AmiGO pipeline

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

 (8)
2017
PMCID: 5442315
PMID: 28513600
DOI: 10.1038/ncomms15120

[…] 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. 69)., amigo 2 versions 2.3.2 and 2.4.24 (ref. 70) 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 [43], whereas their functional annotations were verified by amigo 2 [44]. 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 […]

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 (35). 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 […]

2014
PMCID: 3969325
PMID: 24682084
DOI: 10.1371/journal.pone.0093462

[…] were used to perform differential gene expression analysis among treatments [69]., gene ontology classification of all genes exhibiting significant changes in transcript levels was conducted using amigo online tool [70]. those with only cuff numbers assigned during automatic analysis were manually checked against their positions using tair resources. gene ids and their putative functions […]

2013
PMCID: 3602887
PMID: 23520432
DOI: 10.6026/97320630009182

[…] center for biotechnology information), using the blastx and blastn algorithm [13]. comparison with the homologous sequences was done with clustalw [14]. gene ontology term was assigned through amigo blast [15]. phylogenetic trees were plotted by the maximum likelihood method using mega5 software package [16, 17]., partial cdna fragments of 214 bp and 299 bp, named mg-flp-1 and mg-flp-12 […]

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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