TreeMap protocols

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chevron_left Cophylogeny reconstruction chevron_right
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Associated diseases

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TreeMap specifications

Information


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 in pipelines

 (6)
2017
PMCID: 5223169
PMID: 28071691
DOI: 10.1038/srep40219

[…] maximum parsimony trees were constructed using paup 4.0b10 (sinauer associates, sunderland, ma, usa) with gaps being treated as missing data. a tanglegram was constructed from both trees using treemap 3b1243., sequences of the eight newly assembled mitochondrial genomes of c. militaris were all submitted to genbank under accession numbers as depicted in ., how to cite this article: zhang, […]

2016
PMCID: 4998650
PMID: 26886650
DOI: 10.1097/MD.0000000000002853

[…] web tool, the database for annotation, visualization and integrated discovery (david) provided by national institute of allergy and infectious diseases (http://david.abcc.ncifcrf.gov/home.jsp)., the treemap was generated by revigo to visualize significant (p < 0.01) go terms that were obtained from the functional annotation chart of biological process terms (bp_fat category) on david., […]

2016
PMCID: 5352092
PMID: 27965457
DOI: 10.18632/oncotarget.13857

[…] xeno conditions and at the same time had similar expression levels in 3d3 and xeno conditions. hierarchical clustering revealed two major gene clusters, as indicated in the heatmap (figure )., the treemap (figure ) displays a two-level hierarchy of go terms as a set of nested rectangles. each box is representative of a single cluster. each branch of the tree is given a rectangle, […]

2015
PMCID: 4456939
PMID: 26047021
DOI: 10.1038/srep10917

[…] high semantic similarity. the size of these cluster representatives, which are joined in different superclusters each indicated by 1 colour, is proportional to the p-values derived by revigo. the treemap figures were then adapted by changing the colours of the superclusters., how to cite this article: smolders, k. et al. an effective plasma membrane proteomics approach for small tissue […]

2015
PMCID: 4479327
PMID: 26109289
DOI: 10.1186/s12870-015-0534-1

[…] the enriched go terms. blast2go enrichment analysis was based on a f-fisher test (fdr < 0.05). the relation among go terms was assigned using revigo with the resvik algorithm option [] and r treemap library. degs annotated as related to response to water, including water transport and water deprivation were identified. we used the plant transcription factor database (plntfdb, […]


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TreeMap in publications

 (110)
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 […]

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 […]

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 http://sites.google.com/site/cophylogeny) was used to construct the tanglegram for hosts and symbionts., fish was performed to detect […]

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 […]

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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