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Citations per year

Number of citations per year for the bioinformatics software tool EDGE-Pro
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Protocols

EDGE-Pro specifications

Information


Unique identifier OMICS_28042
Name EDGE-Pro
Alternative name Estimated Degree of Gene Expression in PROkaryotes
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Perl
Computer skills Advanced
Version 1.3.1
Stability Stable
Maintained Yes

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Publication for Estimated Degree of Gene Expression in PROkaryotes

EDGE-Pro citations

 (12)
library_books

Gene Enrichment Analysis Reveals Major Regulators of Mycobacterium tuberculosis Gene Expression in Two Models of Antibiotic Tolerance

2018
Front Microbiol
PMCID: 5893760
PMID: 29670589
DOI: 10.3389/fmicb.2018.00610

[…] Reads were de-multiplexed and adapter sequences removed to yield reads of 100-bp length. Raw reads were mapped to the M. tuberculosis CDC1551 genome (GenBank Assembly GCA_000669715.1) using EDGE-pro v1.3.1 (Magoc et al., ) (running Bowtie2 internally). Samples containing fewer than 5 × 105 reads mapping to the CDC1551 genome were removed from the analysis (one sample) as these were assum […]

call_split

Zinc Acquisition Mechanisms Differ between Environmental and Virulent Francisella Species

2018
J Bacteriol
PMCID: 5786701
PMID: 29109188
DOI: 10.1128/JB.00587-17
call_split See protocol

[…] ads) with the Illumina HiSeq v4 platform.Data analysis was performed by the UVA Bioinformatics Core. Briefly, gene reads were first aligned with reference genomes and read counts were quantified with EDGE-pro software. The Deseq2 Bioconductor package was then used to normalize the read counts and estimate dispersion for each gene. These data were then fitted to a negative binomial model, which was […]

library_books

Gene network analysis identifies a central post transcriptional regulator of cellular stress survival

2018
eLife
PMCID: 5869019
PMID: 29537368
DOI: 10.7554/eLife.33684.044

[…] P7hp-gsrN-3’. The window identification number corresponds to the same sequence across the three different FASTA sequences.Mapping and quantification of reads to these windows was conducted using the EDGE-pro analysis pipeline (). A caveat of EDGE-pro quantification is the potential misattribution of reads to input windows. EDGE-pro quantification does not take strand information into account when […]

call_split

Haem iron plays a key role in the regulation of the Ess/type VII secretion system of Staphylococcus aureus RN6390

2017
Microbiology
PMCID: 5845736
PMID: 29171824
DOI: 10.1099/mic.0.000579
call_split See protocol

[…] eplicates). Total mRNA was extracted, reverse transcribed and sequenced as described previously []. The sequence reads from each individual dataset were mapped to the S. aureus NCTC 8325 genome using EDGE-pro [], and quantification of transcript abundance and calculation of differential gene expression were performed using DEseq2 []. DEseq2 uses the Negative Binomial distribution as a model to com […]

library_books

Endogenously generated 2 aminoacrylate inhibits motility in Salmonella enterica

2017
Sci Rep
PMCID: 5636819
PMID: 29021529
DOI: 10.1038/s41598-017-13030-x

[…] erica subsp. Enterica serovar Typhimurium str. LT2 chromosome, complete genome (RefSeq Accession Number: NC_003197.1) and read counts were generated using the prokaryotic-tailored gene alignment tool EDGE-Pro. Genes differentially expressed (false discovery rate, FDR < 0.05) between the respective wild-type and ridA strains of S. enterica were identified using DEseq,,. Briefly, an FDR < 0.05 cutof […]

library_books

Transcriptomic responses of the olive fruit fly Bactrocera oleae and its symbiont Candidatus Erwinia dacicola to olive feeding

2017
Sci Rep
PMCID: 5320501
PMID: 28225009
DOI: 10.1038/srep42633

[…] Alignment of RNA-seq reads to the draft transcriptome was performed with EDGE-pro v.1.3.1. This program is specifically designed for bacterial gene expression analysis, and takes into account the absence of introns and the overlapping nature of bacterial genes, while it pr […]


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EDGE-Pro institution(s)
Center for computational Biology, McKusick-nathans institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
EDGE-Pro funding source(s)
Supported in part by the National Institutes of Health under grants R01-LM006845S, R01-HG006677, and R01-HG006102.

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