SYSTOMONAS -- an integrated database for systems biology analysis of Pseudomonas

Choi, Claudia; Münch, Richard; Leupold, Stefan; Klein, Johannes; Siegel, I.; Thielen, Bernhard; Benkert, Beatrice; Kucklick, Martin; Schobert, Max; Barthelmes, Jens; Ebeling, Christian; Haddad, Isam; Scheer, Maurice; Grote, Andreas; Hiller, Karsten; Bunk, Boyke; Schreiber, Kerstin; Retter, Ida; Schomburg, Dietmar; Jahn, Dieter

doi:10.1093/nar/gkl823

Cited by 53 publications

(22 citation statements)

References 27 publications

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“…SYSTOMONAS is a dedicated database for system biology studies of Pseudomonas spp. The database utilizes comparative genomic tools to reconstruct metabolic networks and has an extensive transcriptomic, metabolomic and proteomic data from pseudomonads (Choi et al 2007). MetaCyc metabolic pathway database contains both primary and secondary pathways information, enzymes, genes, and associated compounds of several pseudomonad species (Caspi et al 2016).…”

Section: Metabolic Pathways Databases To Identify Secondary Metabolitmentioning

confidence: 99%

A decade of understanding secondary metabolism in Pseudomonas spp. for sustainable agriculture and pharmaceutical applications

Shahid

Malik

Mehnaz

2018

Environmental Sustainability

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Pseudomonas spp. have been widely studied for their plant growth promoting and antimicrobial metabolites. The genus got attention due to the production of array of secondary metabolites involved in the suppression of phytopathogens and ability to stimulate plant growth by means of nitrogen-fixation, production of hydrolytic enzymes, regulatory hormones, and solubilization of inorganic minerals. In recent years, research was focused towards identification of biosynthesis pathways and genes involved in the production of secondary metabolites that led to the discovery of novel metabolites including many new phenazine derivatives, quorum-sensing signals, rhizoxin analogues, cyclic lipopeptides, and a new class of alkylsubstituted aromatic acids. Identification of these biosynthetic pathways provided insights for their successful application in agriculture and for environmental sustainability. In addition, many genomic and metabolomic databases such as; METLIN, KEGG, GNPS, CFM-ID, MassBank, and MetaboLights, allowed exploring intricate metabolic pathways and significant genes involved in the biosynthesis of compounds. Several softwares, genome-mining tools and new techniques, such as MALDI-IMS and MALDI-FTICR MS were developed to facilitate the characterization of new metabolites. Additionally, use of MALDI-imaging techniques facilitated real-time visualization of complex microbial communities and their relationship with pathogens. Secondary metabolites of Pseudomonas spp. were also demonstrated for their apoptotic, anti-mitotic, nematocidal, herbicidal, anthelmintic, insecticidal, and phytotoxic effects. Total biosynthesis of metabolic derivatives and genetic engineering enabled to develop strains with improved yield of targeted bio-products. Availability and access to published genomic sequences and comparative bioinformatics tools helped in identification of strain-specific traits and development of multifunctional inocula. This review highlights significant advances in identification of Pseudomonas secondary metabolites for their successful agricultural and pharmaceutical applications.

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Section: Metabolic Pathways Databases To Identify Secondary Metabolitmentioning

confidence: 99%

A decade of understanding secondary metabolism in Pseudomonas spp. for sustainable agriculture and pharmaceutical applications

Shahid

Malik

Mehnaz

2018

Environmental Sustainability

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“…Store data related to metabolome, proteome and transcriptome data and gene-regulatory networks [33]. The Systems Biology Researcher Database (SysBiolDB) Offers exchange of information worldwide for all systems biology scientists [34] 2.…”

Section: Systomonas Genome Databasementioning

confidence: 99%

System Biology-A Computational Platform for Biological Research

2018

International Journal of Research Studies in Biosciences

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“…In Atlas, the data warehouse, the biological Systomonas is an integrated informatics platform that has been developed for systems biology approach and for the analysis of the biology of pseudomonas in biotechnology and in infection. It stores the prediction information of cellular processes such as gene regulatory networks along with the in-house experimental metabolome, proteome and transcriptome data (Choi et al 2007). Columba integrates several databases like PDB, KEGG, Swiss-Prot, CATH, SCOP, the Gene Ontology, and ENZYME.…”

Section: Bio-data Warehousing Approachmentioning

confidence: 99%

BioSilicoSystems - A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

Hariharaputran

2010

Nat Prec

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The rising field of integrative bioinformatics provides the vital methods to integrate, manage and also to analyze the diverse data and allows gaining new and deeper insights and a clear understanding of the intricate biological systems. The difficulty is not only to facilitate the study of heterogeneous data within the biological context, but it also more fundamental, how to represent and make the available knowledge accessible. Moreover, adding valuable information and functions that persuade the user to discover the interesting relations hidden within the data is, in itself, a great challenge. Also, the cumulative information can provide greater biological insight than is possible with individual information sources. Furthermore, the rapidly growing number of databases and data types poses the challenge of integrating the heterogeneous data types, especially in biology. This rapid increase in the volume and number of data resources drive for providing polymorphic views of the same data and often overlap in multiple resources.In this thesis a multi-pronged approach is proposed that deals with various methods for the analysis and representation of the diverse biological data which are present in different data sources. This is an effort to explain and emphasize on different concepts which are developed for the analysis of molecular data and also to explain its biological significance. The hypotheses proposed are in context with various other results and findings published in the past. The approach demonstrated also explains different ways to integrate the molecular data from various sources along with the need for a comprehensive understanding and clear projection of the concept or the algorithm and its results, but with simple means and methods. The multifarious approach proposed in this work comprises of different tools or methods spanning significant areas of bioinformatics research such as data integration, data visualization, biological network construction / reconstruction and alignment of biological pathways. Each tool deals with a unique approach to utilize the molecular data for different areas of biological research and is built based on the kernel of the thesis. Furthermore these methods are combined with graphical representation that make things simple and comprehensible and also helps to understand with ease the underlying biological complexity. Moreover the human eye is often used to and it is more comfortable with the visual representation of the facts.

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SYSTOMONAS -- an integrated database for systems biology analysis of Pseudomonas

Cited by 53 publications

References 27 publications

A decade of understanding secondary metabolism in Pseudomonas spp. for sustainable agriculture and pharmaceutical applications

A decade of understanding secondary metabolism in Pseudomonas spp. for sustainable agriculture and pharmaceutical applications

System Biology-A Computational Platform for Biological Research

BioSilicoSystems - A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

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