Complex Map Files

• Protein Complex Map
  • Description: Complexes generated from two stage clustering of fully intergrated protein interaction network
  • Format: HuMAP2_ID,Confidence,Uniprot_ACCs,genenames
  • Confidence maps to complexes identified in 5 individual clusterings. 1=Extremely High, 2=Very High, 3=High, 4=Medium High, 5=Medium


• Protein Interaction Network with probability scores (Uniprot gzip), (geneid gzip), (genename gzip)
  • Description: All protein pair predictions with the corresponding svm probability score.
  • Format: protein_id [tab] protein_id [tab] score

Cytoscape Network

• Cytoscape Network
  • Description: Cytoscape network of hu.MAP 2.0
  • Node colors represent complex confidence
    • Extremely High = Green
    • Very High = Blue
    • High = Teal
    • Medium High = Yellow
    • Medium = Gray
  • Edge colors represent gold standard edges
    • Positive Test = Green
    • Positive Train = Blue
    • Negative Test = Yellow
    • Negative Train = Red

Test and training data

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

Feature Matrix

• Feature Matrix (geneid gzip)
  • Description: Table of features from integrated datasets for pairs of proteins (geneids). Also includes Weighted 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).