FUNC protocols

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FUNC specifications

Information


Unique identifier OMICS_17697
Name FUNC
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format CSV
Operating system Unix/Linux
Programming languages C++, Perl, Shell (Bash)
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.4.7
Stability Stable
Requirements
libRmath
Source code URL https://func.eva.mpg.de/func-0.4.7.tar.gz
Maintained Yes

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Publication for FUNC

FUNC in pipeline

2014
PMCID: 3916258
PMID: 24516681
DOI: 10.1371/journal.pntd.0002678

[…] the kegg database using kaas . proteins with signal peptides and transmembrane were identified using the phobius web server, and non-classical secretion was predicted using secretomep 1.0 . func (which considers the hierarchical structure of go) was used to determine significant functional enrichment among the genes overexpressed in each tissue, with a p≤0.01 significance threshold […]


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FUNC in publications

 (27)
PMCID: 5543596
PMID: 28778150
DOI: 10.1186/s12862-017-1018-8

[…] ld with a snp that has been associated with the corresponding phenotype with a p-value of at least 1e-5., enrichment of indels in specific gene categories was tested using the software package func version 0.4.7 []. for this, we selected indels that were assigned to genes based on the vep annotation and further annotated these indels to gene categories used the gene ontology. to account […]

PMCID: 5118908
PMID: 27920789
DOI: 10.3389/fpls.2016.01744

[…] trichomes, and that exhibited either ≥3-fold lower expression or no expression at all in either mutant gl3-sst sim trichomes or wild-type shoots, was then selected as trichome-specific., we used func_hyper and func_hyper_refin in func 0.4.7 () to identify non-redundant go terms that were statistically overrepresented among groups of protein-coding genes. these groups primarily consisted […]

PMCID: 5020434
PMID: 27619014
DOI: 10.1186/s13071-016-1785-x

[…] identity over at least 50 % of the length with the human ortholog but less than 50 % identity (if any) with the s. mediterranea ortholog., functional enrichment of go terms was calculated using func with a p-value cut-off of 0.01 []. in all cases, the target list was comprised of the longest transcript of each unigene associated with the feature of interest and the background list […]

PMCID: 4802047
PMID: 26988143
DOI: 10.1038/ncomms10775

[…] obtained by resampling 5,000 times random alleles from the corresponding danc distribution to fit the number of alleles in the tail., gene ontology analysis was performed using the software package func. we analysed the union of all alleles in the four european danc tails (with p1=yri and p2=gbr, fin, ceu or tsi), for snps that fall into protein-coding genes (ensembl gene annotation […]

PMCID: 4860691
PMID: 26979798
DOI: 10.1093/gbe/evw059

[…] and genomes (kegg) pathway () databases. differentially expressed genes were tested for enrichment by comparing them with all expressed genes using a hypergeometric test. for the go, we used the func package () and defined functional categories to be significantly overrepresented if the corresponding family-wise error rate (fwer) was smaller than 0.05. overrepresentation of differentially […]


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FUNC institution(s)
Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany; Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
FUNC funding source(s)
This work was supported by the Bundesministerium für Bildung und Forschung, the Max Planck Society, the European Commission's Sixth Framework Programme for New and Emerging Science and Technology (PKB140404) and the Deutsche Forschungsgemeinschaft.

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