GOTM statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GOTM
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Tool usage distribution map

This map represents all the scientific publications referring to GOTM per scientific context
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Associated diseases

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Popular tool citations

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Protocols

GOTM specifications

Information


Unique identifier OMICS_18787
Name GOTM
Alternative name GOTree Machine
Interface Web user interface
Restrictions to use None
Programming languages PHP
License GNU General Public License version 3.0
Computer skills Basic
Stability No
Maintained No

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Publication for GOTree Machine

GOTM citations

 (21)
call_split

Delineation of the HPV11E6 and HPV18E6 Pathways in Initiating Cellular Transformation

2017
PMCID: 5672010
PMID: 29164058
DOI: 10.3389/fonc.2017.00258
call_split See protocol

[…] -change cutoff of ±2.0 with significance FDR of ≤0.05, using the Partek® genomics suite™ 6.6 software. A web-based Venn diagram () was used to calculate and identify genes that were induced by HPVE6. GOTree machine (GOTM) () was used for GO analysis of the DEGs. The IPA system was used to identify the top most significantly regulated pathways from the Venn diagram list. The results were presented […]

library_books

IL 6 and Akt are involved in muscular pathogenesis in myasthenia gravis

2015
PMCID: 4308930
PMID: 25627031
DOI: 10.1186/s40478-014-0179-6

[…] Transcriptome analysis was performed on both data sets, human and rats. The data were analyzed using the GOTM [] that generates a tree-like structure and yields two types of data: 1) the subcategories presenting statistical changes and 2) the hierarchy between these different subcategories. In this repre […]

library_books

Integrative analysis of high throughput RNAi screen data identifies the FER and CRKL tyrosine kinases as new regulators of the mitogenic ERK dependent pathways in transformed cells

2014
BMC Genomics
PMCID: 4367906
PMID: 25540073
DOI: 10.1186/1471-2164-15-1169

[…] w) the mitotic index (MI) using a Fisher´s exact test ( http://babelomics3.bioinfo.cipf.es/) []. Di-acyclic graphs for cellular component ontology were generated using the Gene Ontology Tree Machine (GOTM, http://bioinfo.vanderbilt.edu/webgestalt/) [].The kinase interactome networks were built using PhosphoPOINT, the human interactome and phosphoprotein database ( http://kinase.bioinformatics.tw/) […]

library_books

Genome wide methylation profiling of the bronchial mucosa of asthmatics: relationship to atopy

2013
BMC Med Genet
PMCID: 3616917
PMID: 23521807
DOI: 10.1186/1471-2350-14-39

[…] 10 and (2) a P-value of <0.01. Heatmap of the differentially methylated CpG sites was done and viewed by GenomeStudio software. Gene ontology enrichment of DNA methylation profile was performed using GOTM (http://bioinfo.vanderbilt.edu/gotm/), which is based on hypergeometric test to show the overrepresented gene ontology categories (p-value < 0.01) []. The p-value was also calculated according to […]

library_books

Chapter 8: Biological Knowledge Assembly and Interpretation

2012
PLoS Comput Biol
PMCID: 3531281
PMID: 23300429
DOI: 10.1371/journal.pcbi.1002858

[…] resentation helps users to understand biological semantics and contexts. A number of analysis tools with these steps have been introduced: ArrayXPath, Pathway Miner, EASE in pathway analysis, GOFish, GOTree Machine, FatiGO, GOAL, GOMIner, FuncAssociate in ontology analysis and GeneMerge, MAPPFinder, DAVID, GFINDer, OntoTools in both analyses . […]

library_books

Whole transcriptome analysis of a reversible neurodegenerative process in Drosophila reveals potential neuroprotective genes

2012
BMC Genomics
PMCID: 3496630
PMID: 22978642
DOI: 10.1186/1471-2164-13-483

[…] analysis was carried out using VLAD online tool []. Then, functional groups lists of genes were manually elaborated based on the literature and the following databases: VLAD [], AMIGO [], GATHER [], GOTM [] and FlyBase []. Homozygous sall mutant misregulated genes found in our analysis (at stage 16, 17 and at the transition between both stages), were then classified in our “Functional Groups refe […]


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GOTM institution(s)
Graduate School in Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, TN, USA; Oak Ridge National Laboratory, Oak Ridge, TN, USA
GOTM funding source(s)
Supported by the INIA project (NIH/NIAAA, U01-AA013532), the BISTI project (NIH/ NIDA, P01-DA015027) and the ORNL LDRD project (DOE, AC05- 00OR22725).

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