GeneVenn protocols

View GeneVenn computational protocol

GeneVenn statistics

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GeneVenn specifications

Information


Unique identifier OMICS_05568
Name GeneVenn
Interface Web user interface
Restrictions to use None
Input data Some gene lists.
Output data Venn diagrams.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Youping Deng <>

Publication for GeneVenn

GeneVenn in pipelines

 (5)
2018
PMCID: 5919700
PMID: 29698473
DOI: 10.1371/journal.pone.0196590

[…] defined as those with both padj < 0.05 and log2 fold change (fc) > 2 (up-regulated) or < -2 (down-regulated). venn diagrams were plotted from the deg lists generated using deseq using the genevenn webtool (genevenn.sourceforge.net)., the singular enrichment analysis (sea) algorithm was used via the agrigo web tool [] to analyse gene ontology (go) term enrichment of significantly […]

2017
PMCID: 5581396
PMID: 28894456
DOI: 10.3389/fpls.2017.01464

[…] genes were detected using linear regression models in the limma method (), which provides fdr-adjusted p-values for multiple testing problems (). the significance level was set at fdr < 0.05. genevenn was used to generate the venn diagram., the transcript profiles were visualized using mapman (v3.5.1r2) () to inspect coordinated changes in metabolism and other biological process. go […]

2015
PMCID: 4388846
PMID: 25849296
DOI: 10.1371/journal.pone.0121902

[…] to two transcripts, the least significantly aligned transcript(s) were omitted., to determine the tissue or timepoint specificity of degs, venn diagrams and gene lists were obtained using http://genevenn.sourceforge.net/. to determine functionality of degs, genone ontology (go) enrichment analysis was performed using http://bioinfo.cau.edu.cn/agrigo/ []. sequence data are available from ncbi […]

2014
PMCID: 4352135
PMID: 25517099
DOI: 10.1038/nature14021

[…] the benjamini-hochberg correction. enriched go terms were submitted to revigo to remove redundant terms. co-occurrence between our datasets and previously published datasets was visualized with genevenn and bioinforx area-proportional venn diagram., we used two distinct algorithms, weeder and fire to perform an unbiased search for overrepresented sequences in the promoters […]

2013
PMCID: 3725162
PMID: 23866001
DOI: 10.1186/1472-6785-13-25

[…] for multiple testing with the benjamini-hochberg procedure, which controls for false discovery rate., genes that overlapped between gene lists were identified by creating venn diagrams using genevenn []. exact hypergeometric probability test was performed to test the statistical significance of the overlap between two gene lists []. david 6.7 [,] was used to determine the enriched […]


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GeneVenn in publications

 (34)
PMCID: 5876501
PMID: 29616088
DOI: 10.3892/ol.2018.8014

[…] equal to or more than 1.50 are considered upregulated. the number of genes remaining after this step was 9,302, 1,343, and 1,447 genes for tak1, irf3, and irf4 arrays, respectively. next, we used genevenn (genevenn.sourceforge.net) to generate a venn chart demonstrating the set of common genes between the different sets of arrays. the venn chart indicated a list of 706 common genes […]

PMCID: 5820663
PMID: 29568746
DOI: 10.1155/2018/2936257

[…] as phylum, genus, kegg, and eggnog., to address the problem whether these biomarkers are specifically associated with a particular phenotype, venn diagram was plotted with the online program (http://genevenn.sourceforge.net/)., in this study, 806 samples with different phenotypes were analyzed. those samples were from three large available metagenome-wide association studies at present, […]

PMCID: 5751986
PMID: 29298298
DOI: 10.1371/journal.pone.0189668

[…] to identify all candidates with existing gene annotation and fpkm > 0. the identified lists of genes with gene annotation and fpkm > 0 of enthesis, tendon and cartilage were compared using genevenn[]. the venn diagram shows the number of tissue specific genes as well as the number of genes that overlapped between two of the tissues or all tissues (). 13798 genes were expressed […]

PMCID: 5778919
PMID: 29435008
DOI: 10.3892/ol.2017.7660

[…] to non-tumor tissue, were calculated by the t-test method with a linear regression model. kyoto encyclopedia of genes and genomes (kegg) pathway enrichment analysis of the degs was performed. genevenn online analysis software was used for the comparison of the degs between subtypes. a total of 795 degs, including 619 up and 176 downregulated degs were screened from the astrocytoma […]

PMCID: 5745457
PMID: 29088115
DOI: 10.3390/biom7040075

[…] keio collection. inoue et al. [] screened the keio collection for defects in swarming motility using eiken agar and subsequently checked the swarming mutants for reduced swimming motility [,]. using genevenn [], motility genes identified by inoue et al. were compared to the genes identified in our screen (see ). very few genes were found to overlap, especially between swimming motility and curli […]


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GeneVenn institution(s)
Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, USA
GeneVenn funding source(s)
Supported by Dean’s Research Initiative award of the University of Southern Mississippi and the Mississippi Functional Genomics Network (DHHS/NIH/NCRR Grant# 2P20RR016476-04).

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