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Pathway Studio specifications


Unique identifier OMICS_02977
Name Pathway Studio
Interface Web user interface
Restrictions to use License purchase required
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Pathway Studio

Pathway Studio citations


Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia

PMCID: 5929421
PMID: 29731978
DOI: 10.18632/oncotarget.24808

[…] classification stringency (default). For visualization of the enrichment analysis the application Enrichment map [] was used for the program Cytoscape []. Enriched sub-networks were identified using Pathway Studio’s Expression regulatory sub-network enrichment, Elsevier’s Pathway Studio ( ( […]


Connexin 43 Controls the Astrocyte Immunoregulatory Phenotype

Brain Sci
PMCID: 5924386
PMID: 29565275
DOI: 10.3390/brainsci8040050

[…] RNAs with more than 50 reads in Cx43FL were selected;Gene Ontology (GO) analyses: We used the text-mining Pathway Studio ResNet database (Ariadne Genomics, Rockville, MD, USA) and the GSEA tool [] in Pathway Studio 11.0.5 [] to identify over-represented biological processes within our differentially expressed dataset. As parameters for the GSEA method, we selected the Mann-Whitney U-test and a p-v […]


FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets

BMC Genomics
PMCID: 5836822
PMID: 29504895
DOI: 10.1186/s12864-018-4474-7

[…] – for example, KEGG PATHWAY [], BioCyc [], BioGRID [] and IntAct [].There are systems that allow the reconstruction of gene networks for a given set of genes/proteins including FunCoup [], STRING [], Pathway Studio [], Ingenuity Pathway Analysis [], PINA [], GeneMANIA [] and ReactomeFIViz []. These systems use various information sources on interactions of molecular genetic objects, including scie […]


Asymmetric dimethylarginine (ADMA) is identified as a potential biomarker of insulin resistance in skeletal muscle

Sci Rep
PMCID: 5794993
PMID: 29391561
DOI: 10.1038/s41598-018-20549-0

[…] an adult population (p < 0.05, Table  and Supplementary Table ). To find common biological associations between insulin resistance and these metabolites, we performed both pathway analysis using the Pathway Studio and pathway enrichment analysis using ConsensusPathDB and KEGG pathway resources (Supplementary Fig. ). Sub-cellular network analysis demonstrated the metabolites shared biological sign […]


Gene level association analysis of systemic sclerosis: A comparison of African Americans and White populations

PLoS One
PMCID: 5749683
PMID: 29293537
DOI: 10.1371/journal.pone.0189498

[…] oth populations was the same, rs3780540, and the MAF was actually higher in African Americans (0.116) than in Whites (0.0179), yet it was only significant in Whites.An interaction network built using Pathway Studio detected a large number of interactions between genes associated with SSc risk. Genes with the largest number of interactions include ITGAM, AIF1, STAT1, IL12RB2; these genes form hubs […]


Coupling between Myogenesis and Angiogenesis during Skeletal Muscle Regeneration Is Stimulated by Restorative Macrophages

Stem Cell Reports
PMCID: 5785732
PMID: 29198825
DOI: 10.1016/j.stemcr.2017.10.027
call_split See protocol

[…] and analyzed in an unsupervised way by principal component analysis, and a one-way ANOVA was applied to extract DEGs using PartekGS software. Cluster analysis and enrichment were made using DAVID and Pathway Studio software (the strategy is presented in J). A list of genes expressed by both ECs and MPCs was finalized (). […]


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Pathway Studio institution(s)
Ariadne Genomics, Inc, Chinakville, MD, USA

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