Graphite Web protocols

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Graphite Web specifications

Information


Unique identifier OMICS_17607
Name Graphite Web
Interface Web user interface
Restrictions to use None
Input data A data matrix expression file.
Input format TSV
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Chiara Romualdi <>

Publication for Graphite Web

Graphite Web in pipelines

 (2)
2016
PMCID: 5054603
PMID: 27774052
DOI: 10.3389/fncel.2016.00230

[…] at default settings (huang da et al., ,)., for visualization of biological pathways, the data matrix of log2 transformed and rma-normalized microarray data were analyzed using a public web server graphite web (sales et al., ). of the available analytical methods, signaling pathway impact analysis (spia) was used. over the classical probabilistic components, the spia also applies statistical […]

2014
PMCID: 4200275
PMID: 25164807
DOI: 10.1074/jbc.M114.602938

[…] values of the biological replicates for each genotype were log2 transformed and mediated. pathway analyses and network visualization of differentially expressed genes was performed using the graphite web tool that combines topological and multivariate pathway analyses ()., crosses were raised at 20 °c on standard sucrose medium. third instar larvae or freshly enclosed flies […]


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Graphite Web in publications

 (9)
PMCID: 5259824
PMID: 28155707
DOI: 10.1186/s12859-016-1335-8

[…] trap. it means π ∗ are prioritized well in contexttrap by using literature information., we compared the performances of contexttrap with three other pathway analysis methods included in the graphite web server [], also with the original trap. graphite web is a web tool for pathway analysis using gene expression data, providing various analysis methods. for the comparison, three pathway […]

PMCID: 5054603
PMID: 27774052
DOI: 10.3389/fncel.2016.00230

[…] at default settings (huang da et al., ,)., for visualization of biological pathways, the data matrix of log2 transformed and rma-normalized microarray data were analyzed using a public web server graphite web (sales et al., ). of the available analytical methods, signaling pathway impact analysis (spia) was used. over the classical probabilistic components, the spia also applies statistical […]

PMCID: 4706066
PMID: 26834999
DOI: 10.5256/f1000research.7870.r11114

[…] list of genes from analysis, filtering and annotation of variant calls and from differential expression analysis using whole genome micro-arrays, were mapped to pathways using the web version of graphite web employing kegg and reactome databases. the network of interactions between genes was drawn originally using cytoscape (v3.1.1) using the .sif file created by graphite web ( )., we used […]

PMCID: 4552880
PMID: 26317806
DOI: 10.1371/journal.pone.0137128

[…] (database for annotation, visualization, and integrated discovery) & kegg (kyoto encyclopedia of genes and genomes) were used to select, annotate and visualize genes by function and pathway[][]. graphite web software was used to represent signalling pathways present in the analysis[]. the resulting microarray data sets were uploaded at the array express microarray data repository […]

PMCID: 4583640
PMID: 26484227
DOI: 10.1016/j.gdata.2015.05.023

[…] of the tm4 microarray software suite . gene ontology analysis was performed using david web tool , while pathway analysis was performed applying gene set enrichment analysis (gsea) as implemented in graphite web tool . the kegg pathway database was used and only pathways that presented at least 10 mapped genes in common with our gene expression matrix were considered in the analysis. […]


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Graphite Web institution(s)
Department of Biology, University of Padova, Padova, Italy

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