PMID- 25091279
OWN - NLM
STAT- MEDLINE
DCOM- 20150514
LR  - 20211021
IS  - 1471-2229 (Electronic)
IS  - 1471-2229 (Linking)
VI  - 14
DP  - 2014 Aug 5
TI  - Prediction and functional analysis of the sweet orange protein-protein 
      interaction network.
PG  - 213
LID - 10.1186/s12870-014-0213-7 [doi]
AB  - BACKGROUND: Sweet orange (Citrus sinensis) is one of the most important fruits 
      world-wide. Because it is a woody plant with a long growth cycle, genetic studies 
      of sweet orange are lagging behind those of other species. RESULTS: In this 
      analysis, we employed ortholog identification and domain combination methods to 
      predict the protein-protein interaction (PPI) network for sweet orange. The 
      K-nearest neighbors (KNN) classification method was used to verify and filter the 
      network. The final predicted PPI network, CitrusNet, contained 8,195 proteins 
      with 124,491 interactions. The quality of CitrusNet was evaluated using gene 
      ontology (GO) and Mapman annotations, which confirmed the reliability of the 
      network. In addition, we calculated the expression difference of interacting 
      genes (EDI) in CitrusNet using RNA-seq data from four sweet orange tissues, and 
      also analyzed the EDI distribution and variation in different sub-networks. 
      CONCLUSIONS: Gene expression in CitrusNet has significant modular features. 
      Target of rapamycin (TOR) protein served as the central node of the 
      hormone-signaling sub-network. All evidence supported the idea that TOR can 
      integrate various hormone signals and affect plant growth. CitrusNet provides 
      valuable resources for the study of biological functions in sweet orange.
FAU - Ding, Yu-Duan
AU  - Ding YD
FAU - Chang, Ji-Wei
AU  - Chang JW
FAU - Guo, Jing
AU  - Guo J
FAU - Chen, Dijun
AU  - Chen D
FAU - Li, Sen
AU  - Li S
FAU - Xu, Qiang
AU  - Xu Q
FAU - Deng, Xiu-Xin
AU  - Deng XX
FAU - Cheng, Yun-Jiang
AU  - Cheng YJ
AD  - Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong 
      Agricultural University, Wuhan 430070, People's Republic of China. 
      yjcheng@mail.hzau.edu.cn.
FAU - Chen, Ling-Ling
AU  - Chen LL
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140805
PL  - England
TA  - BMC Plant Biol
JT  - BMC plant biology
JID - 100967807
RN  - 0 (Plant Growth Regulators)
SB  - IM
MH  - Citrus sinensis/genetics/*metabolism
MH  - Genome, Plant
MH  - Plant Growth Regulators/metabolism
MH  - *Protein Interaction Maps
MH  - Sequence Analysis, RNA
PMC - PMC4236729
EDAT- 2014/08/06 06:00
MHDA- 2015/05/15 06:00
PMCR- 2014/08/05
CRDT- 2014/08/06 06:00
PHST- 2013/07/16 00:00 [received]
PHST- 2014/07/24 00:00 [accepted]
PHST- 2014/08/06 06:00 [entrez]
PHST- 2014/08/06 06:00 [pubmed]
PHST- 2015/05/15 06:00 [medline]
PHST- 2014/08/05 00:00 [pmc-release]
AID - s12870-014-0213-7 [pii]
AID - 10.1186/s12870-014-0213-7 [doi]
PST - epublish
SO  - BMC Plant Biol. 2014 Aug 5;14:213. doi: 10.1186/s12870-014-0213-7.