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Onto-Express specifications


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



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Publications for Onto-Express

Onto-Express citations


Clinical value of integrated‐signature miRNAs in esophageal cancer

PMCID: 5548877
PMID: 28707457
DOI: 10.1002/cam4.1129

[…] on for various types of data (functional, regulatory, and structural) by searching for frequent patterns among annotations and evaluating statistical relevance . This new approach, superior to DAVID, Onto‐Express, ProfCom or FATIGO+ by overcoming the lack of term–term relationships in these analyses, profiles different sides of the same information and offers a more accurate interpretation of the […]


Bleomycin Treated Chimeric Thy1 Deficient Mice with Thy1 Deficient Myofibroblasts and Thy Positive Lymphocytes Resolve Inflammation without Affecting the Fibrotic Response

PMCID: 4537759
PMID: 26300593
DOI: 10.1155/2015/942179

[…] sing a threshold of >2-fold changes in expression. P < 0.05 was considered statistically significant. The analysis of biological processes affected by Thy1 in lung, myofibroblasts was performed using Onto-Express software (Open Channel Foundation, Chicago, IL, USA). […]


Effect of co administration of Angelicae gigantis radix and Lithospermi radix on rat hepatic injury induced by carbon tetrachloride

PMCID: 4378140
PMID: 25829781
DOI: 10.4103/0973-1296.153095
call_split See protocol

[…] sis. The hierarchical clustering was performed using CLUSTER and TREEVIEW program (M.B. Eisen, http://rana.lbl.gov). We considered 1.5 fold of expression change as baseline of up- or down-regulation. OntoExpress program was applied for ontological analysis,[] and cytoscape program was applied for interaction network analysis[] in which databases of BOND (http://bond.unleashedinformatics.com) and t […]


Adaptive Gene Regulation in the Striatum of RGS9 Deficient Mice

PLoS One
PMCID: 3963927
PMID: 24663062
DOI: 10.1371/journal.pone.0092605

[…] arrays 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 ( […]


Up regulation of CLDN1 in gastric cancer is correlated with reduced survival

BMC Cancer
PMCID: 4029627
PMID: 24321518
DOI: 10.1186/1471-2407-13-586
call_split See protocol

[…] differentially expressed genes, lesser expressed genes were filtered out at a cutoff level of FC > 1.5, producing a list of the 130 most differentially expressed genes. This dataset was imported into Onto-Express and Pathway Express [,], part of the Onto-Tools software suite, for functional analysis, and grouped into Gene Ontology (GO) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) cellu […]


The non negative matrix factorization toolbox for biological data mining

Source Code Biol Med
PMCID: 3736608
PMID: 23591137
DOI: 10.1186/1751-0473-8-10

[…] α1=0.01, α2=0.01, λ1=0, λ2=0.01, t1=1, and t2=1. Next, we obtain 81, 37, and 448 genes for the three factors, respectively. As in [], we then performed gene set enrichment analysis (GSEA) by applying Onto-Express [] on each of these sets of genes. Part of the result is shown in Table . We can see that the factor-specific genes selected by NMF correspond to some biological processes significantly. […]


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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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