Supplementary Information:
Supplementary Figure 1. Pair-wise interconnections between signatures for endpoint C.
Summary: Pair-wise interconnections between signatures for endpoint C.
File type: JPEG image files (.jpg)
Supplementary Figure 2. Pair-wise interconnections between signatures for endpoint D.
Summary: Pair-wise interconnections between signatures for endpoint D.
File type: JPEG image files (.jpg)
Supplementary Table 1. Endpoints, teams and signature description
Summary: Description of the data: endpoints, teams, signatures
File type: MS Excel (.xls)
Supplementary Table 2. Signatures forming DI networks for 13 endpoints
Summary: This file contains information about signatures forming DI networks for 13 endpoints
File type: MS Excel (.xls)
Supplementary Table 3. The most common genes between unions for all endpoints
Summary: This file contains the most common genes between unions for all endpoints
File type: MS Excel (.xls)
Supplementary Table 4. Comparison between three types of similarity trees
Summary: This file contains results of comparison between three types of similarity trees
File type: MS Excel (.xls)
Supplementary Table 5. Similarity between ABT and other signatures
Summary: This file contains results of comparison between ABT and other signatures on gene content
level and ontology level for endpoint A.
File type: MS Excel (.xls)
Supplementary Table 6. Comparison between two types of signature similarity for 13 endpoints
Summary: This file contains results of comparison between signature similarity on gene content level
and signature similarity on ontology level.
File type: MS Excel (.xls)
Supplementary Table 7. Signature congruency vs. model performance for 13 endpoints
The congruence value was compared to the average model performance for an endpoint. Overall, we saw
a strong positive correlation (p < 0.001) between signature congruency and model performance
File type: MS Excel (.xls)
Supplementary File 1. Signature enrichment by protein function
Summary: Genes for each signature were separated into eight broadly-defined protein classes: TFs,
receptors, ligands, kinases, proteases, phosphatases, enzymes and “other” (e.g., binding proteins). This
file contains the results.
File type: MS Excel (.xls)
Supplementary File 2. Signature 1-step network neighborhood enrichment by protein function
Summary: Protein functional composition for the one-step interaction neighborhood of all 262 gene
signatures (i.e. proteins that physically interact with the signature gene proteins) was evaluated. This file
contains the results.
File type: MS Excel (.xls)
Supplementary File 3. Global network topology analysis for all signatures
Summary: This file contains results of network topology analysis.
File type: MS Excel (.xls)
Supplementary File 4. Direct interaction networks for all signatures and unions
Summary: This file includes results of direct interaction network analysis.
File type: MS Excel (.xls)
Supplementary File 5. Ontology enrichment analysis (EA) for signature unions
Summary: This file includes results of ontology enrichment analysis for unions of signatures for each
endpoint and for lists of differentially expressed genes for each endpoint
File type: MS Excel (.xls)
Supplementary File 6. Pairwise gene content overlap between all gene signatures on 13 endpoints
Summary: This file contains pair-wise intersections (overlaps) of gene content between signatures and
their significance by p-value
File type: MS Excel (.xls)
Supplementary File 7. Pairwise kappas on gene content level
Summary: This file contains kappa statistics analysis on gene content level.
File type: MS Excel (.xls)
Supplementary File 8. Similarity trees for all signatures based on gene content, ontology enrichment
and network similarity
Summary: This file contains similarity trees for all signatures based on gene content, ontology
enrichment and network similarity
File type: MS PowerPoint (.ppt)
Supplementary File 9. Pairwise kappas on ontology of disease biomarkers level
Summary: This file contains kappa statistics analysis on ontology enrichment (diseases by biomarkers)
level.
File type: MS Excel (.xls)
Supplementary File 10.
Supplementary File 11. Pairwise connectivity between and within all signatures
Summary: This file contains information about pairwise connectivity between and within all signatures
File type: MS Excel (.xls)
Supplementary File 12. One-step upstream and downstream network objects for all signatures
Summary: This file contains one-step upstream and downstream network objects for all signatures
File type: MS Excel (.xls)
Supplementary File 13. One-step interactions neighborhoods between signatures
Summary: This file contains images which illustrate pairwise connectivity between and within all
signatures
File type: MS PowerPoint (.ppt)
Supplementary File 14. The highest connected transcription factors for all endpoints
Summary: This file contains inreconnected and intraconnected transcription factors for each endpoint.
File type: MS Excel (.xls)
Supplementary File 15. Consistency of EA distributions of signature unions for all endpoints
Summary: This file illustrates consistency of EA distributions of signature unions for all endpoints
File type: MS Excel (.xls)