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. 2015 Jan 6:3:e717.
doi: 10.7717/peerj.717. eCollection 2015.

SATRAT: Staphylococcus aureus transcript regulatory network analysis tool

Tamilselvi Gopal  1 , Vijayaraj Nagarajan  2 , Mohamed O Elasri  3
Affiliations

SATRAT: Staphylococcus aureus transcript regulatory network analysis tool

Tamilselvi Gopal et al. PeerJ. .

Abstract

Staphylococcus aureus is a commensal organism that primarily colonizes the nose of healthy individuals. S. aureus causes a spectrum of infections that range from skin and soft-tissue infections to fatal invasive diseases. S. aureus uses a large number of virulence factors that are regulated in a coordinated fashion. The complex regulatory mechanisms have been investigated in numerous high-throughput experiments. Access to this data is critical to studying this pathogen. Previously, we developed a compilation of microarray experimental data to enable researchers to search, browse, compare, and contrast transcript profiles. We have substantially updated this database and have built a novel exploratory tool-SATRAT-the S. aureus transcript regulatory network analysis tool, based on the updated database. This tool is capable of performing deep searches using a query and generating an interactive regulatory network based on associations among the regulators of any query gene. We believe this integrated regulatory network analysis tool would help researchers explore the missing links and identify novel pathways that regulate virulence in S. aureus. Also, the data model and the network generation code used to build this resource is open sourced, enabling researchers to build similar resources for other bacterial systems.

Keywords: Infectious disease; RNA sequencing; RNA-Seq; Staphylococcus aureus; Staphylococcus aureus microarray meta-database (SAMMD); Staphylococcus aureus transcriptome meta-database (SATMD); Transcript regulatory network; Transcriptome.

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Figures

Figure 1
Figure 1. Redesigned SATMD.
Redesigned Staphylococcus aureus transcriptome meta-database (SATMD) website home page showing 42 strain-based search filters.
Figure 2
Figure 2. Search result.
SATMD basic gene search result for the hypothetical protein SA1030.
Figure 3
Figure 3. SATRAT.
Visualization of associations among regulators of SA1030 using the Staphylococcus aureus transcript regulatory network analysis tool (SATRAT).
Figure 4
Figure 4. SATMD usage.
Distribution of visits to the older version of SATMD.
Figure 5
Figure 5. SATRAT case study.
Transcript regulatory network of SA1030.
See this image and copyright information in PMC

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