544aea9a23cb417e9dd20bb8a4b5bb8c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    152 schema:name Species Specificity
    153 rdf:type schema:DefinedTerm
    154 N5e1e265a80e84d9ca8085b69df5b7110 rdf:first sg:person.0665247717.59
    155 rdf:rest N4859f06af66b413f8536b68dd8309057
    156 N67a2549a7d214e7b801df066e02c1065 rdf:first sg:person.01072107703.46
    157 rdf:rest N5e1e265a80e84d9ca8085b69df5b7110
    158 N6f88834a15714ab9ab9a86898a636b6b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    159 schema:name Protein Binding
    160 rdf:type schema:DefinedTerm
    161 N73062bfd7f804e78a9e2995864bd16c5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    162 schema:name Humans
    163 rdf:type schema:DefinedTerm
    164 N7b953510f664414f84d6f4072d122dfe schema:name Springer Nature - SN SciGraph project
    165 rdf:type schema:Organization
    166 N94f5f1518375408f847b9dceba34714e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    167 schema:name Computational Biology
    168 rdf:type schema:DefinedTerm
    169 N9a3bae8ce301436093031e4ac9828012 schema:issueNumber 1
    170 rdf:type schema:PublicationIssue
    171 Nb239d787c119437ebb0b00cfdcd61286 schema:volumeNumber 11
    172 rdf:type schema:PublicationVolume
    173 Ncef53df60bd74b249a2e3d4f9dcfaed3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    174 schema:name Base Pair Mismatch
    175 rdf:type schema:DefinedTerm
    176 Nd69b1d3c1a6f4c4997ee0063c2f3c4c8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    177 schema:name Sequence Homology, Amino Acid
    178 rdf:type schema:DefinedTerm
    179 Nd7fba64a9aca4f59acb45027bccd99f5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    180 schema:name DNA Repair
    181 rdf:type schema:DefinedTerm
    182 Nda26f1fa6c0d4918b75d0c89b4ac6e9d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    183 schema:name Protein Interaction Mapping
    184 rdf:type schema:DefinedTerm
    185 Nef159c39b4e34a48bf5b4f0f2f555955 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    186 schema:name Proteins
    187 rdf:type schema:DefinedTerm
    188 Nf1fb0b9a90d542688b206a598fe31650 schema:name readcube_id
    189 schema:value 294a62de7fb4f73bd7b062a9855bb295d16edc8e078b1a1d396e6c0e22c3ffc5
    190 rdf:type schema:PropertyValue
    191 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    192 schema:name Biological Sciences
    193 rdf:type schema:DefinedTerm
    194 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
    195 schema:name Biochemistry and Cell Biology
    196 rdf:type schema:DefinedTerm
    197 sg:journal.1023790 schema:issn 1471-2164
    198 schema:name BMC Genomics
    199 rdf:type schema:Periodical
    200 sg:person.01072107703.46 schema:affiliation https://www.grid.ac/institutes/grid.7468.d
    201 schema:familyName Jaeger
    202 schema:givenName Samira
    203 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01072107703.46
    204 rdf:type schema:Person
    205 sg:person.0656252313.13 schema:affiliation https://www.grid.ac/institutes/grid.7468.d
    206 schema:familyName Leser
    207 schema:givenName Ulf
    208 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0656252313.13
    209 rdf:type schema:Person
    210 sg:person.0665247717.59 schema:affiliation https://www.grid.ac/institutes/grid.6363.0
    211 schema:familyName Sers
    212 schema:givenName Christine T
    213 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0665247717.59
    214 rdf:type schema:Person
    215 sg:pub.10.1038/35011540 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019498862
    216 https://doi.org/10.1038/35011540
    217 rdf:type schema:CreativeWork
    218 sg:pub.10.1038/35015694 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005971304
    219 https://doi.org/10.1038/35015694
    220 rdf:type schema:CreativeWork
    221 sg:pub.10.1038/71698 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045849899
    222 https://doi.org/10.1038/71698
    223 rdf:type schema:CreativeWork
    224 sg:pub.10.1038/75556 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044135237
    225 https://doi.org/10.1038/75556
    226 rdf:type schema:CreativeWork
    227 sg:pub.10.1038/82360 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028970743
    228 https://doi.org/10.1038/82360
    229 rdf:type schema:CreativeWork
    230 sg:pub.10.1038/cr.2007.115 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023538498
    231 https://doi.org/10.1038/cr.2007.115
    232 rdf:type schema:CreativeWork
    233 sg:pub.10.1038/nature750 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017837373
    234 https://doi.org/10.1038/nature750
    235 rdf:type schema:CreativeWork
    236 sg:pub.10.1038/nbt825 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019729549
    237 https://doi.org/10.1038/nbt825
    238 rdf:type schema:CreativeWork
    239 sg:pub.10.1038/ng0796-336 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032473067
    240 https://doi.org/10.1038/ng0796-336
    241 rdf:type schema:CreativeWork
    242 sg:pub.10.1038/nrg1272 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018231980
    243 https://doi.org/10.1038/nrg1272
    244 rdf:type schema:CreativeWork
    245 sg:pub.10.1038/nrm1662 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051545057
    246 https://doi.org/10.1038/nrm1662
    247 rdf:type schema:CreativeWork
    248 sg:pub.10.1038/nrm2281 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027198313
    249 https://doi.org/10.1038/nrm2281
    250 rdf:type schema:CreativeWork
    251 sg:pub.10.1038/nrm2787 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001267578
    252 https://doi.org/10.1038/nrm2787
    253 rdf:type schema:CreativeWork
    254 sg:pub.10.1186/1471-2105-4-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013256259
