Integrating phosphorylation network with transcriptional network reveals novel functional relationships.
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 functiona...
Main Authors: | , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Public Library of Science (PLoS)
2012-01-01
|
Series: | PLoS ONE |
Online Access: | http://europepmc.org/articles/PMC3303811?pdf=render |
id |
doaj-38378483481c472193a567a8d8ada549 |
---|---|
record_format |
Article |
spelling |
doaj-38378483481c472193a567a8d8ada5492020-11-24T21:19:26ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0173e3316010.1371/journal.pone.0033160Integrating phosphorylation network with transcriptional network reveals novel functional relationships.Lin WangLin HouMinping QianMinghua DengPhosphorylation 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.http://europepmc.org/articles/PMC3303811?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Lin Wang Lin Hou Minping Qian Minghua Deng |
spellingShingle |
Lin Wang Lin Hou Minping Qian Minghua Deng Integrating phosphorylation network with transcriptional network reveals novel functional relationships. PLoS ONE |
author_facet |
Lin Wang Lin Hou Minping Qian Minghua Deng |
author_sort |
Lin Wang |
title |
Integrating phosphorylation network with transcriptional network reveals novel functional relationships. |
title_short |
Integrating phosphorylation network with transcriptional network reveals novel functional relationships. |
title_full |
Integrating phosphorylation network with transcriptional network reveals novel functional relationships. |
title_fullStr |
Integrating phosphorylation network with transcriptional network reveals novel functional relationships. |
title_full_unstemmed |
Integrating phosphorylation network with transcriptional network reveals novel functional relationships. |
title_sort |
integrating phosphorylation network with transcriptional network reveals novel functional relationships. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2012-01-01 |
description |
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. |
url |
http://europepmc.org/articles/PMC3303811?pdf=render |
work_keys_str_mv |
AT linwang integratingphosphorylationnetworkwithtranscriptionalnetworkrevealsnovelfunctionalrelationships AT linhou integratingphosphorylationnetworkwithtranscriptionalnetworkrevealsnovelfunctionalrelationships AT minpingqian integratingphosphorylationnetworkwithtranscriptionalnetworkrevealsnovelfunctionalrelationships AT minghuadeng integratingphosphorylationnetworkwithtranscriptionalnetworkrevealsnovelfunctionalrelationships |
_version_ |
1726005337807388672 |