CauloBrowser: A systems biology resource for Caulobacter crescentus

Abstract

Caulobacter crescentus is a premier model organism for studying the molecular basis of cellular asymmetry. The Caulobacter community has generated a wealth of high-throughput spatiotemporal databases including data from gene expression profiling experiments (microarrays, RNA-seq, ChIP-seq, ribosome profiling, LC-ms proteomics), gene essentiality studies (Tn-seq), genome wide protein localization studies, and global chromosome methylation analyses (SMRT sequencing). A major challenge involves the integration of these diverse data sets into one comprehensive community resource. To address this need, we have generated CauloBrowser (www.caulobrowser.org), an online resource for Caulobacter studies. This site provides a user-friendly interface for quickly searching genes of interest and downloading genome-wide results. Search results about individual genes are displayed as tables, graphs of time resolved expression profiles, and schematics of protein localization throughout the cell cycle. In addition, the site provides a genome viewer that enables customizable visualization of all published high-throughput genomic data. The depth and diversity of data sets collected by the Caulobacter community makes CauloBrowser a unique and valuable systems biology resource.

Figure 1.

Screenshot of CauloBrowser overview section. The figure shows the overview section search results for genes ctrA, ftsZ and popZ. The results are organized as a table with a row per data category and a column per gene. Links to central databases such as KEGG, BioCyc, NCBI, and UniProt are colored in light blue. The ‘Actions’ row provides two buttons. ‘Go to genome viewer’ links to our Caulobacter genome viewer page zoomed to the region of the corresponding ORF. ‘Remove gene’ removes the gene from the display.

Figure 2.

Screenshot of CauloBrowser sections 2–5. The figure shows sections 2–5 search results for genes ctrA (red), ftsZ (blue), and popZ (green). Time resolved expression data (sections 2,4) is visualized using plots of gene expression across the cell cycle in wild type or different growth conditions and mutant background. Gene expression collection data (section 3) is organized as a table with a row per experiment and a column per gene. Relevant PubMed references (section 5) are listed with links to corresponding PubMed entries.

Figure 3.

Screenshot of the genome viewer. The figure shows our genomic viewer zoomed to genomic coordinates 3 277 948–3 285 141. Nine tracks are open demonstrating the power of simultaneously visualizing data from different experiments. The top ENSEMBL track shows NA1000 genome annotation with forward genes in red and reverse genes in blue. The second track shows the Caulobacter operon structure. Seven additional tracks are shown visualizing multiple Chip-seq and RNS-seq experiments. A list of all available data sets is shown to the right.