GenoBase: comprehensive resource database of Escherichia coli K-12

Abstract

Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the long-term goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12. We have made these experimental resources freely available to the academic community worldwide. Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes. Quality control is extremely important for evaluating results generated by these resources. Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly. Here, we describe GenoBase (http://ecoli.naist.jp/GB/), which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources.

Figure 1.

Chado schema in GenoBase. The portion of the Chado schema is shown that was used to realize the abstract GenoBase schema. Arrows show relationships between a Foreign Key (FK) and Primary Key (PK) of the same name in the database tables, except FK type_id in the feature and featureprop tables are connected to PK cvterm_id in the cvterm table.

Figure 2.

SQL Views in GenoBase. The GenoBase schema was built via SQL Views using the base relations in the Chado schema shown in Figure 1. Views and scripts are downloadable from the GenoBase description page.

Figure 3.

Structure of cloned region of ORF clone libraries. Colored boxes, red, green and blue boxes represent target ORF, eGFP and attL regions, respectively. All of ORF cloning target regions are designed from the second to the last amino acid coding region except the TransBac plasmid clone library.

Figure 4.

Genomic structure of target region of deletion collections. Two sets of deletion collections have been constructed using the same primer set. The deleted regions are the same between Keio and Barcode collections. FRT in the Keio and FRT1 of the Barcode collection are not site-specifically recombined by FLP recombinase.

Figure 5.

Flowchart of evaluation by the latest GenBank annotation. All of resources are generated by DNA primers, which are designed according to the latest annotation at the time of construction.

Figure 6.

Differences with annotation. Each of resource pages for target gene shows inconsistency if it exists. (A) ASKA GFP(+), ASKA GFP(−) and Gateway entry clone validation. (B) TransBac library. (C) Keio and Barcode deletion collections.

Figure 7.

Sample screen images. (A) Sample pages of plasmid clone libraries. Schematic view of inconsistency and cloned region of target genes in nucleotide level. (B) Schematic view of deletion collection. (C) Omics results of each of the target gene. (D) BIOLOG phenotype analysis results in global, gene and plate level view.

Figure 7.

Sample screen images. (A) Sample pages of plasmid clone libraries. Schematic view of inconsistency and cloned region of target genes in nucleotide level. (B) Schematic view of deletion collection. (C) Omics results of each of the target gene. (D) BIOLOG phenotype analysis results in global, gene and plate level view.

Figure 8.

Overlap with no influence. In the case of 4 nt (ATGA) overlap between the target and the upstream genes, the termination codon of the upstream gene is re-generated in deletion strain.