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GenExp specifications

Information


Unique identifier OMICS_09082
Name GenExp
Interface Web user interface
Restrictions to use None
License GNU General Public License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainer


  • person_outline Bernat Gel Moreno

Publication for GenExp

GenExp citations

 (4)
library_books

A Computational Approach towards a Gene Regulatory Network for the Developing Nematostella vectensis Gut

2014
PLoS One
PMCID: 4116165
PMID: 25076223
DOI: 10.1371/journal.pone.0103341

[…] are picked from these average geometries for interpolation of subsequent geometries, to obtain a continuous range of embryo morphologies., published and raw gene expression images are imported into genexp, a matlab interface to quantify gene expression patterns. the expression profile is extracted as described in . a prototype morphology is overlaid with the image (). the selected morphology […]

library_books

Cell Type Specific Features of Circular RNA Expression

2013
PLoS Genet
PMCID: 3764148
PMID: 24039610
DOI: 10.1371/journal.pgen.1003777

[…] for each circular isoform represented by at least 50 counts in one sample (and satisfying an fdr cut-off of .025), we fit a poisson model per gene modeling circle counts by poly(a) gene expression (genexp), celltype and total circles (totcircles) using the glm poisson model in r with the formula:, cir∼log(genexp)+celltype+totcircles−1. coefficients in this model were used to choose genes shown […]

library_books

Inferring robust gene networks from expression data by a sensitivity based incremental evolution method

2012
BMC Bioinformatics
PMCID: 3348052
PMID: 22595005
DOI: 10.1186/1471-2105-13-S7-S8

[…] 5 = 10 . 0 x 4 2 . 0 - 10 . 0 x 5 2 . 0 , the second dataset was taken from []. it was an eight-gene network created manually by the popular grn simulation software tool genexp. the third dataset was a ten-node network previously described in [], given by the following equations:, ẋ 1 = 5 . 0 x 4 x 6 - 2 . 0 - 10 . 0 x 1 2 . 0 […]

library_books

Applying Intelligent Computing Techniques to Modeling Biological Networks from Expression Data

2008
PMCID: 5054112
PMID: 18973867
DOI: 10.1016/S1672-0229(08)60026-1

[…] network model can be built successfully by the gp approach., to evaluate our approach for the network-based model, we firstly used the well-known gene regulatory network simulation software genexp to produce expression data, and then employed our computational approach to infer network models from the data. a four-node network was defined in which the accumulation and degradation rate […]


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GenExp institution(s)
Software Department, UPC-BarcelonaTech, Barcelona, Spain
GenExp funding source(s)
Supported by the Departament d’Universitats, Recerca i Societat de la Informacio de la Generalitat de Catalunya and the projects SweetLogics (TIN2010-21062-C02-01) and LogicTools-2 (TIN 2007-68093-C02-01) funded by the Spanish Ministry of Science and Technology.

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