Pathway-Express protocols

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Pathway-Express specifications

Information


Unique identifier OMICS_18291
Name Pathway-Express
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Registration required Yes
Maintained No

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This tool is not available anymore.

Additional information


http://vortex.cs.wayne.edu/faq.htm#pathwayexpressfaq

Publications for Pathway-Express

Pathway-Express in pipelines

 (5)
2015
PMCID: 4583389
PMID: 26405815
DOI: 10.1371/journal.pone.0138210

[…] variants. genes were identified that uniquely contained variants in each cell line, and within each cytotoxicity group., gene sets found to be significant underwent pathway enrichment analysis via pathway express and gene set enrichment analysis (gsea) using msigdb datasets. significant gene sets and pathways were identified as having a fdr enrichment value of 0.05 for both tools. to ascertain […]

2014
PMCID: 4325706
PMID: 25505077
DOI: 10.1128/JVI.02828-14

[…] (de) during the host response were analyzed using easygo (http://bioinformatics.cau.edu.cn/easygo/). to determine which biological pathways are involved in the responses to viral infection, pathway express (http://vortex.cs.wayne.edu/projects.htm) was used. genes differentially expressed during the host response (fdr < 0.05) were analyzed against a reference background consisting […]

2012
PMCID: 3441782
PMID: 22494416
DOI: 10.1186/1475-2867-12-14

[…] tool of david. the impact factor (if) analysis that considers exact fold changes of differentially expressed genes for generation of the corresponding kegg pathway was performed by using the pathway-express tool (onto-tools, intelligent systems and bioinformatics laboratory) []., ipa is a knowledgebase that contains approximately 2,500,000 biological and chemical interactions […]

2010
PMCID: 2858150
PMID: 20307317
DOI: 10.1186/1471-2164-11-194

[…] in general, and not nf1 in particular. we are not aware of similar analyses in other tumor suppressor genes (e.g. rb)., these observations are largely supported by our analysis with onto-express, pathway-express and metacore tools (biological processes and pathway maps). these methods revealed perturbed cell cycle, mitosis, transcription and dna replication and repair pathways, especially […]

2008
PMCID: 2837362
PMID: 18298660
DOI: 10.1111/j.1582-4934.2008.00284.x

[…] approach available in the metacore software. in addition, an impact analysis was performed on all signalling human pathways available in kyoto encyclopedia of genes and genomes (kegg) with pathway express []., umbilical cord specimens were obtained from women in the following clinical groups: (i) tnl (n= 15), (ii) tl (n= 15), (iii) intrauterine growth restriction at term (iugr-t; n= […]

Pathway-Express in publications

 (39)
PMCID: 5733474
PMID: 29321746
DOI: 10.3389/fpsyt.2017.00271

[…] natick, ma, usa) and (ii) an empirical bayes moderated t-test, implemented by limma package of bioconductor, an r-based open-source software ()., ingenuity pathway analysis (ipa) and onto-tools pathway-express software tools were applied. ipa determines the probability that a given gene set is associated with predefined pathways beyond what would be expected by random chance (). further, […]

PMCID: 5440822
PMID: 28508872
DOI: 10.1038/ncomms15237

[…] experimental variation or batch effect for each gene independently. expression values were transformed in log2, and probesets were mapped using the entrez gene probeset definition. the pathway-express tool from the onto-tools (http://vortex.cs.wayne.edu) was used to assess biological processes and pathways affected at different stages of er+ breast tumour samples. genes encoding […]

PMCID: 5432249
PMID: 28412734
DOI: 10.18632/oncotarget.15428

[…] in the categories of intermediate filament cytoskeleton, intermediate filament and keratin filament (). we further performed an impact analysis for over-represented pathways using a web-based pathway-express [] (http://vortex.cs.wayne.edu/ontoexpress/), and identified 12 pathways and 14 pathways that were significantly enriched at bonferroni corrected p value level of < 0.05 […]

PMCID: 5223107
PMID: 28008160
DOI: 10.14348/molcells.2016.0210

[…] stanford university school of medicine, usa: http://jtreeview.sourceforge.net) (). to investigate the biologically relevant pathways most impacted by the gene input list, the online program pathway-express (onto-tools, wayne state university, detroit, mi, usa; http://vortex.cs.wayne.edu/projects.html) was used (). specific biological pathways were defined using the kyoto encyclopedia […]

PMCID: 5188454
PMID: 27973423
DOI: 10.3390/nu8120799

[…] version 3.02, stanford university, stanford, ca, usa) was performed to identify significantly differentially expressed genes (degs) between hfd and hm groups. the degs were selected and put into pathway-express in onto-tools []. pathway-express searches the kyoto encyclopedia of genes and genomes (kegg) pathway database for each input gene, and the impact analysis was performed in order […]

Pathway-Express institution(s)
Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA; Department of Computer Science, Wayne State University, Detroit, MI, USA; Perinatology Research Branch, NIH/NICHD, Detroit, MI, USA
Pathway-Express funding source(s)
Supported by the following grants: NSF DBI-0234806, CCF-0438970, 1R01HG003491-01A1, 1U01CA117478-01, 1R21CA100740-01, 1R01NS045207-01, 5R21EB000990-03, 2P30 CA022453-24.

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