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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 citations

 (6)
library_books

A mechanism underlying position specific regulation of alternative splicing

2017
Nucleic Acids Res
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 […]

library_books

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

2017
Nucleic Acids Res
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 […]

library_books

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

2016
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 […]

library_books

Polarizing the Neuron through Sustained Co expression of Alternatively Spliced Isoforms

2016
Cell Rep
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 […]

library_books

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

2015
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 […]

library_books

Characterization of FUS Mutations in Amyotrophic Lateral Sclerosis Using RNA Seq

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

[…] 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 […]


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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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