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Genome2D specifications


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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Publication for Genome2D

Genome2D citations


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

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 […]


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

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 (). […]


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

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 DNA microarray data were obtained from two independent biological replicates and one technical replicate (inclu […]


Global Screening of Salmonella enterica Serovar Typhimurium Genes for Desiccation Survival

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 ( Interestingly, only IG_STM14_3165 had the predicted promoter. […]


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

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. […]


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

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 () (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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