ArticlePloS one2012
Integrating phosphorylation network with transcriptional network reveals novel functional relationships.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 9 citations in OpenAlex.
- Fusing gene expressions and transitive protein-protein interactions for inference of gene regulatory networks.BMC systems biology · 2019Article
- A biomolecular proportional integral controller based on feedback regulations of protein level and activity.Royal Society open science · 2018Article
- RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals.Database : the journal of biological databases and curation · 2014Article
- PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data.Bioinformatics (Oxford, England) · 2013Article
- SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks.BMC systems biology · 2013Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phosphorylation and transcriptional regulation events are critical for cells to transmit and respond to signals. In spite of its importance, systems-level strategies that couple these two networks have yet to be presented. Here we introduce a novel approach that integrates the physical and functional aspects of phosphorylation network together with the transcription network in S.cerevisiae, and demonstrate that different network motifs are involved in these networks, which should be considered in interpreting and integrating large scale datasets. Based on this understanding, we introduce a HeRS score (hetero-regulatory similarity score) to systematically characterize the functional relevance of kinase/phosphatase involvement with transcription factor, and present an algorithm that predicts hetero-regulatory modules. When extended to signaling network, this approach confirmed the structure and cross talk of MAPK pathways, inferred a novel functional transcription factor Sok2 in high osmolarity glycerol pathway, and explained the mechanism of reduced mating efficiency upon Fus3 deletion. This strategy is applicable to other organisms as large-scale datasets become available, providing a means to identify the functional relationships between kinases/phosphatases and transcription factors.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.