    255 https://doi.org/10.1186/1471-2105-4-2
    256 rdf:type schema:CreativeWork
    257 sg:pub.10.1186/1471-2105-8-s4-s8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016062280
    258 https://doi.org/10.1186/1471-2105-8-s4-s8
    259 rdf:type schema:CreativeWork
    260 sg:pub.10.1186/gb-2006-7-11-120 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015165657
    261 https://doi.org/10.1186/gb-2006-7-11-120
    262 rdf:type schema:CreativeWork
    263 sg:pub.10.1186/gb-2009-10-2-207 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040399255
    264 https://doi.org/10.1186/gb-2009-10-2-207
    265 rdf:type schema:CreativeWork
    266 https://app.dimensions.ai/details/publication/pub.1074873306 schema:CreativeWork
    267 https://app.dimensions.ai/details/publication/pub.1074882107 schema:CreativeWork
    268 https://app.dimensions.ai/details/publication/pub.1075243181 schema:CreativeWork
    269 https://doi.org/10.1002/0471250953.bi0207s21 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015402311
    270 rdf:type schema:CreativeWork
    271 https://doi.org/10.1002/prot.22172 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011291951
    272 rdf:type schema:CreativeWork
    273 https://doi.org/10.1002/yea.706 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011830580
    274 rdf:type schema:CreativeWork
    275 https://doi.org/10.1006/mcne.1995.0001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032255513
    276 rdf:type schema:CreativeWork
    277 https://doi.org/10.1016/j.bbrc.2003.11.092 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017182855
    278 rdf:type schema:CreativeWork
    279 https://doi.org/10.1016/j.canlet.2005.12.009 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032533792
    280 rdf:type schema:CreativeWork
    281 https://doi.org/10.1016/j.cell.2006.07.003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025997887
    282 rdf:type schema:CreativeWork
    283 https://doi.org/10.1016/j.datak.2006.05.003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004259965
    284 rdf:type schema:CreativeWork
    285 https://doi.org/10.1016/j.dnarep.2007.04.013 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028124587
    286 rdf:type schema:CreativeWork
    287 https://doi.org/10.1016/j.febslet.2006.02.053 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025225657
    288 rdf:type schema:CreativeWork
    289 https://doi.org/10.1016/j.mad.2008.02.012 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039114399
    290 rdf:type schema:CreativeWork
    291 https://doi.org/10.1016/j.molcel.2006.04.023 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044829373
    292 rdf:type schema:CreativeWork
    293 https://doi.org/10.1016/j.pnpbp.2004.05.025 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012702292
    294 rdf:type schema:CreativeWork
    295 https://doi.org/10.1016/j.str.2004.10.015 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001335576
    296 rdf:type schema:CreativeWork
    297 https://doi.org/10.1016/s0955-0674(03)00009-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002143112
    298 rdf:type schema:CreativeWork
    299 https://doi.org/10.1016/s0960-9822(06)00337-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1019836351
    300 rdf:type schema:CreativeWork
    301 https://doi.org/10.1016/s1357-2725(02)00096-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051844460
    302 rdf:type schema:CreativeWork
    303 https://doi.org/10.1021/cr068303k schema:sameAs https://app.dimensions.ai/details/publication/pub.1053927079
    304 rdf:type schema:CreativeWork
    305 https://doi.org/10.1038/msb4100129 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030436057
    306 rdf:type schema:CreativeWork
    307 https://doi.org/10.1073/pnas.0409522102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026062100
    308 rdf:type schema:CreativeWork
    309 https://doi.org/10.1073/pnas.0809583105 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013847515
    310 rdf:type schema:CreativeWork
    311 https://doi.org/10.1073/pnas.1534710100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022732383
    312 rdf:type schema:CreativeWork
    313 https://doi.org/10.1073/pnas.192159399 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018429006
    314 rdf:type schema:CreativeWork
    315 https://doi.org/10.1073/pnas.2032324100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026727582
    316 rdf:type schema:CreativeWork
    317 https://doi.org/10.1074/jbc.m106120200 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024622554
    318 rdf:type schema:CreativeWork
    319 https://doi.org/10.1089/106652703322756168 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059204990
    320 rdf:type schema:CreativeWork
    321 https://doi.org/10.1093/bioinformatics/bth919 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051576699
    322 rdf:type schema:CreativeWork
    323 https://doi.org/10.1093/bioinformatics/bti115 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000935925
    324 rdf:type schema:CreativeWork
    325 https://doi.org/10.1093/bioinformatics/btl145 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033113903
    326 rdf:type schema:CreativeWork
    327 https://doi.org/10.1093/bioinformatics/btl683 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049590204
    328 rdf:type schema:CreativeWork
    329 https://doi.org/10.1093/bioinformatics/btm194 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021186259
    330 rdf:type schema:CreativeWork
    331 https://doi.org/10.1093/bioinformatics/btm195 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006143058
    332 rdf:type schema:CreativeWork
