PMID- 18030341
OWN - NLM
STAT- MEDLINE
DCOM- 20080821
LR  - 20211020
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 2
IP  - 11
DP  - 2007 Nov 21
TI  - Hubs with network motifs organize modularity dynamically in the protein-protein 
      interaction network of yeast.
PG  - e1207
LID - e1207
AB  - BACKGROUND: It has been recognized that modular organization pervades biological 
      complexity. Based on network analysis, 'party hubs' and 'date hubs' were proposed 
      to understand the basic principle of module organization of biomolecular 
      networks. However, recent study on hubs has suggested that there is no clear 
      evidence for coexistence of 'party hubs' and 'date hubs'. Thus, an open question 
      has been raised as to whether or not 'party hubs' and 'date hubs' truly exist in 
      yeast interactome. METHODOLOGY: In contrast to previous studies focusing on the 
      partners of a hub or the individual proteins around the hub, our work aims to 
      study the network motifs of a hub or interactions among individual proteins 
      including the hub and its neighbors. Depending on the relationship between a 
      hub's network motifs and protein complexes, we define two new types of hubs, 
      'motif party hubs' and 'motif date hubs', which have the same characteristics as 
      the original 'party hubs' and 'date hubs' respectively. The network motifs of 
      these two types of hubs display significantly different features in spatial 
      distribution (or cellular localizations), co-expression in microarray data, 
      controlling topological structure of network, and organizing modularity. 
      CONCLUSION: By virtue of network motifs, we basically solved the open question 
      about 'party hubs' and 'date hubs' which was raised by previous studies. 
      Specifically, at the level of network motifs instead of individual proteins, we 
      found two types of hubs, motif party hubs (mPHs) and motif date hubs (mDHs), 
      whose network motifs display distinct characteristics on biological functions. In 
      addition, in this paper we studied network motifs from a different viewpoint. 
      That is, we show that a network motif should not be merely considered as an 
      interaction pattern but be considered as an essential function unit in organizing 
      modules of networks.
FAU - Jin, Guangxu
AU  - Jin G
AD  - Academy of Mathematics and Systems Science, Chinese Academy of Science, Beijing, 
      China.
FAU - Zhang, Shihua
AU  - Zhang S
FAU - Zhang, Xiang-Sun
AU  - Zhang XS
FAU - Chen, Luonan
AU  - Chen L
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20071121
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (Saccharomyces cerevisiae Proteins)
SB  - IM
MH  - *Amino Acid Motifs
MH  - Protein Binding
MH  - Saccharomyces cerevisiae Proteins/chemistry/*metabolism
MH  - Signal Transduction
PMC - PMC2065901
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2007/11/22 09:00
MHDA- 2008/08/22 09:00
PMCR- 2007/11/21
CRDT- 2007/11/22 09:00
PHST- 2007/04/26 00:00 [received]
PHST- 2007/10/30 00:00 [accepted]
PHST- 2007/11/22 09:00 [pubmed]
PHST- 2008/08/22 09:00 [medline]
PHST- 2007/11/22 09:00 [entrez]
PHST- 2007/11/21 00:00 [pmc-release]
AID - 07-PONE-RA-01168R2 [pii]
AID - 10.1371/journal.pone.0001207 [doi]
PST - epublish
SO  - PLoS One. 2007 Nov 21;2(11):e1207. doi: 10.1371/journal.pone.0001207.