Identification of common coexpression modules based on quantitative network comparison
| العنوان: | Identification of common coexpression modules based on quantitative network comparison |
|---|---|
| المؤلفون: | Sanghyeon Kim, Yousang Jo, Doheon Lee |
| المصدر: | BMC Bioinformatics BMC Bioinformatics, Vol 19, Iss S8, Pp 19-28 (2018) |
| بيانات النشر: | BioMed Central, 2018. |
| سنة النشر: | 2018 |
| مصطلحات موضوعية: | 0301 basic medicine, Cell signaling, Aging, Computational biology, Biology, lcsh:Computer applications to medicine. Medical informatics, Biochemistry, 03 medical and health sciences, 0302 clinical medicine, Huntington's disease, Similarity (network science), Structural Biology, medicine, Humans, Gene Regulatory Networks, Coexpression network, lcsh:QH301-705.5, Molecular Biology, Gene, Microarray analysis techniques, Applied Mathematics, Research, Gene Expression Profiling, Network similarity, Brain, Reproducibility of Results, Network comparison, medicine.disease, Computer Science Applications, 030104 developmental biology, Gene Ontology, Huntington Disease, lcsh:Biology (General), Gene Expression Regulation, lcsh:R858-859.7, Identification (biology), DNA microarray, 030217 neurology & neurosurgery, Huntington’s disease |
| الوصف: | Background Finding common molecular interactions from different samples is essential work to understanding diseases and other biological processes. Coexpression networks and their modules directly reflect sample-specific interactions among genes. Therefore, identification of common coexpression network or modules may reveal the molecular mechanism of complex disease or the relationship between biological processes. However, there has been no quantitative network comparison method for coexpression networks and we examined previous methods for other networks that cannot be applied to coexpression network. Therefore, we aimed to propose quantitative comparison methods for coexpression networks and to find common biological mechanisms between Huntington’s disease and brain aging by the new method. Results We proposed two similarity measures for quantitative comparison of coexpression networks. Then, we performed experiments using known coexpression networks. We showed the validity of two measures and evaluated threshold values for similar coexpression network pairs from experiments. Using these similarity measures and thresholds, we quantitatively measured the similarity between disease-specific and aging-related coexpression modules and found similar Huntington’s disease-aging coexpression module pairs. Conclusions We identified similar Huntington’s disease-aging coexpression module pairs and found that these modules are related to brain development, cell death, and immune response. It suggests that up-regulated cell signalling related cell death and immune/ inflammation response may be the common molecular mechanisms in the pathophysiology of HD and normal brain aging in the frontal cortex. Electronic supplementary material The online version of this article (10.1186/s12859-018-2193-3) contains supplementary material, which is available to authorized users. |
| اللغة: | English |
| تدمد: | 1471-2105 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::34905c84eabccb294eefe50cb9b66f51 http://europepmc.org/articles/PMC5998758 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....34905c84eabccb294eefe50cb9b66f51 |
| قاعدة البيانات: | OpenAIRE |
Find this article in full text from Springer Verlag. | تدمد: | 14712105 |
|---|