GeneSCF protocols

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GeneSCF specifications

Information


Unique identifier OMICS_10275
Name GeneSCF
Alternative name Gene Set Clustering based on Functional annotation
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data The standard input for GeneSCF is plain text document (text/plain) containing a list of genes in the form of official gene symbols.
Output data The final output from GeneSCF is a table (text/tab-separated file, TSV) with list of ranked functions based on the number of hits from the user provided gene list. It also contains column with probability value (P-value) obtained by Fisher’s exact test using the contingency table and also columns containing false discovery rate (FDR) values using different multiple hypothesis correction methods.
Operating system Unix/Linux
Programming languages Perl, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1
Stability Stable
Requirements
R, ggplot
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

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Documentation


Maintainer


  • person_outline Chandrasekhar Kanduri <>

Publications for Gene Set Clustering based on Functional annotation

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GeneSCF: a real-time based functional enrichment tool with support for multiple organisms.

2016 BMC Bioinformatics
PMCID: 5020511
PMID: 27618934
DOI: 10.1186/s12859-016-1250-z

GeneSCF in pipeline

2018
PMCID: 5830406
PMID: 29491376
DOI: 10.1038/s41467-018-03265-1

[…] the significant candidates were filtered with log-fold change > ± 1 and fdr ≤ 0.05., the significantly deregulated genes from sirna knockdown samples were tested for pathway enrichment using tool genescf v1.1. the parameters for genescf were set to database reactome with background genes 20,345 (all protein-coding genes from gencode v19 annotation used in this study). the enriched functions […]


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GeneSCF in publications

 (2)
PMCID: 5830406
PMID: 29491376
DOI: 10.1038/s41467-018-03265-1

[…] using the serum starvation method (supplementary fig. ).fig. 1, since lncrnas exert their actions via regulating protein-coding rnas in cis and/or trans–, we performed enrichment analysis using genescf for the neighboring protein-coding genes (within ±50 kb window of s-phase-specific lncrnas). interestingly, the neighboring protein-coding genes associated with etu-labeled s-phase-specific […]

PMCID: 5062931
PMID: 27777635
DOI: 10.1186/s13148-016-0274-6

[…] repeat elements obtained.fig. 2 , the pathway enrichment analysis and cancer enrichment analysis on clldmgs was carried out with the help of a command line functional enrichment tool called genescf v1.1 (gene set clustering based on functional annotation) [, ]. we used genescf with parameters, two different database kegg pathways and ncg (network of cancer genes 4.0) [], ensembl […]


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GeneSCF institution(s)
Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
GeneSCF funding source(s)
This work was supported by the grants from the Knut and Alice Wallenberg Foundation (KAW) (Dnr KAW 2014.0057), Swedish Foundation for Strategic Research (RB13-0204), Swedish Cancer Research foundation (Cancerfonden: Kontrakt no. 150796), the Swedish Research Council (VR-M: K2014-67X-20781-07-4), Barncancerfonden (PR2014/0147), Ingabritt Och Arne Lundbergs forskningsstiftelse and LUA/ALF.

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