maSigPro protocols

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Associated diseases

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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

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Publications for maSigPro

maSigPro in pipelines

 (14)
2018
PMCID: 5923024
PMID: 29703138
DOI: 10.1186/s12864-018-4679-9

[…] in the gene expression of human bronchial epithelial cells (beas-2b) by the exposure to ufp generated from diesel and biomass combustion. a combination of different bioinformatics tools (edger, next-masigpro and reactome fi app-cytoscape and prioritization strategies) facilitated the analyses the temporal transcriptional pattern, functional gene set enrichment and gene networks related […]

2017
PMCID: 5222877
PMID: 28119706
DOI: 10.3389/fpls.2016.02007

[…] temporal expression changes in time-course experiments. rna-seq raw counts were normalized by the deseq normalization (). time-series differential expression analysis was carried out using the masigpro package (). the p-values were corrected for multiple comparisons by the benjamini and hochberg false discovery rate (fdr) procedure. we set q = 0.05 and rsq = 0.7 to get significant genes, […]

2017
PMCID: 5412052
PMID: 28464824
DOI: 10.1186/s12864-017-3743-1

[…] integrating both common and tagwise dispersion []. second, to accommodate the time-series nature of the experimental design, we also conducted step-wise regression analysis of gene expression in masigpro []. regression analysis enabled the detection of genes with significant patterns of differential expression across all three time points. gene expression heatmaps were generated in r […]

2017
PMCID: 5532269
PMID: 28751729
DOI: 10.1038/s41598-017-06110-5

[…] periodically expressed genes were identified as having the same calculated dominant cycling frequency between biological replicates. time-dependent expression signatures were established using masigpro with a replicate correlation coefficient cutoff of 0.8. target genes of potential regulatory (top 50 most highly and/or variably expressed) lncrnas were identified using the genereg package […]

2017
PMCID: 5634787
PMID: 28994389
DOI: 10.7554/eLife.26851.034

[…] probes). signal intensities were transformed to log2 scale. to investigate the differences in temporal gene expression profiles between genotypes, a regression-based approach was performed using masigpro (rrid:scr_001349), a package for time-course microarray analysis available from bioconductor (). we defined a regression model where the dependent variable was the signal intensity […]


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maSigPro in publications

 (59)
PMCID: 5937035
PMID: 29730990
DOI: 10.1186/s12915-018-0518-3

[…] linear model of the negative binomial family with time as a discrete factor; (2) a deseq2 generalized linear model of the negative binomial family with a natural cubic spline of time; and (3) a masigpro [] third degree polynomial regression. we define the variable describing the different treatments as ‘group’, with the following levels: g01, unstimulated cells; g02, mock-stimulated cells […]

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

[…] only the diseases with fdr corrected p-value ≤0.05., groups of genes with a differential temporal expression profile in exposed cells (as compared to controls) were identified using the next-masigpro method of the masigpro [, ] r package (version 1.34.1). briefly, the p.vector function was used to compute a regression fit for each gene in both matrixes of cpm counts for beas-2s exposed […]

PMCID: 5902570
PMID: 29692768
DOI: 10.3389/fmicb.2018.00698

[…] for mrnas. instead, a time series analysis method was used to determine if sirna-dicer feeding significantly changed the expression pattern using the data from all 6 days post-infection using masigpro package ()., the target genes of mirnas were predicted using sequence-based algorithms. annotated 3′utrs of protein-coding genes were used for mirna target prediction using the miranda […]

PMCID: 5855815
PMID: 29462945
DOI: 10.3390/ijms19020593

[…] 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 […]

PMCID: 5753469
PMID: 29298685
DOI: 10.1186/s12864-017-4389-8

[…] 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 […]


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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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