CDAP

Complex Detection Analyzer Package (CADP) helps you to execute protein complex detection methods and compare their results in a quick and compact ways. It computes a wide range of evaluation criteria and visualize the comparison of methods in tables and multiplots. It assists you in filtering detected clusters by providing a protein name (STRING ID) as a query and by setting constraint on maximum and minimum number of proteins in detected clusters. The list of methods for detecting protein complexes is as follows:

  • CFinder
  • MCL
  • ClusterOne
  • RNSC
  • RRW
  • ProRank
  • IMHRC
  • PEWCC
  • Prorank Plus

  • You can also upload the result of any other method for evaluating its results. The valid format for uploaded file is described here.

    The list of evaluation criteria is as follows:

  • Sensitivity(Sn), Positive Predictive Value(PPV), Accuracy (ACC)
  • Maximal Margin Relevance (MMR)
  • Precision, Recall, Fmeasure
  • Precision+, Recall+, Fmeasure+
  • PrecN, RecN, FmeasureN
  • Area Under MMR+Fmeasure+ curve (AUMF)

  • You may look for the values of evaluation criteria for a specific threshold. This can also be done by CDAP. The PPI datasets are:

  • Collins
  • Gavin
  • Krogan-Core
  • Krogan-Extended

  • And the Gold Standards used in assessment of results are:

  • MIPS: catalog of protein complexes
  • SGD: Gene Ontology based protein complex
  • CYC2008: Manually curated heteromeric protein complexes

  • Moreover, you can upload your custom PPI dataset or Gold Standard. The valid formats for uploaded files are declared here.

    The required files for applying ProRank on each datasets: Collins, Gavin, Krogan-Core, Krogan-Extended

    +98 21 22431653
    ch-eslahchi@sbu.ac.ir
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