Paintomics protocols

View Paintomics computational protocol

Paintomics statistics

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Paintomics specifications

Information


Unique identifier OMICS_03546
Name Paintomics
Interface Web user interface
Restrictions to use None
Programming languages Perl, Python
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline A Conesa <>
  • person_outline Ana Conesa <>
  • person_outline PaintOmics Team <>

Additional information


The previous version of the application can be run at http://www.paintomics.org/cgi-bin/main2.cgi http://paintomics.readthedocs.io/en/latest/

Publications for Paintomics

Paintomics in pipelines

 (2)
2017
PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] microarray and pathway data (incromap) [], integrated interactome system (iis) [], kazusa plant pathway viewer (kappa-view4) [], mapman [], prometra (which is integrated with meltdb 2.0) [], paintomics [], visualization and analysis of networks containing experimental data (vanted) [], mbrole [], and integrated molecular pathway level analysis (impala) [] go 1 step further and integrate […]

2016
PMCID: 4728800
PMID: 26813401
DOI: 10.1186/s13059-016-0881-8

[…] has been used to identify pathways that are regulated at both the gene expression and the metabolite level, and tools are available that visualize results within the pathway context (masstrix [], paintomics [], vanted v2 [], and steinernet [])., integration of more than two genomic data types is still at its infancy and not yet extensively applied to functional sequencing techniques, […]


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Paintomics in publications

 (11)
PMCID: 5845109
PMID: 29556248
DOI: 10.3389/fgene.2018.00058

[…] pr+bc animals (the adjusted p < 0.10; the log fold change was 0.58). commonly changed genes, both up- and downregulated, were mapped to kegg biological pathways using the david bioinformatics and paintomics platform. commonly deregulated pathways included the pi3k-akt signaling pathway, protein digestion and absorption, ecm-receptor interactions, and neuroactive ligand-receptor interactions […]

PMCID: 5749025
PMID: 29291722
DOI: 10.1186/s12859-017-2006-0

[…] analysis (ipa®, qiagen, redwood city, ca), kegg [], masstrix [], mbrole [], metaboanalyst, metabox [], metacore™ (thomson reuters inc., carlsbad, ca), metamapp [], metexplore, metscape [], mpea [], paintomics [], papi [], pathvisio [], reactome [], small molecule pathway database (smpdb) [], wikipathways [] and xcms []., the main features of these tools were summarized on a binary matrix […]

PMCID: 5604420
PMID: 28923083
DOI: 10.1186/s13024-017-0210-z

[…] ontology (go) enrichment by metascape (http://metascape.org) [] using a hypergeometric test corrected p-value lower than 0.05. masigpro clusters were also analyzed for kegg pathway enrichments using paintomics 3 [] with significant pathways selected based on fisher’s exact test p-value lower than 0.05., rna was converted to cdna using superscript iii reverse transcriptase (life technologies) […]

PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] microarray and pathway data (incromap) [], integrated interactome system (iis) [], kazusa plant pathway viewer (kappa-view4) [], mapman [], prometra (which is integrated with meltdb 2.0) [], paintomics [], visualization and analysis of networks containing experimental data (vanted) [], mbrole [], and integrated molecular pathway level analysis (impala) [] go 1 step further and integrate […]

PMCID: 5333161
PMID: 28252038
DOI: 10.1038/srep43518

[…] of cho cell culture., the omics approaches mentioned above are highly dependent on data analysis to accurately process information from the high-throughput data acquisition. software tools including paintomics, inmex, and multialign were developed for transcriptomic, metabolomic, and liquid chromatography mass spectrometry (lc-ms) proteomic data analysis. paintomics provides a web-based tool […]


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Paintomics institution(s)
Genomics of Gene Expression Lab, Centro de Investigacion Prıncipe Felipe, Valencia, Spain; Department of Applied Statistics, Operations Research and Quality, Universitat Politecnica de Valencia, Spain; Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA; Department of Cellular Biology, University of Brasilia, Biological Sciences Institute, Brasilia, Brazil; Genetics Institute, University of Florida, Gainesville, FL, USA
Paintomics funding source(s)
Supported by European Union Seventh Framework Programme [FP7/2007–2013] under the grant agreement [306000-STATegra]; Marie Curie International Research Staff Exchange Scheme under grant agreement [612583-DEANN]; Spanish MINECO [BIO2012-40244]; and by INB Grant [PT17/0009/0015 - ISCIII-SGEFI / ERDF].

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