The Negatome Database

Summary

The Negatome is a collection of protein and domain pairs which are unlikely engaged in direct physical interactions. The database currently contains experimentally supported non-interacting protein pairs derived from two distinct sources: by manual curation of literature and by analysing protein complexes from the PDB. More stringent lists of non-interacting pairs were derived from these two datasets by excluding interactions from IntAct. It can be used to evaluate newly derived experimental interactions. The Negatome is much less biased towards functionally dissimilar proteins than the negative data derived by randomly selecting proteins from different cellular locations. Thus, the negatome is complementary to such random data for training protein interaction prediction algorithms.

Supplement

The supplement to the paper can be downloaded here.

References and Data Used

Smialowski, P., Pagel, P., Wong, P., Brauner, B., Dunger, I., Fobo, G., Frishman, G., Montrone, C., Rattei, T., Frishman, D., Ruepp, A. (2010) "The Negatome Database: a reference set of non-interacting protein pairs", Nucleic Acids Research 38(Database issue): D540-4. LINK.
Finn, R. D., M. Marshall, et al. (2005). "iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions." Bioinformatics 21(3): 410-2. Web Data
Kerrien, S., Y. Alam-Faruque, et al. (2007). "IntAct--open source resource for molecular interaction data." Nucleic Acids Res 35(Database issue): D561-5. Web Data
Kouranov, A., L. Xie, et al. (2006). "The RCSB PDB information portal for structural genomics." Nucleic Acids Res 34(Database issue): D302-5. Web
Stein, A., R. B. Russell, et al. (2005). "3did: interacting protein domains of known three-dimensional structure." Nucleic Acids Res 33(Database issue): D413-7. Web Data

Download

We provide a 'Linked view' on the left side of the table below. Text download can be done on the right.

Dataset	Derived from	Description	Number of Pairs
Manual	Manual literature annotation	Manually annotated literature data describing the lack of protein interaction. High-throughput data are not included. The data is restricted only to mammalian proteins.	1291
Manual-stringent	Manual	The Manual dataset filtered against the IntAct dataset	1162
Manual-PFAM	Manual-stringent	PFAM domain pairs found in the Manual dataset filtered using iPFAM and 3did	523
PDB	The PDB database	Protein pairs that are members of at least one structural complex but do not interact directly. Organism of origin is not restricted	809
PDB-stringent	PDB	The PDB dataset filtered against the IntAct dataset.	745
PDB-PFAM	PDB-stringent	Non-interacting PFAM domains found in the same structural complex filtered using iPFAM and 3did	458
Combined	Manual and PDB-stringent	A combined non-interacting Protein dataset	1892
Combined Pfam	Manual-PFAM and PDB-PFAM	A combined non-interacting Protein domain dataset	979

Additional Mappings

Additional mappings to IntAct, KEGG, GO for our data can be found here and as text download here .

Acknowledgements

This work was partially funded by the Biosapiens Network of Excellence. We thank Roland Arnold for the name and Alexei Antonov.