AmiGO protocols

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AmiGO specifications

Information


Unique identifier OMICS_02266
Name AmiGO
Interface Web user interface
Restrictions to use None
Programming languages Javascript
Computer skills Basic
Version 2.4.24
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Seth Carbon <>

Publications for AmiGO

AmiGO in pipelines

 (16)
2017
PMCID: 5442315
PMID: 28513600
DOI: 10.1038/ncomms15120

[…] with annotated genes to obtain lists of genes with specific coverage by h3k4me3 and h3k27me3. spearman rank correlation coefficients were computed and tested for significance in genstat 18 (ref. )., amigo 2 versions 2.3.2 and 2.4.24 (ref. ) were used for go analysis to assess the over- and underrepresentation in biological processes of significantly differentially-h3k4me3-modified genes […]

2017
PMCID: 5573286
PMID: 28846681
DOI: 10.1371/journal.pone.0182469

[…] duf221 domain., the number of ests (expression sequence tags) for osddp genes were determined using data of rice genome annotation project [], whereas their functional annotations were verified by amigo 2 []. to provide a simple nomenclature, members of the studied gene family from rice were named from 1 to10 as per their appearance in chronological order (from top to bottom on the respective […]

2016
PMCID: 4823825
PMID: 27048880
DOI: 10.1038/ncomms11185

[…] using deseq2 (ref. ). the top 200 over expressed and top 200 under expressed genes in dipg3-pons 2 (the sub-clone with pik3ca activating mutation) were analysed for geneset enrichment using both amigo 2 tool (http://amigo.geneontology.org/amigo) provided by gene ontology and david (https://david.ncifcrf.gov/). we used panther overrepresentation test (release 20,150,430) for analysis type […]

2016
PMCID: 5217106
PMID: 27836907
DOI: 10.1534/g3.116.033241

[…] associated with an eqtl hotspot, we defined hotspot confidence boundaries as being the most frequently observed 95% confidence limits of all significant eqtl centered in the hotspot. we used amigo2 () to identify “molecular function” or “biological process” gene ontology (go) terms associated with transcriptional regulation by applying the search term “transcription regulation and – […]

2015
PMCID: 4770214
PMID: 26553800
DOI: 10.1093/nar/gkv1162

[…] euclidean distance on the rlog-transformed counts. heatmap were generated using the z-scored-transformed rlog values of significantly changed genes., gene ontology analysis was carried out using the amigo 2 tools (). multiple comparisons were corrected using bonferroni correction., differential methylation analysis was carried out in the context of promoter (−2 kb ∼ tss) and gene body using […]


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AmiGO in publications

 (118)
PMCID: 5942847
PMID: 29702646
DOI: 10.1371/journal.pntd.0006459

[…] searched using the interproscan [] and ncbi conserved domains database (cdd) []. gene ontology (go) for specific biological process, molecular function, and cellular component were assigned using amigo ver. 2.4.26 []., the amino acid sequences of ost subunits were retrieved from the uniprotkb/swiss-prot database []. multiple sequence alignments were carried out with the parameters of g-ins-i […]

PMCID: 5910380
PMID: 29679077
DOI: 10.1038/s41467-018-04003-3

[…] analysis. enrichment analyses of recon 2 and go categories, were performed using perseus. to further analyse the individual proteins contained in enriched go categories, they were queried using the amigo web application. the gobp category of cell redox homoeostasis (go:0045454) for mus musculus was downloaded on 07/10/2017. global protein cysteine content analysis of the metabolic […]

PMCID: 5875016
PMID: 29598829
DOI: 10.1186/s13072-018-0182-4

[…] in quotients and combined p value across sites in the region: the enrichment analysis used the combined rank among the 1000 best-ranking regions and a hypergeometric test to identify go terms in the amigo 2 database []. pairwise comparison of triplicate samples from each cell line against wt htert was also made to determine change in beta value and associated combined p-value, adjusted […]

PMCID: 5882314
PMID: 29662623
DOI: 10.18632/oncotarget.24664

[…] determined by fdr corrected p-value from multiple t-tests < 0.05. microarray data were deposited in geo with accession number gse104383., gene ontology analyses were performed using the programs amigo 2 [] and revigo []. the gene networks, pathways and functional analyses were generated through the use of qiagen’s ingenuity pathway analysis (ipa®, qiagen redwood city, […]

PMCID: 5915032
PMID: 29455577
DOI: 10.1080/15548627.2017.1415189

[…] manual go annotation was performed essentially as described by patel et al []. the most specific go terms, representing the experimental data presented in each paper, were identified using the amigo or quickgo browsers [,,] and a consistent annotation approach was used []. the type of experimental data reported in the paper guides the selection of evidence codes associated […]


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AmiGO institution(s)
CALIPHO group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland; Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA; Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, CA, USA
AmiGO funding source(s)
National Institutes of Health/National Human Genome Research Institute grant [HG002273].

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