expressionplot protocols

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expressionplot specifications

Information


Unique identifier OMICS_01939
Name expressionplot
Software type Application/Script
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Brad A. Friedman <>

Publication for expressionplot

expressionplot in pipeline

2013
PMCID: 3620060
PMID: 23577159
DOI: 10.1371/journal.pone.0060788

[…] the vector condition to wild-type fus, the two fus mutants and sirna against fus, using an online tool (http://bioinfogp.cnb.csic.es/tools/venny/index.html). our data has been deposited to the expressionplot web server (http://als-research.dyndns-server.com/cgi-bin/expressionplot/home.pl) , and will be accessible from the date of publication., to confirm gene expression levels detected […]

expressionplot in publications

 (6)
PMCID: 5716086
DOI: 10.1093/nar/gkx901

[…] millipore)., cad cells treated with sicontrol, siptbp1 or siptbp1/2 were analyzed by rna-seq as described [(); ncbi geo accession number gse37933]. alternative splicing changes were quantified using expressionplot () and cassette exons consistently up- or down-regulated in both siptbp1 and siptbp1/2 samples compared to the sicontrol (p < 0.01) were shortlisted for further analyses. genes […]

PMCID: 5499739
PMID: 28379442
DOI: 10.1093/nar/gkx225

[…] the motifs as described previously ()., published rna-seq and par-clip data () were downloaded from ncbi geo database (accession number: gse44976). analysis of alternative splicing was done using expressionplot pipeline (). par-clip reads were processed using parpipe pipeline (https://ohlerlab.mdc-berlin.de/software/parpipe_119/) based on the paralyzer tool (). two replicates were processed […]

PMCID: 5046175
PMID: 27683878
DOI: 10.1177/1759091416670749

[…] center for biotechnology information through the national library of medicine under accession number prjna338665., rna sequencing reads were mapped to the mm9 genome using bowtie v.1 and the expressionplot pipeline (; ). differential expression was performed using deseq in the expressionplot software package (). the bonferroni correction was used within deseq to control for multiple […]

PMCID: 4870516
PMID: 27134173
DOI: 10.1016/j.celrep.2016.04.012

[…] our understanding of the part played by as in the development and evolution of eukaryotic organisms., annotated ua3es were extracted from the ucsc known genes dataset (http://genome.ucsc.edu/) using expressionplot utility scripts () and further filtered to remove other types of regulated rna processing, e.g., cassette exons or alternative polyadenylation. mouse glutamatergic neurogenesis rna-seq […]

PMCID: 4534681
PMID: 26288846
DOI: 10.1016/j.ebiom.2015.05.028

[…] analysis, total rna (n = 5 per group) was labeled and hybridized to affymetrix mouse genome 430 2.0 arrays. expression intensity for each probe set was calculated and heatmap generated using expressionplot application suit (). data are available at the ncbi (geo accession number gse68152)., tissue extracts were generated by homogenizing freshly isolated tissues in t-per tissue protein […]

expressionplot institution(s)
Department of Molecular and Cell Biology, Harvard University, Cambridge, MA, USA; The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, USA; Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, New York, NY, USA

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