Onto-Express protocols

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description
Onto-Express computational protocol

Onto-Express specifications

Information


Unique identifier OMICS_18286
Name Onto-Express
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Sorin Draghici <>

Additional information


http://vortex.cs.wayne.edu/Onto-Tools%20User%20Manual/Onto-Express/Onto-Express.html

Publications for Onto-Express

Onto-Express IN pipelines

 (3)
2014
PMCID: 3963927
PMID: 24663062
DOI: 10.1371/journal.pone.0092605

[…] of one group (wt or rgs9-deficient mice) [21]. statistical testing was done using a two-tailed student’s t-test. for gene ontology profiling, mas5 normalized data with p≤0.01 were subjected to the onto express algorithm [22]–[23]. the settings were: hypergeometric distribution, correction for false discovery rate (fdr). the mas5 processed data were also analyzed using the gene set enrichment […]

2008
PMCID: 2227948
PMID: 18237449
DOI: 10.1186/1755-8794-1-2

[…] diseased (ms) and control (normal siblings) samples. the ms samples were 8923, 8922 a, 8830, 8839, 9013 and 9016, respectively. the unaffected siblings were 9017, 9018, 9023 and 8921a, respectively. onto-express analyses depicted in figure 4 shows that transcription factor binding is a highly significant component in our microarray data. results from pathway-express analysis are listed in table […]

2008
PMCID: 2386486
PMID: 18442417
DOI: 10.1186/1471-2164-9-197

[…] (the database for annotation, visualization and integrated discovery) [59]., pathway classification of the differentially expressed genes was performed using the pathway express tool available in onto-express [60]. enriched pathways among the differentially expressed genes below a p-value of 0.1 were identified and those associated with mammary gland development are listed in table 1. […]

Onto-Express institution(s)
Department of Computer Science, Wayne State University, Detroit, MI, USA; Department of Obstetrics and Gynecology, Karmanos Cancer Institute, Detroit, MI, USA; Department of Molecular Biology and Genetics, Karmanos Cancer Institute, Detroit, MI, USA
Onto-Express funding source(s)
Supported by the NSF grant number NSF- 0234806, USMRMC grant number DAMD17-03-2-0035, NIH grant numbers RO1-NS045207-01 and R21-EB000990-01, and Michigan Life Sciences Corridor grant number MLSC-27.

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