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TreeMap specifications


Unique identifier OMICS_08814
Name TreeMap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes


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TreeMap citations


Time resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

BMC Biol
PMCID: 5937035
PMID: 29730990
DOI: 10.1186/s12915-018-0518-3

[…] to filter out weak associations. the enrichment was tested as above with a hypergeometric test. the categories with a nominal p value below 0.05 were grouped by their therapeutic areas to draw a treemap using the treemap library. diseases were included into all the therapeutic areas they belonged to., we considered data from three different public ppi data repositories (human interactome […]


De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution

Sci Rep
PMCID: 5882950
PMID: 29615780
DOI: 10.1038/s41598-018-23749-w

[…] to gain insights into the potential biological function underlying these ortholog groups, we analysed the distribution of gene ontology (go) terms for each cluster and visualized these using revigo/treemap (figs  and ). given that the proteins identified by orthomcl clustering are potentially novel to colonial ascidians, a cross-species approach for go enrichment was performed using the human […]


Extensive and systematic rewiring of histone post translational modifications in cancer model systems

Nucleic Acids Res
PMCID: 5934616
PMID: 29618087
DOI: 10.1093/nar/gky224

[…] cultures (219 up and 244 down) were used as target sets. significantly enriched go terms are reported in dataset s4, and were summarized by reducing functional redundancies and visualized by treemap using the revigo web server (), with allowed similarity 0.5 (small), database homo sapiens, and semantic similarity measure simrel., to investigate the consequences of the transition […]


Host Symbiont Cospeciation of Termite Gut Cellulolytic Protists of the Genera Teranympha and Eucomonympha and their Treponema Endosymbionts

PMCID: 5877339
PMID: 29367472
DOI: 10.1264/jsme2.ME17096

[…] that minimized the overall cost of a historical reconstruction. the default event costs were as follows: 0 for a codivergence event, 1 for duplication and host switch events, and 2 for loss events. treemap (charleston, m. treemap 3.0 beta. available at was used to construct the tanglegram for hosts and symbionts., fish was performed to detect […]


Long lived rodents reveal signatures of positive selection in genes associated with lifespan

PLoS Genet
PMCID: 5884551
PMID: 29570707
DOI: 10.1371/journal.pgen.1007272

[…] gene ontologies based on fold-changes (). gene ontologies with fdr≤0.1 were summarized using revigo (allowed similarity = 0.5) []. four of the six largest summarized categories of the resulting treemap (/ tables) were further analyzed due their aging relevance (representative terms given): “translation” (go:0006412), “cellular respiration” (go:0045333), “response to oxidative stress” […]


Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens

Mol Ecol
PMCID: 5900718
PMID: 29421852
DOI: 10.1111/mec.14523

[…] simplified host–pathogen association set to reduce the amount of losses and failure to diverge predicted and facilitate comparisons with core‐pa and paco results. we visualized the interactions with treemap3 (charleston & robertson, ), using the untangling function to improve the layout., refers to the set of host association tested for cophylogeny: “full set” corresponds to the complete […]

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