| Summary of GenoBase |
Scope of database (GenoBase ) is to understand comprehensively the living-cell
system of Escherichia coli K-12 (W3110). Untill now, GenoBase is the public
repository for Sequence Information, Proteome, Transcriptome, Bioinformatics,
and Knowledge based on literature concerning E.coli. |
| Sequence Information |
Sequence information involving the whole genome sequence is compiled
in GenoBase In ORFs, functions, DNA and amino acid sequences, and positions
in genome are compiled based on "JW" index number. |
| Proteome and transcriptome |
2-D protein maps are constructed. Positions for individual protein spots
are visualized. Spot positions are linked with sequence information. Expression
profiles of DNA microarray data are also compiled. |
| Bioinformatics |
To infer the function of individual ORFs and the relationships between
them, we have three approaches, which are(i) gene-clustering analysis based
on the amino acid sequence of each ORF, (ii) multivariate analysis for deducing
the functions of genes in view of codon usage heterogeneity, and (iii) investigation
of the gene network based on the data from DNA micro-array. Self-Organizing
Mapping for classifying genes by expression profile in transcription for
eleven points in the time series is now available. |
Knowledge based on literature concerning
E.coli |
We collected literature concerning mutants and transcription regulations.
The knowledge for the literature is reflected in GenoBase (A) Literature
on operon and transcription regulation for E.coli K-12 has been collected.
About 700 transcription initiation sites reported by these papers are located
in E.coli K-12 (W3110) genome sequence. (B) Literature on mutants for E.coli
K-12 has been collected. Until now, about 4,000 papers are compiled
in GenoBase. |
| Resource |
Materials for systematic genome analysis such as ORF clones (Archive clone),
disruption mutants (Transposon insertion mutants), deletion mutants (constructed
by Wanner's method) etc are available. |
| Resource requests, Comments and questions to ecoli_admin@gtc.naist.jp
|
