Complex Map Files

• Protein Complex Map
  • Description: Complexes generated from two stage clustering of fully intergrated protein interaction network
  • Format: geneid geneid geneid ... (one complex per line)
• Protein Complex Map (genenames)
  • Description: Complexes generated from two stage clustering of fully intergrated protein interaction network
  • Format: genename genename genename ... (one complex per line)
  • Note: ids that did not map properly have original geneid or ensembl id
• Protein Interaction Network with probability scores
  • Description: Co-complex protein pairs that are observed in the protein complex map with the corresponding svm probability score.
  • Format: geneid [tab] geneid [tab] score
• Protein Interaction Network with probability scores (genenames)
  • Description: Co-complex protein pairs that are observed in the protein complex map with the corresponding svm probability score.
  • Format: genename [tab] genename [tab] score
  • Note: ids that did not map properly have original geneid or ensembl id

Additional database input files

• Node Table
  • Description: Cluster ids and additional identifiers for proteins in the complex map
  • Format: acc,clustid,clustid_key,genename,key(geneid),proteinname,uniprot_link
• Enrichment Table
  • Description: Output from gprofiler for each complex, FDR-corrected hypergeometric p <= 0.05 (updated 2017-05-01)
  • Format: complex_id, corr_pval, t_count, q_count, qandt_count, qandt_by_q, qandt_by_t, term_id, t_type, t_group, t_name, depth_in_group, qandt_list
• Edge Table
  • Description: List of edges in the complex map with svm probability score and boolean values for each evidence type determining support for the edge
  • Format: id1 score fractions bioplex hein bioplex_prey hein_prey

Cytoscape Network

• Cytoscape Network

Test and training data

• Train Complexes
  • Description: List of training complexes used in protein complex discovery pipeline
  • Format: geneid geneid geneid ... (one complex per line)
• Test Complexes
  • Description: List of test complexes used in protein complex discovery pipeline
  • Format: geneid geneid geneid ... (one complex per line)
• Train Positive PPIs
  • Description: List of train postive ppis used in protein complex discovery pipeline
  • Format: geneid geneid
• Train Negative PPIs
  • Description: List of train negative ppis used in protein complex discovery pipeline
  • Format: geneid geneid
• Test Positive PPIs
  • Description: List of test positive ppis used in protein complex discovery pipeline
  • Format: geneid geneid
• Test Negative PPIs
  • Description: List of test negative ppis used in protein complex discovery pipeline
  • Format: geneid geneid

Feature Matrix

• Feature Matrix (gz)
  • Description: Table of features from Wan et al., Hein et al. and BioPlex for pairs of proteins. Also includes hypergeometric matrix model features
  • Format: protein_id,protein_id,[features]

Code

• Protein Complex Maps (GitHub)

License

• CC0 (+BY)
• Data associated with this website are free to download and share. They are governed by the Creative Commons Zero license, which means that they are a part of the public domain, and every use of them is allowed. If you make extensive use of data from this data set, please credit the authors and when appropriate the authors of the source data (see about for references).