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FungiFun specifications

Information


Unique identifier OMICS_05903
Name FungiFun
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.2.8
Stability Beta
Maintained Yes

Maintainer


  • person_outline Steffen Priebe <>

Publications for FungiFun

FungiFun in pipelines

 (7)
2017
PMCID: 5298990
PMID: 28232843
DOI: 10.3389/fpls.2017.00148

[…] ), respectively. those genes encoding proteins with a signal peptide and no transmembrane segment were identified as effector candidates. for go annotation, genes of interest were submitted to the fungifun (priebe et al., , ) and the venn diagram was constructed using venny v2.1 (bioinfogp)., jw analyzed the data and wrote the manuscript; ss analyzed the data and contributed to the manuscript; […]

2017
PMCID: 5381528
PMID: 28338982
DOI: 10.1093/gbe/evx052

[…] f. graminearum editing sites found by and with putative editing sites identified in sexual tissue from p. confluens. functional classification of genes with putative editing sites was done using fungifun 2 () with the funcat ontology (), or ontologizer () based on gene ontology (go) annotations from uniprot (, )., to verify that the observed variants are indeed editing sites and not errors […]

2017
PMCID: 5415137
PMID: 28467453
DOI: 10.1371/journal.pone.0176485

[…] discovery rate (fdr) <0.01 and fold changes >2 [,,]. the degs were annotated by blast searching against non-redundant protein sequences (nr) and swiss-prot databases and then subjected to the fungifun2 web-based sever to interrogate the functional enrichment of funcat and gene ontologies []. rna-seq data were deposited in ncbi's sequence read archive (sra) with accession number srp073233. […]

2017
PMCID: 5435353
PMID: 28467421
DOI: 10.1371/journal.pgen.1006737

[…] bam files were first processed using the htseq package v0.6.0 [] to generate raw counts, and the raw counts are subjected to differential analysis using the deseq2 package version 1.10.1 []., the fungifun2 online resource tool was used in functional enrichment analysis (https://elbe.hki-jena.de/fungifun/fungifun.php) []. the gene to category associations was tested for over-representation […]

2017
PMCID: 5559454
PMID: 28814742
DOI: 10.1038/s41598-017-08239-9

[…] p-values were adjusted to determine differentially regulated genes. venn diagrams were created by venny 2.0.2 (http://bioinfogp.cnb.csic.es/tools/venny/index.html). go analysis was carried out with fungifun2 (https://elbe.hki-jena.de/fungifun/fungifun.php). the whole dataset of detected protein-coding genes and their expression can be found in table ., sequence information for all c. albicans […]


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FungiFun in publications

 (38)
PMCID: 5946477
PMID: 29747589
DOI: 10.1186/s12864-018-4730-x

[…] ion count (≥2 for medium confidence, ≥4 for high confidence). furthermore, the average variability was observed as a function of the differential regulation and the precursor ion count., the fungifun2 package (https://elbe.hki-jena.de/fungifun/fungifun.php), with default settings was used to test the enrichment of genes related to funcat and kegg pathway categories in stress responsive […]

PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] accessed through interpro version 64.0 (https://www.ebi.ac.uk/interpro/) using interproscan 5,. in addition, the secreted proteins in aspergillus species were annotated with go terms using fungifun2 (https://elbe.hki-jena.de/fungifun/fungifun.php). supplementary table  contains detailed annotations for secreted and cell membrane proteins in aspergillus species., in the predicted […]

PMCID: 5925793
PMID: 29491142
DOI: 10.1074/jbc.M117.813741

[…] process annotations, in differentially expressed genes (degs), we employed david (database for annotation, visualization, and integrated discovery; https://david.ncifcrf.gov)5 (, ) and the fungifun2 tool (https://elbe.hki-jena.de/fungifun/fungifun.php)5 (). go categories ion transport (go:0006811; p = 0.0002) and oxidation-reduction process (go:0055114; p = 0.0002) were enriched […]

PMCID: 5780349
PMID: 29403478
DOI: 10.3389/fimmu.2017.01997

[…] to the different condition. data were expressed as fold change in logarithmic scale. microarray data are public available to the geo repository, under the accession number gse85138. david () and fungifun 2.0 tools () were used for functional enrichment analysis on degs, using default parameters (therefore considering as valid results with a p-value <0.05). heatmap visualization […]

PMCID: 5793092
PMID: 29271897
DOI: 10.3390/toxins10010005

[…] principle component analysis plots and heat maps were generated using r. venn diagrams were created by biovenn []. gene ontology term enrichment analysis for wgcna clusters was conducted using fungifun2 []. rendering of gene networks was performed using cytoscape v3.4.0 []. kegg annotation was produced through the blastkoala [] service., rna for qpcr was isolated using the rneasy plant […]


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FungiFun institution(s)
Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute (HKI), Jena, Germany

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