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FIDEA specifications

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Unique identifier OMICS_01539
Name FIDEA
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for FIDEA

FIDEA in pipelines

 (2)
2016
PMCID: 5099522
PMID: 27877172
DOI: 10.3389/fmicb.2016.01786

[…] by the grants from the national natural science foundation of china (31330005 and 20875061)., http://support.illumina.com/sequencing/sequencing_software/igenome.html , http://www.biocomputing.it/fidea , http://www-huber.embl.de/users/anders/htseq/ , http://bioinfogp.cnb.csic.es/tools/venny/index.html , http://www.informatics.jax.org/ , the supplementary material for this article […]

2016
PMCID: 5099522
PMID: 27877172
DOI: 10.3389/fmicb.2016.01786

[…] genes and transcripts whose |log2 (foldchange)|≥ 1 and adjusted p-value < 0.05 (fdr adjusted with benjamini–hochberg) were picked as significant ones., the enrichment analysis was performed with fidea (), and both up-regulated and down-regulated genes were considered. a threshold of 0.05 for q-value (fdr adjusted with benjamini–hochberg) was used to select significant enriched go and pathway […]

FIDEA in publications

 (7)
PMCID: 5830977
PMID: 28988989
DOI: 10.1016/j.stemcr.2017.09.004

[…] the change in the transcriptome detected in fus mutant cells might be informative of pathways potentially involved in als mn degeneration. gene ontology (go) term enrichment analysis with the fidea tool () highlighted relevant categories that cooperate in pathways and distinct molecular functions. in particular, we noticed a striking enrichment for categories related to cell adhesion […]

PMCID: 5511350
PMID: 28703137
DOI: 10.1038/ncomms16058

[…] overlap with pchi-c baits±10 kb and assigned to the gene(s) on the overlapping bait as we know that we lack sensitivity to detect short-range interactions between promoters and regulatory elements., fidea was used to determine enrichment of go terms in gene lists., the proteins encoded by the 781 protein-coding genes assigned to a gwas variant based on pchi-c and ld data were used as primary […]

PMCID: 5491171
PMID: 28662214
DOI: 10.1371/journal.pone.0180258

[…] processes but not visa versa. to determine the functional relevance of these common targets, we performed pathway analyses using the functional interpretation of differential expression analysis (fidea) program, a program that can be used to analyze various types of differential expression data []. two different databases were used with the fidea program; (1) the kyoto encyclopedia of genes […]

PMCID: 5316204
PMID: 28212627
DOI: 10.1186/s12864-017-3561-5

[…] referred to the ensembl annotation and for micrornas to the mirbase database v18 []., all protein-coding genes with putative hbx binding sites (promoters or intragenic) were analysed by david [] and fidea [] web servers using kegg [] and reactome pathways [, ], the interpro families [] and the gene ontology (go) biological processes []. only biological terms with benjamini-corrected p-value <  […]

PMCID: 5241696
PMID: 28098217
DOI: 10.1038/srep40775

[…] targets. moreover, 105 genes from this list were positive for rorc binding based on chip-seq results by takeda et al. and a further 49 differentially expressed (mostly downregulated) in runts (, ). fidea showed that these genes are primarily involved amino acid metabolism ( and 7)., the progressive increase in the number of de genes between males and females () is in agreement with the current […]

FIDEA institution(s)
Department of Physics, Sapienza University, Rome, Italy

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