Investigating ego modules involved in TGFβ3-induced chondrogenesis in mesenchymal stem cells based on ego network.
OBJECTIVE
This paper aimed to investigate ego modules for TGFβ3-induced chondrogenesis in mesenchymal stem cells (MSCs) using ego network algorithm.


METHODS
The ego network algorithm comprised three parts, extracting differential expression network (DEN) based on gene expression data and protein-protein interaction (PPI) data; exploring ego genes by reweighting DEN; and searching ego modules by ego gene expansions. Subsequently, permutation test was carried out to evaluate the statistical significance of the ego modules. Finally, pathway enrichment analysis was conducted to investigate ego pathways enriched by the ego modules.


RESULTS
A total of 15 ego genes were obtained from the DEN, such as PSMA4, HNRNPM and WDR77. Starting with each ego genes, 15 candidate modules were gained. When setting the thresholds of the area under the receiver operating characteristics curve (AUC) ≥0.9 and gene size ≥4, three ego modules (Module 3, Module 8 and Module 14) were identified, and all of them had statistical significances between normal and TGFβ3-induced chondrogenesis in MSCs. By mapping module genes to confirmed pathway database, their ego pathways were detected, Cdc20:Phospho-APC/C mediated degradation of Cyclin A for Module 3, Mitotic G1-G1/S phases for Module 8, and mRNA Splicing for Module 14.


CONCLUSIONS
We have successfully identified three ego modules, evaluated their statistical significances and investigated their functional enriched ego pathways. The findings might provide potential biomarkers and give great insights to reveal molecular mechanism underlying this process.
Department of Orthopedics, Affiliated Hospital of Taishan Medical University, Tai'an, 271000, Shandong Province, China.
Jing-Guo
JG
Wu
Department of Orthopedics, Affiliated Hospital of Taishan Medical University, Tai'an, 271000, Shandong Province, China.
Qing-Wei
QW
Jia
Department of Orthopedics, Tai'an Centre Hospital Branch, Tai'an, 271000, Shandong Province, China.
Yong
Y
Li
Department of Orthopedics, Tai'an Centre Hospital Branch, Tai'an, 271000, Shandong Province, China.
Fei-Fei
FF
Cao
Department of Orthopedics, Affiliated Hospital of Taishan Medical University, Tai'an, 271000, Shandong Province, China.
Xi-Shan
XS
Zhang
Department of Orthopedics, Tai'an Centre Hospital, Tai'an, 271000, No.29 on Longtan Road, Shandong Province, China. Electronic address: congliu2016@163.com.
Cong
C
Liu
D020219:Chondrogenesis / Q000502:physiology*; D020869:Gene Expression Profiling; D006801:Humans; D059630:Mesenchymal Stem Cells / Q000166:cytology*; D053782:Transforming Growth Factor beta3 / Q000502:physiology*
D053782:Transforming Growth Factor beta3
Ego; Gene expression; Mesenchymal stem cells; Module; Network; Pathway; TGFβ3