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FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species.

Priebe S, Kreisel C, Horn F, Guthke R, Linde J - Bioinformatics (2014)

Bottom Line: Enrichment analysis is often used to identify characteristic patterns in candidate lists.FungiFun is a user-friendly Web tool for functional enrichment analysis of fungal genes and proteins.The novel tool FungiFun2 uses a completely revised data management system and thus allows enrichment analysis for 298 currently available fungal strains published in standard databases.

View Article: PubMed Central - PubMed

Affiliation: Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.

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Overview of FungiFun2 functionality. (A) With help of a semi-automatic procedure, gene to category associations for three ontologies as well as gene names and functions are downloaded. The numbers in the Venn diagram indicate the number of available strains. (B) The user selects a strain and ontology. (C) On the Web server, gene to category association and significance tests are performed. (D) Schematic visualization of the output (dynamical figures, charts and tables) is shown
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btu627-F1: Overview of FungiFun2 functionality. (A) With help of a semi-automatic procedure, gene to category associations for three ontologies as well as gene names and functions are downloaded. The numbers in the Venn diagram indicate the number of available strains. (B) The user selects a strain and ontology. (C) On the Web server, gene to category association and significance tests are performed. (D) Schematic visualization of the output (dynamical figures, charts and tables) is shown

Mentions: Our group implemented the tool FungiFun (Priebe et al., 2010) supporting enrichment analysis for 28 species with a focus on fungal pathogens. In this article, we present the novel tool FungiFun2, which allows the systematic analysis of candidate lists from all the currently available fungal strains published in standard databases (Fig. 1). Users can choose from 298 strains of 240 species. For data collection, FungiFun2 uses a semi-automatic procedure, which downloads gene to category associations and annotations (names and functions) from online databases. This procedure allows the database to be kept up-to-date and simplifies the addition of further species. In comparison to the previous version, which worked with flat files for annotations, FungiFun2 parses annotation into a standardized database allowing higher data connectivity and flexibility, e. g. alternative input identifiers (IDs), gene annotation and complex search queries. Finally, FungiFun2 offers a modern and user-friendly interface.Fig. 1.


FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species.

Priebe S, Kreisel C, Horn F, Guthke R, Linde J - Bioinformatics (2014)

Overview of FungiFun2 functionality. (A) With help of a semi-automatic procedure, gene to category associations for three ontologies as well as gene names and functions are downloaded. The numbers in the Venn diagram indicate the number of available strains. (B) The user selects a strain and ontology. (C) On the Web server, gene to category association and significance tests are performed. (D) Schematic visualization of the output (dynamical figures, charts and tables) is shown
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4308660&req=5

btu627-F1: Overview of FungiFun2 functionality. (A) With help of a semi-automatic procedure, gene to category associations for three ontologies as well as gene names and functions are downloaded. The numbers in the Venn diagram indicate the number of available strains. (B) The user selects a strain and ontology. (C) On the Web server, gene to category association and significance tests are performed. (D) Schematic visualization of the output (dynamical figures, charts and tables) is shown
Mentions: Our group implemented the tool FungiFun (Priebe et al., 2010) supporting enrichment analysis for 28 species with a focus on fungal pathogens. In this article, we present the novel tool FungiFun2, which allows the systematic analysis of candidate lists from all the currently available fungal strains published in standard databases (Fig. 1). Users can choose from 298 strains of 240 species. For data collection, FungiFun2 uses a semi-automatic procedure, which downloads gene to category associations and annotations (names and functions) from online databases. This procedure allows the database to be kept up-to-date and simplifies the addition of further species. In comparison to the previous version, which worked with flat files for annotations, FungiFun2 parses annotation into a standardized database allowing higher data connectivity and flexibility, e. g. alternative input identifiers (IDs), gene annotation and complex search queries. Finally, FungiFun2 offers a modern and user-friendly interface.Fig. 1.

Bottom Line: Enrichment analysis is often used to identify characteristic patterns in candidate lists.FungiFun is a user-friendly Web tool for functional enrichment analysis of fungal genes and proteins.The novel tool FungiFun2 uses a completely revised data management system and thus allows enrichment analysis for 298 currently available fungal strains published in standard databases.

View Article: PubMed Central - PubMed

Affiliation: Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.

Show MeSH
Related in: MedlinePlus