ComPPI, a cellular compartment-specific database for protein-protein interaction network analysis
Here we present ComPPI, a cellular compartment specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis (http://ComPPI.LinkGroup.hu). ComPPI enables the user to filter biologically unlikely interactions, where the two interacting proteins have no common subcellular localizations and to predict novel properties, such as compartment-specific biological functions. ComPPI is an integrated database covering four species (S. cerevisiae, C. elegans, D. melanogaster and H. sapiens). The compilation of nine protein-protein interaction and eight subcellular localization data sets had four curation steps including a manually built, comprehensive hierarchical structure of more than 1600 subcellular localizations. ComPPI provides confidence scores for protein subcellular localizations and protein-protein interactions. ComPPI has user-friendly search options for individual proteins giving their subcellular localization, their interactions and the likelihood of their interactions considering the subcellular localization of their interacting partners. Download options of search results, whole proteomes, organelle-specific interactomes and subcellular localization data are available on its website. Due to its novel features, ComPPI is useful for the analysis of experimental results in biochemistry and molecular biology, as well as for proteome-wide studies in bioinformatics and network science helping cellular biology, medicine and drug design.
Code (0)
등록된 구현이 없습니다.
Tasks
Drug DesignSimilar Papers 제목 키워드 기반
Translocatome: a novel resource for the analysis of protein translocation between cellular organelles
Here we present Translocatome, the first dedicated database of human translocating proteins. The core of the Translocatome database is the manually curated data set of 213 human translocating proteins listing the source …
Structural Controllability to Unveil Hidden Regulation Mechanisms in Unfolded Protein Response: the Role of Network Models
The Unfolded Protein Response is the cell mechanism for maintaining the balance of properly folded proteins in the endoplasmic reticulum , the specialized cellular compartment. Although it is largely studied from a biolo…
Microfluidic production of porous polymer cell-mimics capable of gene expression
Engineering simple, artificial models of living cells allows synthetic biologists to study cellular functions under well-controlled conditions. Reconstituting multicellular behaviors with synthetic cell-mimics is still a…
Multi class intracellular protein targeting predictions in diatoms and other algae with complex plastids: ASAFind 2.0
Cells of diatoms and related algae with complex plastids of red algal origin are highly compartmentalized. These plastids are surrounded by four envelope membranes, which also define the periplastidic compartment (PPC), …
Phosphatidylserine transport in cell life and death
Phosphatidylserine (PS) is a negatively-charged glycerophospholipid found mainly in the plasma membrane (PM) and in the late secretory/endocytic compartments, where it regulates cellular activity and can mediate apoptosi…