Bert O'Malley

Analysis of the Human Endogenous Complexome

Elucidation of endogenous cellular protein-protein interactions and their networks is most desirable for biological studies. Here we report our study of endogenous human coregulator protein complex networks obtained from integrative mass spectrometry-based analysis of 3290 affinity purifications. By preserving weak protein interactions during complex isolation and utilizing high levels of reciprocity in the large dataset, we identified many unreported protein associations, such as a transcriptional network formed by ZMYND8, ZNF687, and ZNF592. Furthermore, our work revealed a tiered interplay within networks that share common proteins, providing a conceptual organization of a cellular proteome composed of minimal endogenous modules (MEMOs), complex isoforms (uniCOREs), and regulatory complex-complex interaction networks (CCIs). This resource will effectively fill a void in linking correlative genomic studies with an understanding of transcriptional regulatory protein functions within the proteome for formulation and testing of future hypotheses.

The dataset can be accessed in one of two ways:

1. CCI networks are available either as downloadable QuickView PDFs or scrollable lists in the Interactions section of the Coregulator Molecule Pages. For example, visit the Interactions section for AIB1/SRC-3. We encourage you to read the Help PDF to familiarize yourself with the dataset.
2. Searching a website developed by the Proteomics Resource.
3. The full dataset may be downloaded here.

NURSA Phase II | Proteomics Resource

Malovannaya A, Lanz RB, Jung SY, Bulynko Y, Le N, Chan DW, Ding C, Shi Y, Yucer N, Krenciute G, Jim B-J, Li C, Chen R, Li W, Wang Y, O'Malley BW and Qin J

Bert O'Malley

May 27, 2011