Complex Assembly and Activity States as Multifaceted Protein Attributes Explaining Phenotypic Variability | Zenodo Skip to main Communities My dashboard Log in Sign up Published April 24, 2026 | Version v2 Dataset Open Complex Assembly and Activity States as Multifaceted Protein Attributes Explaining Phenotypic Variability Authors/Creators Rosenberger, George (Researcher) 1 Show affiliations 1. Columbia University Description Cell function studies primarily focus on measuring overall molecular abundances while often overlooking critical clues—including protein modifications and molecular interaction networks—that critically determine the functional properties of the cell. In prior work, we introduced a suite of methods to reveal context-specific transcription factor-gene regulatory networks, kinase-substrate networks, and protein interaction networks and leveraged them to gain deeper insights into transcriptional regulation and signal transduction. However, the complex interdependencies between these networks are still elusive. To address this challenge, we introduce a multi-omics framework, aimed at harnessing measured or inferred protein activity in context-specific networks, which yields deeper functional insights into mechanisms underlying molecular phenotypes, compared to protein abundance alone. As proof of concept, we utilized progressively differentiated instances of HeLa CCL2 and Kyoto cell lines to explore the role of protein complexes and interactions in cell doubling time and susceptibility to Salmonella Typhimurium infection. Notably, this analysis underscores the pivotal role of protein interaction networks in linking molecular profiles to phenotypic outcomes, thus providing a highly generalizable framework for multi-omics dataset analysis. Files Files (33.2 GB) Name Size external.tgz md5:56a3b8ce2a9c185bf3e645643c187c04 867.8 MB Download intermediate_fig_ev1_benchmark_detection.tgz md5:f19bafc8201311c60fc565d33bb4ac66 17.2 GB Download intermediate_preprocessing_phosphoproteomics.tgz md5:1106b8c96e16b52d49d9fe046160258c 8.5 MB Download intermediate_preprocessing_proteomics.tgz md5:84a82dc37cf7e21e394588649292f372 55.6 MB Download intermediate_secat_secswath.tgz md5:6bb540af755193fa93a11b178e4c80a5 7.0 GB Download intermediate_vespa_phosphoproteomics.tgz md5:b0f779c93a03e55934ff6422e5e55a20 81.6 MB Download intermediate_viper_transcriptomics.tgz md5:24d31b75036644b55111f12f7d9d8927 165.5 MB Download raw.tgz md5:d303f9fe39846aed0e2b7f3e71841dee 2.7 GB Download reference.tgz md5:7d2bc0218d58d08471b2a1aecfbb1f4b 5.3 GB Download 123 Views 270 Downloads Show more details All versions This version Views Total views 123 48 Downloads Total downloads 270 114 Data volume Total data volume 1.3 TB 409.7 GB More info on how stats are collected.... Versions External resources Indexed in OpenAIRE Communities Details DOI DOI Badge DOI 10.5281/zenodo.19733975 Markdown [](https://doi.org/10.5281/zenodo.19733975) reStructuredText .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.19733975.svg :target: https://doi.org/10.5281/zenodo.19733975 HTML <a href="https://doi.org/10.5281/zenodo.19733975"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.19733975.svg" alt="DOI"></a> Image URL https://zenodo.org/badge/DOI/10.5281/zenodo.19733975.svg Target URL https://doi.org/10.5281/zenodo.19733975 Resource type Dataset Publisher Zenodo Rights License Creative Commons Attribution 4.0 International The Creative Commons Attribution license allows re-distribution and re-use of a licensed work on the condition that the creator is appropriately credited. Read more Citation Export Technical metadata Created April 24, 2026 Modified April 24, 2026 Jump up About About Policies Infrastructure Principles Projects Roadmap Contact Blog Blog Support Help FAQ Developers REST API OAI-PMH Contribute GitHub Donate Funded by Powered by CERN Data Centre & InvenioRDM Status Privacy policy Cookie policy Terms of Use This site uses cookies. Find out more on how we use cookies Accept all cookies Accept only essential cookies