PMID- 34383650
OWN - NLM
STAT- MEDLINE
DCOM- 20221012
LR  - 20221025
IS  - 1557-9964 (Electronic)
IS  - 1545-5963 (Linking)
VI  - 19
IP  - 5
DP  - 2022 Sep-Oct
TI  - Inferring Gene Co-Expression Networks by Incorporating Prior Protein-Protein 
      Interaction Networks.
PG  - 2894-2906
LID - 10.1109/TCBB.2021.3103407 [doi]
AB  - Inferring gene co-expression networks from high-throughput gene expression data 
      is an important task in bioinformatics. Many gene networks often exhibit modular 
      structures. Although several Gaussian graphical model-based methods have been 
      developed to estimate gene co-expression networks by incorporating the modular 
      structural prior, none of them takes into account the modular structures captured 
      by the prior networks (e.g., protein interaction networks). In this study, we 
      propose a novel prior network-dependent gene network inference (pGNI) method to 
      estimate gene co-expression networks by integrating gene expression data and 
      prior protein interaction network data. The underlying modular structure is 
      learned from both sets of data. Through simulation studies, we demonstrate the 
      feasibility and effectiveness of our method. We also apply our method to two real 
      datasets. The modular structures in the networks estimated by our method are 
      biological significant.
FAU - Wang, Meng-Guo
AU  - Wang MG
FAU - Ou-Yang, Le
AU  - Ou-Yang L
FAU - Yan, Hong
AU  - Yan H
FAU - Zhang, Xiao-Fei
AU  - Zhang XF
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20221010
PL  - United States
TA  - IEEE/ACM Trans Comput Biol Bioinform
JT  - IEEE/ACM transactions on computational biology and bioinformatics
JID - 101196755
SB  - IM
MH  - Algorithms
MH  - Computational Biology/methods
MH  - Computer Simulation
MH  - Gene Expression Profiling/methods
MH  - *Gene Regulatory Networks/genetics
MH  - Normal Distribution
MH  - *Protein Interaction Maps/genetics
EDAT- 2021/08/13 06:00
MHDA- 2022/10/13 06:00
CRDT- 2021/08/12 17:18
PHST- 2021/08/13 06:00 [pubmed]
PHST- 2022/10/13 06:00 [medline]
PHST- 2021/08/12 17:18 [entrez]
AID - 10.1109/TCBB.2021.3103407 [doi]
PST - ppublish
SO  - IEEE/ACM Trans Comput Biol Bioinform. 2022 Sep-Oct;19(5):2894-2906. doi: 
      10.1109/TCBB.2021.3103407. Epub 2022 Oct 10.