    333 https://doi.org/10.1093/bioinformatics/btm576 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001327568
    334 rdf:type schema:CreativeWork
    335 https://doi.org/10.1093/bioinformatics/btn161 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025732104
    336 rdf:type schema:CreativeWork
    337 https://doi.org/10.1093/bioinformatics/btn312 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045432146
    338 rdf:type schema:CreativeWork
    339 https://doi.org/10.1093/bioinformatics/btp309 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028922385
    340 rdf:type schema:CreativeWork
    341 https://doi.org/10.1093/bioinformatics/btp551 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019469116
    342 rdf:type schema:CreativeWork
    343 https://doi.org/10.1093/emboj/20.19.5521 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047285323
    344 rdf:type schema:CreativeWork
    345 https://doi.org/10.1093/hmg/4.11.2033 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059645233
    346 rdf:type schema:CreativeWork
    347 https://doi.org/10.1093/nar/25.17.3389 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047265454
    348 rdf:type schema:CreativeWork
    349 https://doi.org/10.1093/nar/gkg056 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009644940
    350 rdf:type schema:CreativeWork
    351 https://doi.org/10.1093/nar/gkg094 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053722790
    352 rdf:type schema:CreativeWork
    353 https://doi.org/10.1093/nar/gkg095 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027045924
    354 rdf:type schema:CreativeWork
    355 https://doi.org/10.1093/nar/gkh052 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002546052
    356 rdf:type schema:CreativeWork
    357 https://doi.org/10.1093/nar/gkh086 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039774953
    358 rdf:type schema:CreativeWork
    359 https://doi.org/10.1093/nar/gkj109 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007734343
    360 rdf:type schema:CreativeWork
    361 https://doi.org/10.1093/nar/gkl1094 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010536783
    362 rdf:type schema:CreativeWork
    363 https://doi.org/10.1093/nar/gkl818 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042758114
    364 rdf:type schema:CreativeWork
    365 https://doi.org/10.1093/nar/gkl950 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026903670
    366 rdf:type schema:CreativeWork
    367 https://doi.org/10.1093/nar/gkl988 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012601238
    368 rdf:type schema:CreativeWork
    369 https://doi.org/10.1093/nar/gkm1000 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015047250
    370 rdf:type schema:CreativeWork
    371 https://doi.org/10.1093/nar/gkm909 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051781785
    372 rdf:type schema:CreativeWork
    373 https://doi.org/10.1093/nar/gkm961 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038250419
    374 rdf:type schema:CreativeWork
    375 https://doi.org/10.1101/gr.1224503 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000505228
    376 rdf:type schema:CreativeWork
    377 https://doi.org/10.1101/gr.1680803 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051307680
    378 rdf:type schema:CreativeWork
    379 https://doi.org/10.1101/gr.205301 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031531293
    380 rdf:type schema:CreativeWork
    381 https://doi.org/10.1126/science.1072165 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004577893
    382 rdf:type schema:CreativeWork
    383 https://doi.org/10.1126/science.1090289 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029676590
    384 rdf:type schema:CreativeWork
    385 https://doi.org/10.1146/annurev.genet.40.110405.090439 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009563788
    386 rdf:type schema:CreativeWork
    387 https://doi.org/10.1158/0008-5472.can-08-3232 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008767384
    388 rdf:type schema:CreativeWork
    389 https://doi.org/10.1371/journal.pcbi.0010045 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040557220
    390 rdf:type schema:CreativeWork
    391 https://doi.org/10.1371/journal.pcbi.0030237 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027342833
    392 rdf:type schema:CreativeWork
    393 https://doi.org/10.1371/journal.pcbi.1000160 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013373824
    394 rdf:type schema:CreativeWork
    395 https://doi.org/10.1371/journal.pcbi.1000431 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017687419
    396 rdf:type schema:CreativeWork
    397 https://doi.org/10.1371/journal.pone.0000383 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046430504
    398 rdf:type schema:CreativeWork
    399 https://doi.org/10.1371/journal.pone.0001562 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029608735
    400 rdf:type schema:CreativeWork
    401 https://doi.org/10.1534/genetics.106.055616 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012788378
    402 rdf:type schema:CreativeWork
    403 https://www.grid.ac/institutes/grid.6363.0 schema:alternateName Charité
    404 schema:name Institute of Pathology, Molecular Tumorpathology, University Medicine Charite, Chariteplatz 1, 10117, Berlin, Germany
    405 rdf:type schema:Organization
    406 https://www.grid.ac/institutes/grid.7468.d schema:alternateName Humboldt University of Berlin
    407 schema:name Knowledge Management in Bioinformatics, Humboldt-Universitat zu Berlin Unter den Linden 6, 10099, Berlin, Germany
    408 rdf:type schema:Organization
     




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


    ...