IIIDB: a database for isoform-isoform interactions and isoform network modules

doi:10.1186/1471-2164-16-S2-S10

CSpace > 应用数学研究所

	IIIDB: a database for isoform-isoform interactions and isoform network modules
	Tseng,Yu-Ting 1; Li,Wenyuan 2; Chen,Ching-Hsien 3; Zhang,Shihua4 ; Chen,Jeremy JW 5,6,7; Zhou,Xianghong Jasmine 2; Liu,Chun-Chi 1,5,7
	2015-01-21
发表期刊	BMC Genomics
ISSN	1471-2164
卷号	16 期号:Suppl 2
摘要	AbstractBackgroundProtein-protein interactions (PPIs) are key to understanding diverse cellular processes and disease mechanisms. However, current PPI databases only provide low-resolution knowledge of PPIs, in the sense that "proteins" of currently known PPIs generally refer to "genes." It is known that alternative splicing often impacts PPI by either directly affecting protein interacting domains, or by indirectly impacting other domains, which, in turn, impacts the PPI binding. Thus, proteins translated from different isoforms of the same gene can have different interaction partners.ResultsDue to the limitations of current experimental capacities, little data is available for PPIs at the resolution of isoforms, although such high-resolution data is crucial to map pathways and to understand protein functions. In fact, alternative splicing can often change the internal structure of a pathway by rearranging specific PPIs. To fill the gap, we systematically predicted genome-wide isoform-isoform interactions (IIIs) using RNA-seq datasets, domain-domain interaction and PPIs. Furthermore, we constructed an III database (IIIDB) that is a resource for studying PPIs at isoform resolution. To discover functional modules in the III network, we performed III network clustering, and then obtained 1025 isoform modules. To evaluate the module functionality, we performed the GO/pathway enrichment analysis for each isoform module.ConclusionsThe IIIDB provides predictions of human protein-protein interactions at the high resolution of transcript isoforms that can facilitate detailed understanding of protein functions and biological pathways. The web interface allows users to search for IIIs or III network modules. The IIIDB is freely available at http://syslab.nchu.edu.tw/IIIDB.
DOI	10.1186/1471-2164-16-S2-S10
语种	英语
WOS记录号	BMC:10.1186/1471-2164-16-S2-S10
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/215
专题	应用数学研究所
通讯作者	Liu,Chun-Chi
作者单位	1.National Chung Hsing University; Institute of Genomics and Bioinformatics 2.University of Southern California; Molecular and Computational Biology 3.University of California Davis; Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine and Center for Comparative Respira-tory Biology and Medicine 4.National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, CAS 5.National Chung Hsing University; Institute of Biomedical Sciences 6.National Chung Hsing University; Institute of Molecular Biology 7.National Chung Hsing University; Agricultural Biotechnology Center
推荐引用方式 GB/T 7714	Tseng,Yu-Ting,Li,Wenyuan,Chen,Ching-Hsien,et al. IIIDB: a database for isoform-isoform interactions and isoform network modules[J]. BMC Genomics,2015,16(Suppl 2).
APA	Tseng,Yu-Ting.,Li,Wenyuan.,Chen,Ching-Hsien.,Zhang,Shihua.,Chen,Jeremy JW.,...&Liu,Chun-Chi.(2015).IIIDB: a database for isoform-isoform interactions and isoform network modules.BMC Genomics,16(Suppl 2).
MLA	Tseng,Yu-Ting,et al."IIIDB: a database for isoform-isoform interactions and isoform network modules".BMC Genomics 16.Suppl 2(2015).