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GoGene specifications


Unique identifier OMICS_16314
Name GoGene
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No


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Publication for GoGene

GoGene citations


Var2GO: a web based tool for gene variants selection

BMC Bioinformatics
PMCID: 5123234
PMID: 28185576
DOI: 10.1186/s12859-016-1197-0

[…] type. While this approach might help in reducing the size of the data, it greatly increase the risk of losing meaningful pieces of information.Examples of available tools for gene annotation include: GoGene [], which is conceived to allow gene annotation through GO and MeSH (Medical Subject Headings) vocabularies. It requires a list containing gene names/identifiers as input. The output list with […]


miRNA Profiling Reveals Dysregulation of RET and RET Regulating Pathways in Hirschsprung's Disease

PLoS One
PMCID: 4774952
PMID: 26933947
DOI: 10.1371/journal.pone.0150222

[…] he putative targets, only genes with previously reported functions in the pathology of Hirschsprung’s Disease were considered to represent true targets of miRNAs differentially expressed in HSCR. The GoGene (http://gopubmed.org/gogene) [] and NCBI Pubmed databases (http://www.ncbi.nlm.nih.gov/pubmed/) were used for literature retrieval. […]


Transcriptional response of porcine skeletal muscle to feeding a linseed enriched diet to growing pigs

PMCID: 4746901
PMID: 26862397
DOI: 10.1186/s40104-016-0064-1

[…] ially expressed genes as follows. We constructed a synthesized gene set containing genes related to muscle mass regulation based on gene ontology (GO) annotation and literature mining. Pubgene [] and GOGene [] are literature mining tools that can retrieve genes involved in skeletal muscle growth in our data. Database for Annotation, Visualization and Integrated Discovery software [] was used to an […]


Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database

Source Code Biol Med
PMCID: 4106183
DOI: 10.1186/1751-0473-9-15

[…] most relevant to a given gene. A small number of literature search tools are also specifically designed to support the analysis of lists of genes. The most directly comparable in aims to Annokey are GoGene [] and GeneValorization [].GoGene is a tool that draws on associations between genes and functionally-related terms extracted from the literature, in combination with structured information in […]


From Data towards Knowledge: Revealing the Architecture of Signaling Systems by Unifying Knowledge Mining and Data Mining of Systematic Perturbation Data

PLoS One
PMCID: 3634064
PMID: 23637789
DOI: 10.1371/journal.pone.0061134

[…] nalysis of the original paper. Given a list of differentially expressed genes responding to a perturbation instance, we represent the genes and their annotations using a data structure referred to as GOGene graph . In such a graph, a node represents a GO term and a directed edge between a pair of nodes reflects an “is-a” relationship between the GO terms; in addition, each node keeps track of the […]


The Mammalian Adult Neurogenesis Gene Ontology (MANGO) Provides a Structural Framework for Published Information on Genes Regulating Adult Hippocampal Neurogenesis

PLoS One
PMCID: 3489671
PMID: 23139788
DOI: 10.1371/journal.pone.0048527

[…] Query of the GoGene database (http://www.gopubmed.com) was made on April 19, 2011. The search term used was [adult AND neurogenesis]. The 1735 hits retrieved were filtered for the MeSH term “Hippocampus” (ID: D00 […]

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GoGene institution(s)
Biotechnology Center, Technische Universität Dresden, Dresden, Germany; Department of Computer Science and Engineering, Arizona State University, Tempe, AZ, USA
GoGene funding source(s)
This work was supported by the EU project SEALIFE and the BMBF project ForMaT.

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