ArrayXPath protocols

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ArrayXPath specifications

Information


Unique identifier OMICS_09771
Name ArrayXPath
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publications for ArrayXPath

ArrayXPath in pipeline

2007
PMCID: 2140066
PMID: 17897448
DOI: 10.1186/1471-2105-8-360

[…] gene ontology (go) classification [,-]. a complementary approach is to interpret the data in a biological way by making use of pathway visualization tools, such as genmapp [,], metacore [] and/or arrayxpath ii []. these tools link an element in a pathway with a specific identifier, usually by an ensembl, uniprot, unigene, entrez gene or go id. hence, to allow the biological interpretation […]


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ArrayXPath in publications

 (9)
PMCID: 3919110
PMID: 24579087
DOI: 10.1155/2014/763237

[…] significance of gene expression microarray data []. when pathways are extracted from pathway miner, the levels of gene expression can be discerned, but four samples could be shown at a time. arrayxpath functions by focusing on mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway information and by displaying the results […]

PMCID: 3397482
PMID: 22837650
DOI: 10.3390/ijms13066561

[…] [,] and gene-sifter use a standardized z-score. pathwayprocessor [], pathmapa [], cytoscape [], and pathwaymine [] use fisher’s exact test. metacore uses a hypergeometric model, while arrayxpath [] offers both fisher’s exact test and a false discovery rate. vitapad [] and pathway studio [] focus on visualization approaches alone and do not offer any detailed analyses. finally, […]

PMCID: 3278848
PMID: 22373334
DOI: 10.1186/1471-2105-12-S13-S8

[…] interpretation. such functional categorization was accomplished using go terms and biological pathways. we used david 2.1 (http://david.abcc.ncifcrf.gov/) for go term enrichment analysis and arrayxpath [,] for pathway annotation. a modified fisher’s exact test is performed to determine whether the proportions of members falling into each category differ by group, when those in two […]

PMCID: 2734540
PMID: 19664232
DOI: 10.1186/1755-8794-2-51

[…] for the functional category classification (student's t-test was used in gene ontology (go)). potential pathways involved in fibrosing steatohepatitis were investigated using a web-based service (arrayxpath; ), where fisher's exact test and the fdr following storey's scheme were applied to evaluate the statistical significance., in the line exhibiting "high" hcv core protein, over 70% […]

PMCID: 2702506
PMID: 19584916
DOI: 10.1155/2009/917084

[…] designed mainly for identification of important genes. other tools like genmapp [], pharmgkb [], and kegg [] only show the positions of the genes on a known pathway. although some softwares such as arrayxpath [] integrate the pathway resources and provide analysis and visualization tools for deciphering the important genes and pathway structures, no notion of chaining or aggregating regulatory […]


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ArrayXPath institution(s)
Seoul National University Biomedical Informatics (SNUBI); Human Genome Research Institute, Seoul National University College of Medicine, Seoul, Korea

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