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Onto-Express specifications

Information


Unique identifier OMICS_18286
Name Onto-Express
Alternative name Ontoexpress
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Documentation


Maintainer


This tool is not available anymore.

Additional information


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

Publications for Onto-Express

Onto-Express in pipelines

 (5)
2014
PMCID: 3963927
PMID: 24663062
DOI: 10.1371/journal.pone.0092605

[…] of one group (wt or rgs9-deficient mice) . 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 –. the settings were: hypergeometric distribution, correction for false discovery rate (fdr). the mas5 processed data were also analyzed using the gene set enrichment analysis […]

2013
PMCID: 3751509
PMID: 23880092
DOI: 10.1186/1742-2094-10-92

[…] to the public database at the geo website (http://www.ncbi.nih.gov/geo; record number: gse46695). selected genes were classified according to gene ontology category “biological process” using onto-express []. pathway analysis was performed with webgestalt []. hierachical clustering was performed using genespring 10.0 (agilent technologies). all experiments were performed in three […]

2013
PMCID: 3869932
PMID: 24376830
DOI: 10.1371/journal.pone.0084646

[…] first was database for annotation, visualization and integrated discovery (david; http://david.abcc.ncifcrf.gov/) [], which relies on a modified fisher's exact test (ease score), and the second is onto-express [,] (http://vortex.cs.wayne.edu/projects.htm) which implements a hypergeometric statistical method. both of the tools rely on gene ontology (go) as a primary annotation source, but also […]

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, […]

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

[…] t-test. the resulting p-values were adjusted using the false discovery rate method []. the differentially expressed genes underwent a functional analysis based on gene ontology (go) terms using onto express [, ]. canonical metabolic and signalling pathways from the metacore® database (st. joseph, mi, usa) were used to annotate the genes differentially expressed between the ua and uv. […]


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Onto-Express in publications

 (78)
PMCID: 5908625
PMID: 29642183
DOI: 10.1097/MD.0000000000010362

[…] controls. the differentially expressed genes (degs) were identified using linear models for microarray data package. then, gene ontology (go) enrichment analysis for degs was performed by onto-express. subsequently, the protein–protein interaction (ppi) network was constructed and pathway enrichment analysis was performed by search tool for the retrieval of interacting genes (string). […]

PMCID: 5733474
PMID: 29321746
DOI: 10.3389/fpsyt.2017.00271

[…] tpm groups based on the following criteria: detected by either ingenuity pathway analysis (ipa; http://www.ingenuity.com/) or onto-tools pathway-express (https://bioportal.bioontology.org/projects/onto-express) with (i) number of genes ≥3, (ii) nominal p values < 0.05 at both weeks 8 and 12, and further restricting by false discovery rates (fdrs) < 0.15 at both time points. pathways […]

PMCID: 5337511
PMID: 28321227
DOI: 10.3389/fpls.2017.00283

[…] 20,000 × g for 10 min. liquid protein samples were combined with 5x loading buffer (0.3 m tris-hcl ph 8.0, 5% sds, 10% glycerol, 100 mm dtt, 0.05% phenol red), heated at 99°c for 5 min, then loaded onto express plus page 4-20% gels (genscript inc., piscataway, nj, usa). gels were run at 100 v for 100–110 min, then transferred to polyvinylidine difluoride (pvdf) membrane using the trans-blot […]

PMCID: 5325330
PMID: 27588498
DOI: 10.18632/oncotarget.11716

[…] at least 2-fold difference in expression either up- or downregulated. finally, the biological functions of the differentially expressed mrna or target genes of mirna were categorized using the onto-express gene ontology software (http://vortex.cs.wayne.edu/projects.htm)., we found that in total pax3-foxo1 altered the expression of 846 genes, with 562 being upregulated and 284 […]

PMCID: 5548323
PMID: 28936255
DOI: 10.5772/62975

[…] also display a preference for the liver. subsequent experiments have demonstrated that exosomal uptake by kupffer cells leads to tgf-β synthesis and release, activating hepatostellate cells that go onto express fibronectin. this, then, attracts bone marrow-derived macrophages and granulocytes, which are now determined to be a prerequisite for metastasis, opening an avenue for future work., […]


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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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