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Protocols

maSigPro specifications

Information


Unique identifier OMICS_01990
Name maSigPro
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.52.0
Stability Stable
Requirements
stats, graphics, Biobase, grDevices, MASS, mclust, R(>=2.3.1), venn
Maintained Yes

Subtool


  • Iso-maSigPro

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Documentation


Publications for maSigPro

maSigPro citations

 (50)
library_books

Transcriptional profiling of human bronchial epithelial cell BEAS 2B exposed to diesel and biomass ultrafine particles

2018
BMC Genomics
PMCID: 5923024
PMID: 29703138
DOI: 10.1186/s12864-018-4679-9

[…] es of inflammation and oxidative stress, vasculature developments, was validated using qPCR (Table ). The 23 selected targets were manually chosen according to their inclusion in the gene set of next-maSigPro cluster and of GSEA hallmarks. Moreover, we proceeded with a deep literature mining analysis referring to specific keywords such as lung diseases, cardiovascular. Further details are reported […]

library_books

ArgR of Streptomyces coelicolor Is a Pleiotropic Transcriptional Regulator: Effect on the Transcriptome, Antibiotic Production, and Differentiation in Liquid Cultures

2018
Front Microbiol
PMCID: 5839063
PMID: 29545785
DOI: 10.3389/fmicb.2018.00361

[…] of these 45 genes (64%) had the profile of group 1 (Figure ), including the 15 genes related to arginine and pyrimidine biosynthesis. The other 16 genes did not fit any of the 10 groups determined by maSigPro. The function of many of these 29 genes is unknown, although SCO6824-SCO6827 resembles a polyketide synthesis gene cluster and sigM (SCO7314) has been reported to be involved in osmotic stres […]

call_split

Luminal lncRNAs Regulation by ERα Controlled Enhancers in a Ligand Independent Manner in Breast Cancer Cells

2018
Int J Mol Sci
PMCID: 5855815
PMID: 29462945
DOI: 10.3390/ijms19020593
call_split See protocol

[…] ault settings. A gene was considered as differentially expressed if associated with an adjusted p-value < 0.001. To identify genes differentially expressed in the time-course E2-treatment experiment, maSigPro R package [] was applied in default setting by considering the adjusted p-value computed using the p.vector function of the package. A gene was considered as differentially expressed if assoc […]

call_split

Time course transcriptome analysis of human cellular reprogramming from multiple cell types reveals the drastic change occurs between the mid phase and the late phase

2018
BMC Genomics
PMCID: 5753469
PMID: 29298685
DOI: 10.1186/s12864-017-4389-8
call_split See protocol

[…] nal intensities of each gene in the biological replicates were averaged. Next, to extract dynamically expressed genes across all cell types during reprogramming process, we individually proceeded the maSigPro package [] in each cell and screened genes which showed the significance in all five cell types (P-value <0.01, FDR < 0.05, R2 > 0.6). The filtration yielded 3615 extracted genes (Fig. ). Whe […]

library_books

Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence

2017
BMC Genomics
PMCID: 5698953
PMID: 29162050
DOI: 10.1186/s12864-017-4304-3

[…] . Differentially expressed genes between post and pre samples were identified using the glmTreat function in edgeR (v3.18.1) [] with a FDR < 0.05 and FC > 2. Age-regulated genes were identified using maSigPro [] with a FDR < 0.05 and clustered using k-means clustering based on relative mean expression values (maximum normalized count value set to one) for each time point. […]

library_books

Transcriptional regulation of endothelial cell behavior during sprouting angiogenesis

2017
Nat Commun
PMCID: 5620061
PMID: 28959057
DOI: 10.1038/s41467-017-00738-7

[…] nt (version 0.6.1). DESeq2 was used to identify DEGs across the samples. To identify genes with significant expression profile differences over time between retinal developmental stages, we used Next-maSigPro, an R Bioconductor package that works by fitting a generalized linear model with negative binomial dispersion to the library-corrected gene reads counts, but explicitly accounting for the tim […]

Citations

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maSigPro institution(s)
Mathematics Department, University of Alicante, Spain; Genomics of Gene Expression Laboratory, Centro de Investigaciones Prıncipe Felipe, Valencia, Spain; Statistics and Operational Research Department, Politechnical University of Valencia, Valencia, Spain; Microbiology and Cell Science Department, Institute for Food and Agricultural Research, University of Florida, FL, USA
maSigPro funding source(s)
Supported by the European Union Seventh Framework Programme STATegra project under the grant agreement 306000 and the Spanish MINECO grants BIO2012-40244 and BIO2015-71658-R.

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