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Genome2D specifications

Information


Unique identifier OMICS_23246
Name Genome2D
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability No
Maintained No

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This tool is not available anymore.

Publication for Genome2D

Genome2D citations

 (21)
library_books

Dynamic sporulation gene co expression networks for Bacillus subtilis 168 and the food borne isolate Bacillus amyloliquefaciens: a transcriptomic model

2018
Microb Genom
PMCID: 5857382
PMID: 29424683
DOI: 10.1099/mgen.0.000157

[…] the top 10 % most expressed genes in both the B. subtilis 168 and B. amyloliquefaciens RNA-seq data. The list of genes for each strain was then subjected to downstream gene set enrichment analysis in Genome2D []. The gene set enrichment results for the analysis for the top 10 % most expressed genes across time points for B. subtilis 168 and B. amyloliquefaciens are given in Tables S6 and S7, respe […]

library_books

The Streptococcus agalactiae Stringent Response Enhances Virulence and Persistence in Human Blood

2017
Infect Immun
PMCID: 5736797
PMID: 29109175
DOI: 10.1128/IAI.00612-17

[…] 7.0. The Tn-seq Circos plot () was generated using Circos 0.67-7 (). Heat map data for were generated using HeatmapGenerator 5.0 (). Gene set enrichment analysis for the data in was performed with Genome2D (). […]

call_split

The Relationship among Tyrosine Decarboxylase and Agmatine Deiminase Pathways in Enterococcus faecalis

2017
Front Microbiol
PMCID: 5672081
PMID: 29163401
DOI: 10.3389/fmicb.2017.02107
call_split See protocol

[…] ed States) and images were analyzed using GenePix Pro v.6.0 software. Background subtraction and locally weighted scatterplot smoothing normalization were done using the standard routines provided by GENOME2D software available at http://genome2d.molgenrug.nl/index.php/analysis-pipeline. DNA microarray data were obtained from two independent biological replicates and one technical replicate (inclu […]

library_books

Global Screening of Salmonella enterica Serovar Typhimurium Genes for Desiccation Survival

2017
Front Microbiol
PMCID: 5596212
PMID: 28943871
DOI: 10.3389/fmicb.2017.01723

[…] that contains a hypothetical protein (fig|588858.6.peg.1457) on the negative strand. Moreover, we looked for the promoter regions in the desiccation resistance intergenic regions using Pepper (http://genome2d.molgenrug.nl/index.php/prokaryote-promoters). Interestingly, only IG_STM14_3165 had the predicted promoter. […]

call_split

Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates

2017
Front Microbiol
PMCID: 5543090
PMID: 28824604
DOI: 10.3389/fmicb.2017.01487
call_split See protocol

[…] of root exudates. The significance threshold was p-value < 0.05 and fold-change > 2 (“TopHits” in T-Rex). Functional categorization including GO, InterPro, KEGG and PFAM domains, was performed on the Genome2D web server. The RNA-seq data from this study have been submitted to the NCBI Gene Expression Omnibus (GEO) under the accession number GSE98148. […]

library_books

The Staphylococcus aureus α Acetolactate Synthase ALS Confers Resistance to Nitrosative Stress

2017
Front Microbiol
PMCID: 5504149
PMID: 28744267
DOI: 10.3389/fmicb.2017.01273

[…] ng RNA extracted from cells grown on galactose and submitted to 250 μM spermine NONOate for 3 h. Following data acquisition, the RNA-Seq results were analyzed using the T-Rex pipeline web tool http://genome2d.molgenrug.nl/index.php/rnaseq-expression-analysis () (Supplementary Table ), and the data validated by quantitative real-time RT-PCR (Supplementary Table ).Exposure of S. aureus to NO altered […]

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Genome2D institution(s)
Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands

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