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expressionplot specifications


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


  • person_outline Brad A. Friedman

Publication for expressionplot

expressionplot citations


A mechanism underlying position specific regulation of alternative splicing

Nucleic Acids Res
PMCID: 5716086
DOI: 10.1093/nar/gkx901

[…] 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 with >1 […]


An RRM–ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion

Nucleic Acids Res
PMCID: 5499739
PMID: 28379442
DOI: 10.1093/nar/gkx225

[…] 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 ( based on the PARalyzer tool (). Two replicates were processed se […]


Transcriptional Fingerprint of Hypomyelination in Zfp191null and Shiverer (Mbpshi) Mice

PMCID: 5046175
PMID: 27683878
DOI: 10.1177/1759091416670749
call_split See protocol

[…] 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 compa […]


Polarizing the Neuron through Sustained Co expression of Alternatively Spliced Isoforms

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

[…] Annotated UA3Es were extracted from the UCSC Known Genes dataset ( 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 […]


Sustained Brown Fat Stimulation and Insulin Sensitization by a Humanized Bispecific Antibody Agonist for Fibroblast Growth Factor Receptor 1/βKlotho Complex

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

[…] croarray 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). […]


Characterization of FUS Mutations in Amyotrophic Lateral Sclerosis Using RNA Seq

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

[…] re amplified by PCR and size selected by gel electrophoresis prior to sequencing on an Illumina Genome Analyzer (Illumina, San Diego, CA). Analysis of RNA-Seq was performed utilizing software package ExpressionPlot : gene expression levels were estimated by counting the number of reads mapping to constitutive exons for each gene and determining RPKM values (reads per kilobase of exon model per mil […]

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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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