Limits...
Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.

Hermida L, Poussin C, Stadler MB, Gubian S, Sewer A, Gaidatzis D, Hotz HR, Martin F, Belcastro V, Cano S, Peitsch MC, Hoeng J - BMC Genomics (2013)

Bottom Line: Therefore, it is important to systematically store the full list of genes with their associated statistical analysis results (differential expression, t-statistics, p-value) corresponding to one or more effect(s) or contrast(s) of interest (shortly termed as " contrast data") in a comparable manner and extract gene sets in order to efficiently support downstream analyses and further leverage data on a long-term basis.Filling this gap would open new research perspectives for biologists to discover disease-related biomarkers and to support the understanding of molecular mechanisms underlying specific biological perturbation effects (e.g. disease, genetic, environmental, etc.).To illustrate Confero platform functionality we walk through major aspects of the Confero workflow and results using the Bioconductor estrogen package dataset.

View Article: PubMed Central - HTML - PubMed

Affiliation: Philip Morris International Research & Development, Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland. leandro@leandrohermida.com

ABSTRACT

Background: High-throughput omics technologies such as microarrays and next-generation sequencing (NGS) have become indispensable tools in biological research. Computational analysis and biological interpretation of omics data can pose significant challenges due to a number of factors, in particular the systems integration required to fully exploit and compare data from different studies and/or technology platforms. In transcriptomics, the identification of differentially expressed genes when studying effect(s) or contrast(s) of interest constitutes the starting point for further downstream computational analysis (e.g. gene over-representation/enrichment analysis, reverse engineering) leading to mechanistic insights. Therefore, it is important to systematically store the full list of genes with their associated statistical analysis results (differential expression, t-statistics, p-value) corresponding to one or more effect(s) or contrast(s) of interest (shortly termed as " contrast data") in a comparable manner and extract gene sets in order to efficiently support downstream analyses and further leverage data on a long-term basis. Filling this gap would open new research perspectives for biologists to discover disease-related biomarkers and to support the understanding of molecular mechanisms underlying specific biological perturbation effects (e.g. disease, genetic, environmental, etc.).

Results: To address these challenges, we developed Confero, a contrast data and gene set platform for downstream analysis and biological interpretation of omics data. The Confero software platform provides storage of contrast data in a simple and standard format, data transformation to enable cross-study and platform data comparison, and automatic extraction and storage of gene sets to build new a priori knowledge which is leveraged by integrated and extensible downstream computational analysis tools. Gene Set Enrichment Analysis (GSEA) and Over-Representation Analysis (ORA) are currently integrated as an analysis module as well as additional tools to support biological interpretation. Confero is a standalone system that also integrates with Galaxy, an open-source workflow management and data integration system. To illustrate Confero platform functionality we walk through major aspects of the Confero workflow and results using the Bioconductor estrogen package dataset.

Conclusion: Confero provides a unique and flexible platform to support downstream computational analysis facilitating biological interpretation. The system has been designed in order to provide the researcher with a simple, innovative, and extensible solution to store and exploit analyzed data in a sustainable and reproducible manner thereby accelerating knowledge-driven research. Confero source code is freely available from http://sourceforge.net/projects/confero/.

Show MeSH

Related in: MedlinePlus

Screenshot of Confero platform integrated in Galaxy. Confero platform is a standalone application that can be used via the command line. However, for non-programmatic users and to provide flexibility, Confero platform has been integrated into Galaxy. The window shows three main frames: 1) the first frame on the left contains all Confero tools (also see Additional file 1: Table S1) to import data (DATA IMPORT), manage and export data from Confero (DATA MANAGEMENT AND EXPORT), run GSEA or ORA and manage results (FUNCTIONAL ENRICHMENT ANALYSIS MODULE); 2) the second frame in the middle generally displays the web page with the menu when selecting a tool, and results once the job is done; 3) the third frame on the right contains all the history of actions/results performed during an analysis. This history is saved and the user can investigate the results of the analysis at any time. The user has also the possibility to share the history with other users that have an account in Galaxy.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3750322&req=5

Figure 3: Screenshot of Confero platform integrated in Galaxy. Confero platform is a standalone application that can be used via the command line. However, for non-programmatic users and to provide flexibility, Confero platform has been integrated into Galaxy. The window shows three main frames: 1) the first frame on the left contains all Confero tools (also see Additional file 1: Table S1) to import data (DATA IMPORT), manage and export data from Confero (DATA MANAGEMENT AND EXPORT), run GSEA or ORA and manage results (FUNCTIONAL ENRICHMENT ANALYSIS MODULE); 2) the second frame in the middle generally displays the web page with the menu when selecting a tool, and results once the job is done; 3) the third frame on the right contains all the history of actions/results performed during an analysis. This history is saved and the user can investigate the results of the analysis at any time. The user has also the possibility to share the history with other users that have an account in Galaxy.

Mentions: The Confero platform enables one to 1) convert contrast data coming from statistical analysis into a simple and standard data format, 2) process contrast data and extract gene sets, 3) store contrast data, gene sets and metadata, 4) process and store external ID lists of interest as gene sets, 5) analyze and interpret stored data using integrated tools (e.g. GSEA, ORA) and a priori knowledge sources (e.g. Confero DB, MSigDB [17], GeneSigDB [23,24]), and 6) facilitate subsequent downstream analysis with a variety of data transformation and export tools. Confero runs as a standalone system and, as shown in FigureĀ 3, all platform modules are also integrated with the Galaxy workflow management system [11-13]. An overview of all available Confero tools with high-level description is summarized in the Additional file 1: Table S1.


Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.

Hermida L, Poussin C, Stadler MB, Gubian S, Sewer A, Gaidatzis D, Hotz HR, Martin F, Belcastro V, Cano S, Peitsch MC, Hoeng J - BMC Genomics (2013)

Screenshot of Confero platform integrated in Galaxy. Confero platform is a standalone application that can be used via the command line. However, for non-programmatic users and to provide flexibility, Confero platform has been integrated into Galaxy. The window shows three main frames: 1) the first frame on the left contains all Confero tools (also see Additional file 1: Table S1) to import data (DATA IMPORT), manage and export data from Confero (DATA MANAGEMENT AND EXPORT), run GSEA or ORA and manage results (FUNCTIONAL ENRICHMENT ANALYSIS MODULE); 2) the second frame in the middle generally displays the web page with the menu when selecting a tool, and results once the job is done; 3) the third frame on the right contains all the history of actions/results performed during an analysis. This history is saved and the user can investigate the results of the analysis at any time. The user has also the possibility to share the history with other users that have an account in Galaxy.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750322&req=5

Figure 3: Screenshot of Confero platform integrated in Galaxy. Confero platform is a standalone application that can be used via the command line. However, for non-programmatic users and to provide flexibility, Confero platform has been integrated into Galaxy. The window shows three main frames: 1) the first frame on the left contains all Confero tools (also see Additional file 1: Table S1) to import data (DATA IMPORT), manage and export data from Confero (DATA MANAGEMENT AND EXPORT), run GSEA or ORA and manage results (FUNCTIONAL ENRICHMENT ANALYSIS MODULE); 2) the second frame in the middle generally displays the web page with the menu when selecting a tool, and results once the job is done; 3) the third frame on the right contains all the history of actions/results performed during an analysis. This history is saved and the user can investigate the results of the analysis at any time. The user has also the possibility to share the history with other users that have an account in Galaxy.
Mentions: The Confero platform enables one to 1) convert contrast data coming from statistical analysis into a simple and standard data format, 2) process contrast data and extract gene sets, 3) store contrast data, gene sets and metadata, 4) process and store external ID lists of interest as gene sets, 5) analyze and interpret stored data using integrated tools (e.g. GSEA, ORA) and a priori knowledge sources (e.g. Confero DB, MSigDB [17], GeneSigDB [23,24]), and 6) facilitate subsequent downstream analysis with a variety of data transformation and export tools. Confero runs as a standalone system and, as shown in FigureĀ 3, all platform modules are also integrated with the Galaxy workflow management system [11-13]. An overview of all available Confero tools with high-level description is summarized in the Additional file 1: Table S1.

Bottom Line: Therefore, it is important to systematically store the full list of genes with their associated statistical analysis results (differential expression, t-statistics, p-value) corresponding to one or more effect(s) or contrast(s) of interest (shortly termed as " contrast data") in a comparable manner and extract gene sets in order to efficiently support downstream analyses and further leverage data on a long-term basis.Filling this gap would open new research perspectives for biologists to discover disease-related biomarkers and to support the understanding of molecular mechanisms underlying specific biological perturbation effects (e.g. disease, genetic, environmental, etc.).To illustrate Confero platform functionality we walk through major aspects of the Confero workflow and results using the Bioconductor estrogen package dataset.

View Article: PubMed Central - HTML - PubMed

Affiliation: Philip Morris International Research & Development, Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland. leandro@leandrohermida.com

ABSTRACT

Background: High-throughput omics technologies such as microarrays and next-generation sequencing (NGS) have become indispensable tools in biological research. Computational analysis and biological interpretation of omics data can pose significant challenges due to a number of factors, in particular the systems integration required to fully exploit and compare data from different studies and/or technology platforms. In transcriptomics, the identification of differentially expressed genes when studying effect(s) or contrast(s) of interest constitutes the starting point for further downstream computational analysis (e.g. gene over-representation/enrichment analysis, reverse engineering) leading to mechanistic insights. Therefore, it is important to systematically store the full list of genes with their associated statistical analysis results (differential expression, t-statistics, p-value) corresponding to one or more effect(s) or contrast(s) of interest (shortly termed as " contrast data") in a comparable manner and extract gene sets in order to efficiently support downstream analyses and further leverage data on a long-term basis. Filling this gap would open new research perspectives for biologists to discover disease-related biomarkers and to support the understanding of molecular mechanisms underlying specific biological perturbation effects (e.g. disease, genetic, environmental, etc.).

Results: To address these challenges, we developed Confero, a contrast data and gene set platform for downstream analysis and biological interpretation of omics data. The Confero software platform provides storage of contrast data in a simple and standard format, data transformation to enable cross-study and platform data comparison, and automatic extraction and storage of gene sets to build new a priori knowledge which is leveraged by integrated and extensible downstream computational analysis tools. Gene Set Enrichment Analysis (GSEA) and Over-Representation Analysis (ORA) are currently integrated as an analysis module as well as additional tools to support biological interpretation. Confero is a standalone system that also integrates with Galaxy, an open-source workflow management and data integration system. To illustrate Confero platform functionality we walk through major aspects of the Confero workflow and results using the Bioconductor estrogen package dataset.

Conclusion: Confero provides a unique and flexible platform to support downstream computational analysis facilitating biological interpretation. The system has been designed in order to provide the researcher with a simple, innovative, and extensible solution to store and exploit analyzed data in a sustainable and reproducible manner thereby accelerating knowledge-driven research. Confero source code is freely available from http://sourceforge.net/projects/confero/.

Show MeSH
Related in: MedlinePlus