23 research outputs found
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts
We report the extended database and data mining resources newly released in the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). H-InvDB is a comprehensive annotation resource of human genes and transcripts, and consists of two main views and six sub-databases. The latest release of H-InvDB (release 6.2) provides the annotation for 219 765 human transcripts in 43 159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources—‘Navigation search’, ‘H-InvDB Enrichment Analysis Tool (HEAT)’ and web service APIs. ‘Navigation search’ is an extended search system that enables complicated searches by combining 16 different search options. HEAT is a data mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. H-InvDB now has web service APIs of SOAP and REST to allow the use of H-InvDB data in programs, providing the users extended data accessibility
Large-scale Identification of <i>N-</i>Glycosylated Proteins of Mouse Tissues and Construction of a Glycoprotein Database, GlycoProtDB
Protein glycosylation is a common post-translational
modification
that plays important roles in terms of protein function. However,
analyzing the relationship between glycosylation and protein function
remains technically challenging. This problem arises from the fact
that the attached glycans possess diverse and heterogeneous structures.
We believe that the first step to elucidate glycan function is to
systematically determine the status of protein glycosylation under
physiological conditions. Such studies involve analyzing differences
in glycan structure on cell type (tissue), sex, and age, as well as
changes associated with perturbations as a result of gene knockout
of glycan biosynthesis-related enzyme, disease and drug treatment.
Therefore, we analyzed a series of glycoproteomes in several mouse
tissues to identify glycosylated proteins and their glycosylation
sites. Comprehensive analysis was performed by lectin- or HILIC-capture
of glycopeptide subsets followed by enzymatic deglycosylation in stable
isotope-labeled water (H<sub>2</sub><sup>18</sup>O, IGOT) and finally
LC–MS analyses. In total, 5060 peptides derived from 2556 glycoproteins
were identified. We then constructed a glycoprotein database, GlycoProtDB,
using our experimental-based information to facilitate future studies
in glycobiology
Large-scale Identification of <i>N-</i>Glycosylated Proteins of Mouse Tissues and Construction of a Glycoprotein Database, GlycoProtDB
Protein glycosylation is a common post-translational
modification
that plays important roles in terms of protein function. However,
analyzing the relationship between glycosylation and protein function
remains technically challenging. This problem arises from the fact
that the attached glycans possess diverse and heterogeneous structures.
We believe that the first step to elucidate glycan function is to
systematically determine the status of protein glycosylation under
physiological conditions. Such studies involve analyzing differences
in glycan structure on cell type (tissue), sex, and age, as well as
changes associated with perturbations as a result of gene knockout
of glycan biosynthesis-related enzyme, disease and drug treatment.
Therefore, we analyzed a series of glycoproteomes in several mouse
tissues to identify glycosylated proteins and their glycosylation
sites. Comprehensive analysis was performed by lectin- or HILIC-capture
of glycopeptide subsets followed by enzymatic deglycosylation in stable
isotope-labeled water (H<sub>2</sub><sup>18</sup>O, IGOT) and finally
LC–MS analyses. In total, 5060 peptides derived from 2556 glycoproteins
were identified. We then constructed a glycoprotein database, GlycoProtDB,
using our experimental-based information to facilitate future studies
in glycobiology
Large-scale Identification of <i>N-</i>Glycosylated Proteins of Mouse Tissues and Construction of a Glycoprotein Database, GlycoProtDB
Protein glycosylation is a common post-translational
modification
that plays important roles in terms of protein function. However,
analyzing the relationship between glycosylation and protein function
remains technically challenging. This problem arises from the fact
that the attached glycans possess diverse and heterogeneous structures.
We believe that the first step to elucidate glycan function is to
systematically determine the status of protein glycosylation under
physiological conditions. Such studies involve analyzing differences
in glycan structure on cell type (tissue), sex, and age, as well as
changes associated with perturbations as a result of gene knockout
of glycan biosynthesis-related enzyme, disease and drug treatment.
Therefore, we analyzed a series of glycoproteomes in several mouse
tissues to identify glycosylated proteins and their glycosylation
sites. Comprehensive analysis was performed by lectin- or HILIC-capture
of glycopeptide subsets followed by enzymatic deglycosylation in stable
isotope-labeled water (H<sub>2</sub><sup>18</sup>O, IGOT) and finally
LC–MS analyses. In total, 5060 peptides derived from 2556 glycoproteins
were identified. We then constructed a glycoprotein database, GlycoProtDB,
using our experimental-based information to facilitate future studies
in glycobiology