YPIBP: A repository for phosphoinositide-binding proteins in yeast

Autor: Yan Yuan Tseng, Wei Sheng Wu, Chien Sheng Chen, Biqing Liang, Jagat Rathod, Han-Chen Yen
Rok vydání: 2021
Předmět:
PI3P
phosphatidylinositol-3-phosphate
PI4P
phosphatidylinositol-4-phosphate
S. cerevisiae
LRD
Lipid-Related Domain
ITC
Isothermal Titration Calorimetry
PI5P
phosphatidylinositol-5-phosphate
Biochemistry
Interactome
OSBP
Oxysterol-Binding Protein
chemistry.chemical_compound
0302 clinical medicine
LMPD
LIPID MAPS Proteome Database
Structural Biology
PtdIns
Phosphatidylinositol
LBD
Lipid-Binding Domain
0303 health sciences
PIs
Phosphoinositides
Lipid-binding domain
Computer Science Applications
Transport protein
Cvt
Cytoplasm-to-vacuole targeting
030220 oncology & carcinogenesis
QCM
Quartz Crystal Microbalance
BAR
Bin-Amphiphysin-Rvs
LMSD
LIPID MAPS Structure Database
Biotechnology
FYVE
Fab 1 (yeast orthologue of PIKfyve)
YOTB
Vac 1 (vesicle transport protein)
and EEA1
OMIM
Online Mendelian Inheritance in Man
Phosphoinositides (PIs)
SNX
Sorting Nexin
SPR
Surface Plasmon Resonance
Protein domain
Phosphatidylinositol (PtdIns)
Biophysics
CAFA
Critical Assessment of Functional Annotation
PX
Phox Homology
Computational biology
Biology
Domain (software engineering)
03 medical and health sciences
Interaction network
PH
Pleckstrin Homology
GO
Gene Ontology
Genetics
Phosphatidylinositol
030304 developmental biology
ComputingMethodologies_COMPUTERGRAPHICS
Data Article
FDR
False Discovery Rate
ANTH
AP180 N-terminal Homology
PI(3
4)P2
phosphatidylinositol-3
4-bisphosphate
PI(3
5)P2
phosphatidylinositol-3
5-bisphosphate
PMID
PubMed ID
Phosphoinositide binding
YPIBP
Yeast Phosphoinositide-Binding Proteins
Yeast
PI-binding protein
chemistry
ENTH
Epsin N-terminal Homology
PI(4
5)P2
phosphatidylinositol-4
5-bisphosphate
CRAL-TRIO
cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor
PI(3
4
5)P3
phosphatidylinositol-3
4
5-trisphosphate
TP248.13-248.65
Zdroj: Computational and Structural Biotechnology Journal
Computational and Structural Biotechnology Journal, Vol 19, Iss, Pp 3692-3707 (2021)
ISSN: 2001-0370
Popis: Graphical abstract
Highlights • YPIBP contains 679 PI-binding yeast proteins and their PI-binding evidence. • YPIBP contains 181 lipid-binding domains and 103 lipid-related domains. • YPIBP provides PI-binding enrichment analysis and domain enrichment analysis. • YPIBP provides visualization of PI-domain-protein interactome.
Phosphoinositides (PIs) are a family of eight lipids consisting of phosphatidylinositol (PtdIns) and its seven phosphorylated forms. PIs have important regulatory functions in the cell including lipid signaling, protein transport, and membrane trafficking. Yeast has been recognized as a eukaryotic model system to study lipid-protein interactions. Hundreds of yeast PI-binding proteins have been identified, but this research knowledge remains scattered. Besides, the complete PI-binding spectrum and potential PI-binding domains have not been interlinked. No comprehensive databases are available to support the lipid-protein interaction research on phosphoinositides. Here we constructed the first knowledgebase of Yeast Phosphoinositide-Binding Proteins (YPIBP), a repository consisting of 679 PI-binding proteins collected from high-throughput proteome-array and lipid-array studies, QuickGO, and a rigorous literature mining. The YPIBP also contains protein domain information in categories of lipid-binding domains, lipid-related domains and other domains. The YPIBP provides search and browse modes along with two enrichment analyses (PI-binding enrichment analysis and domain enrichment analysis). An interactive visualization is given to summarize the PI-domain-protein interactome. Finally, three case studies were given to demonstrate the utility of YPIBP. The YPIBP knowledgebase consolidates the present knowledge and provides new insights of the PI-binding proteins by bringing comprehensive and in-depth interaction network of the PI-binding proteins. YPIBP is available at http://cosbi7.ee.ncku.edu.tw/YPIBP/.
Databáze: OpenAIRE
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