Dataset Information

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.

ABSTRACT: The BRENDA (BRaunschweig ENzyme DAtabase) enzyme portal (http://www.brenda-enzymes.org) is the main information system of functional biochemical and molecular enzyme data and provides access to seven interconnected databases. BRENDA contains 2.7 million manually annotated data on enzyme occurrence, function, kinetics and molecular properties. Each entry is connected to a reference and the source organism. Enzyme ligands are stored with their structures and can be accessed via their names, synonyms or via a structure search. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are based on text mining methods and represent a complete survey of PubMed abstracts with information on enzymes in different organisms, tissues or organelles. The supplemental database DRENDA provides more than 910 000 new EC number-disease relations in more than 510 000 references from automatic search and a classification of enzyme-disease-related information. KENDA (Kinetic ENzyme DAta), a new amendment extracts and displays kinetic values from PubMed abstracts. The integration of the EnzymeDetector offers an automatic comparison, evaluation and prediction of enzyme function annotations for prokaryotic genomes. The biochemical reaction database BKM-react contains non-redundant enzyme-catalysed and spontaneous reactions and was developed to facilitate and accelerate the construction of biochemical models.

SUBMITTER: Schomburg I

PROVIDER: S-EPMC3531171 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature

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BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.

Schomburg Ida I Chang Antje A Placzek Sandra S Söhngen Carola C Rother Michael M Lang Maren M Munaretto Cornelia C Ulas Susanne S Stelzer Michael M Grote Andreas A Scheer Maurice M Schomburg Dietmar D

Nucleic acids research 20121129 Database issue

The BRENDA (BRaunschweig ENzyme DAtabase) enzyme portal (http://www.brenda-enzymes.org) is the main information system of functional biochemical and molecular enzyme data and provides access to seven interconnected databases. BRENDA contains 2.7 million manually annotated data on enzyme occurrence, function, kinetics and molecular properties. Each entry is connected to a reference and the source organism. Enzyme ligands are stored with their structures and can be accessed via their names, synony ...[more]

PMID: 23203881

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Project description:Singapore grouper iridovirus (SGIV) is the major agent that causes severe iridovirus diseases in grouper maricluture. Based on the genomic information, a DNA microarray, containing probes corresponding to 162 putative SGIV open reading frames (ORFs) was constucted. The viral microarrays wereused to classify the majority of SGIV transcripts into three temporal kinetic classes (immediate-early, IE; early, E; late, L) during an in vitro infection by their dependence on de novo protein synthesis inhibitor and viral DNA replication. Keywords: drug response To map the SGIV transcripts into temporal kinetic classes during the infection in vitro, GS cells were treated with drug inhibitors as previously described with some slight modifications. Briefly, GS monolayers were treated for 1 h prior to, during and throughout the viral infection with either CHX or PAA, which inhibited de novo protein synthesis and viral DNA replication mechanisms, respectively. To distinguish between viral IE transcripts and other transcripts, cells infected with SGIV (MOI of 5) or mock infected were treated with CHX (100 Âµg/ml), and then harvested at 8 h p.i. Whereas, viral E and L transcripts were categorized when cells infected with SGIV (MOI of 5) in the presence and absence of PAA (200 Âµg/ml), respectively. Until at 36 h p.i., cells were collected for RNA extraction. In a comparison analysis, we used Significance Analysis of Microarrays (SAM) software to identify the groups of different expression genes between the drug-treated samples and untreated samples. SAM identifies genes with statistically significant changes in expression by assimilating a set of gene-specific t tests. Significance is based on an estimated of FDRâ¤5% and a 2 fold-change cutoff. Only the genes that met the following three criteria could be categorized into various temporal kinetic classes: (i) a viral gene was considered to be a IE transcript if its expression level increased or weakly affected under CHX treatment, (ii) a viral gene was considered to be a L transcript if its median intensity ratio in the PAA-treated samples was at least two-fold lower than that in the untreated samples and (iii) a viral gene was considered to be a E transcript if it expressed higher or remained within the two- fold range after PAA treatment but was inhibited distinctly by CHX treatment. To identify the significant differences in gene expression, a criterion with at least two-fold change combined with studentâs one sample t-test p value <0.05 was adopted.

Dataset Information

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.

Publications

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.

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