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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

Maintainer


This tool is not available anymore.

Additional information


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

Publications for Pathway-Express

Pathway-Express citations

 (33)
library_books

Highly Expressed Integrin α8 Induces Epithelial to Mesenchymal Transition Like Features in Multiple Myeloma with Early Relapse

2016
Mol Cells
PMCID: 5223107
PMID: 28008160
DOI: 10.14348/molcells.2016.0210

[…] PFS point, 77 genes upregulated more than two-fold in the < 12 months group were defined and the altered biological pathways were investigated ( and ). Pathway enrichment analysis was performed using Pathway-Express identifying KEGG pathways from the process of an input list of genes (). We found eight pathways that were associated with the PFS < 12 months relapsed MM group (corrected P < 0.05), f […]

call_split

Regressive Effect of Myricetin on Hepatic Steatosis in Mice Fed a High Fat Diet

2016
PMCID: 5188454
PMID: 27973423
DOI: 10.3390/nu8120799
call_split See protocol

[…] SAM, 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 to bu […]

call_split

Systems Medicine as an Emerging Tool for Cardiovascular Genetics

2016
PMCID: 5003874
PMID: 27626034
DOI: 10.3389/fcvm.2016.00027
call_split See protocol

[…] complexity, has increased explanatory power () and investigates biological pathways rather than genome-scale networks. Methods and tools for pathway analysis have been developed and studied, such as Pathway-Express, an impact analysis including classical statistics along with crucial factors such as the magnitude of each gene’s expression change, their type and position in the given pathways, and […]

library_books

Transcriptional profiling of foam cells in response to hypercholesterolemia

2016
Genom Data
PMCID: 4925893
PMID: 27408807
DOI: 10.1016/j.gdata.2016.06.006

[…] variances. Differences were considered significant when P < 0.01. To determine the main biological pathways affected in foam cells in response to WD feeding for 2 or 14 weeks, data were analyzed with Pathway Express . A P value was generated based on the number of genes differentially expressed in each pathway with respect to the number expected to change by chance. Pathway Express was also used t […]

library_books

Transcriptional Profiling of Foam Cells Reveals Induction of Guanylate‐Binding Proteins Following Western Diet Acceleration of Atherosclerosis in the Absence of Global Changes in Inflammation

2016
PMCID: 4859273
PMID: 27091181
DOI: 10.1161/JAHA.115.002663

[…] ions are listed in Table S1 (2‐week WD vs CHOW) and Table S2 (14‐week WD vs CHOW). To determine the main biological processes affected in response to hypercholesterolemia, the data were analyzed with Pathway Express. Two pathways, “antigen processing and presentation” and “ubiquitin‐mediated proteolysis,” were commonly affected in both WD groups (Figure C). Changes in genes in the antigen processi […]

library_books

Systems Analysis of Adaptive Responses to MAP Kinase Pathway Blockade in BRAF Mutant Melanoma

2015
PLoS One
PMCID: 4583389
PMID: 26405815
DOI: 10.1371/journal.pone.0138210

[…] toff (). The CGA, CGC, CGD and CGE groups () showed 2614, 7310, 2383, and 2993 probes detecting differential gene expression at a 1% FDR, respectively. When each of these gene lists was put through a Pathway Express [,] enrichment analysis, the top two pathways in all four groups were always leukocyte transendothelial migration and cell adhesion molecules, and the third ranked pathway in every gro […]

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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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