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1,289
MIPS: analysis and annotation of proteins from whole genomes
- Nucleic Acids Res
, 2004
"... resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of.400 genomes automatically annotated w ..."
Abstract
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Cited by 206 (14 self)
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with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
- Nature
, 2006
"... Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation ..."
Abstract
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Cited by 296 (9 self)
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into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics
Relating Whole-Genome Expression Data with Protein-Protein Interactions
, 2002
"... this paper is the interactions occurring within specific complexes. These were obtained from the MIPS complexes catalog (Fellenberg et al. 2000), which represents a carefully annotated, comprehensive data set of protein complexes culled from the scientific literature. In addition, we looked at other ..."
Abstract
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Cited by 229 (14 self)
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at other types of protein-protein interactions from large "aggregated" data sets collecting many heterogeneous pair-wise interactions. We collected these from the MIPS catalogs of physical and genetic interactions (Fellenberg et al. 2000), databases of interacting proteins (DIP and BIND) (Bader
MIPS: a database for protein sequences and complete genomes
, 1998
"... The MIPS group [Munich Information Center for Protein Sequences of the German National Center for Environment and Health (GSF)] at the Max-PlanckInstitute for Biochemistry, Martinsried near Munich, Germany, is involved in a number of data collection activities, including a comprehensive database of ..."
Abstract
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Cited by 52 (0 self)
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The MIPS group [Munich Information Center for Protein Sequences of the German National Center for Environment and Health (GSF)] at the Max-PlanckInstitute for Biochemistry, Martinsried near Munich, Germany, is involved in a number of data collection activities, including a comprehensive database
Reverse engineering of regulatory networks in human B cells.
- Nat. Genet.
, 2005
"... Cellular phenotypes are determined by the differential activity of networks linking coregulated genes. Available methods for the reverse engineering of such networks from genome-wide expression profiles have been successful only in the analysis of lower eukaryotes with simple genomes. Using a new m ..."
Abstract
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Cited by 178 (2 self)
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of both protein-protein interaction and metabolic networks is of a hierarchical scale-free nature 1,2 , characterized by an inverse relationship between the number of nodes and their connectivity (scale-free) and by a preferential interaction among highly connected genes, called hubs (hierarchical
Mammalian TOR complex 2 controls the actin cytoskeleton and is rapamycin insensitive.
- Nature Cell Biol.
, 2004
"... The target of rapamycin (TOR) is a highly conserved protein kinase and a central controller of cell growth. In budding yeast, TOR is found in structurally and functionally distinct protein complexes: TORC1 and TORC2. A mammalian counterpart of TORC1 (mTORC1) has been described, but it is not known ..."
Abstract
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Cited by 109 (3 self)
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genomes revealed fragments of a probable vertebrate homologue of the TORC2-specific protein AVO3. Mammalian AVO3 (mAVO3) was cloned from mouse C2C12 cDNA and sequenced, revealing a putative protein of 1,708 amino acids that shares about 25% identity with S. cerevisiae AVO3. Although there are no obvious
MIPS: analysis and annotation of genome information in 2007
- Nucleic Acids Research
, 2008
"... combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known to ortholo ..."
Abstract
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Cited by 23 (0 self)
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interactions based on scrutinized information from the literature to serve as an accepted set of reliable annotated interaction data (MPACT, MPPI, CORUM). All databases and tools described as well as the detailed descriptions of our projects can be accessed through the MIPS web server
2003a) Assessment of the reliability of protein–protein interactions and protein function prediction. Pacific Symposium of Biocomputing (PSB2003
"... As more and more high-throughput protein-protein interaction data are collected, the task of estimating the reliability of different data sets becomes increasingly important. In this paper, we present our study of two groups of protein-protein interaction data, the physical interaction data and the ..."
Abstract
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Cited by 93 (4 self)
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develop a maximum likelihood method to estimate the reliability of protein interaction data sets according to the distribution of correlation coefficients of gene expression profiles of putative interact-ing protein pairs. The results of the three measurements are consistent with each other. The MIPS
An Essential Role for DYF-11/MIP-T3 in Assembling Functional Intraflagellar Transport Complexes
"... MIP-T3 is a human protein found previously to associate with microtubules and the kinesin-interacting neuronal protein DISC1 (Disrupted-in-Schizophrenia 1), but whose cellular function(s) remains unknown. Here we demonstrate that the C. elegans MIP-T3 ortholog DYF-11 is an intraflagellar transport ( ..."
Abstract
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Cited by 4 (0 self)
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MIP-T3 is a human protein found previously to associate with microtubules and the kinesin-interacting neuronal protein DISC1 (Disrupted-in-Schizophrenia 1), but whose cellular function(s) remains unknown. Here we demonstrate that the C. elegans MIP-T3 ortholog DYF-11 is an intraflagellar transport
3did: Interacting protein domains of known three-dimensional structure
- D413-D417. http://dx.doi.org/10.1093/nar/gki037 Copyright © 2014 SciRes. OPEN ACCESS
, 2005
"... The database of 3D Interacting Domains (3did) is a collection of domain–domain interactions in proteins for which high-resolution three-dimensional struc-tures are known. 3did exploits structural information to provide critical molecular details necessary for understanding how interactions occur. It ..."
Abstract
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Cited by 62 (4 self)
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The database of 3D Interacting Domains (3did) is a collection of domain–domain interactions in proteins for which high-resolution three-dimensional struc-tures are known. 3did exploits structural information to provide critical molecular details necessary for understanding how interactions occur
Results 1 - 10
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1,289
