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Genes 2017, 8(10), 252; doi:10.3390/genes8100252

Network-Based Method for Identifying Co-Regeneration Genes in Bone, Dentin, Nerve and Vessel Tissues

1,2,†
,
3,4,†
,
5,†
,
6
,
5,* , 5,* and 1,*
1
School of Life Sciences, Shanghai University, Shanghai 200444, China
2
College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
3
Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Harvard University, Boston, MA 02115, USA
4
Department of Orthopedic Surgery, Brigham and Women’s Hospital, Harvard University, Boston, MA 02115, USA
5
Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
6
Department of Computer Science, Guangdong AIB Polytechnic, Guangzhou 510507, Guangdong, China
*
Authors to whom correspondence should be addressed.
Received: 28 July 2017 / Revised: 15 September 2017 / Accepted: 28 September 2017 / Published: 2 October 2017
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Abstract

Bone and dental diseases are serious public health problems. Most current clinical treatments for these diseases can produce side effects. Regeneration is a promising therapy for bone and dental diseases, yielding natural tissue recovery with few side effects. Because soft tissues inside the bone and dentin are densely populated with nerves and vessels, the study of bone and dentin regeneration should also consider the co-regeneration of nerves and vessels. In this study, a network-based method to identify co-regeneration genes for bone, dentin, nerve and vessel was constructed based on an extensive network of protein–protein interactions. Three procedures were applied in the network-based method. The first procedure, searching, sought the shortest paths connecting regeneration genes of one tissue type with regeneration genes of other tissues, thereby extracting possible co-regeneration genes. The second procedure, testing, employed a permutation test to evaluate whether possible genes were false discoveries; these genes were excluded by the testing procedure. The last procedure, screening, employed two rules, the betweenness ratio rule and interaction score rule, to select the most essential genes. A total of seventeen genes were inferred by the method, which were deemed to contribute to co-regeneration of at least two tissues. All these seventeen genes were extensively discussed to validate the utility of the method. View Full-Text
Keywords: co-regeneration; bone; dentin; nerve; vessel; protein–protein interaction co-regeneration; bone; dentin; nerve; vessel; protein–protein interaction
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Chen, L.; Pan, H.; Zhang, Y.-H.; Feng, K.; Kong, X.; Huang, T.; Cai, Y.-D. Network-Based Method for Identifying Co-Regeneration Genes in Bone, Dentin, Nerve and Vessel Tissues. Genes 2017, 8, 252.

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