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Protocols

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 citations

 (223)
call_split

The transcription factor Spores Absent A is a PKA dependent inducer of Dictyostelium sporulation

2018
Sci Rep
PMCID: 5923282
PMID: 29704004
DOI: 10.1038/s41598-018-24915-w
call_split See protocol

[…] 00 bp shift in positions of peak summits between experiments. Peaks were annotated to the gene with the closest start codon, using ChIPpeakAnno. Gene ontology (GO) enrichment was determined using the Amigo tool at the GO consortium (www.geneontology.org/) with a threshold cutoff of p ≥ 0.05. […]

library_books

Proteome wide analysis of cysteine oxidation reveals metabolic sensitivity to redox stress

2018
Nat Commun
PMCID: 5910380
PMID: 29679077
DOI: 10.1038/s41467-018-04003-3

[…] t 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 and mitochondr […]

library_books

Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression

2018
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 for multip […]

call_split

Cancer reversion with oocyte extracts is mediated by cell cycle arrest and induction of tumour dormancy

2018
Oncotarget
PMCID: 5882314
PMID: 29662623
DOI: 10.18632/oncotarget.24664
call_split See protocol

[…] on was 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, www.qiagen.com/ingenuity […]

library_books

Detection of genomic structural variations in Guizhou indigenous pigs and the comparison with other breeds

2018
PLoS One
PMCID: 5860705
PMID: 29558483
DOI: 10.1371/journal.pone.0194282

[…] luding SLC16A4, SLC16A12, SLC5A12, SLC16A5, and SLC16A7. For all of the five genes involved DEL variation located in the intron region. However, we retrieved 252 GO terms related with ion transports (AmiGO 2, http://amigo.geneontology.org/amigo/landing). It seemed that the effects of SV on the ion transports might be compensated by other members of SLC family.The Xiang pig is well known Chinese mi […]

library_books

Integrative analysis of competing endogenous RNA network focusing on long noncoding RNA associated with progression of cutaneous melanoma

2018
PMCID: 5911588
PMID: 29522273
DOI: 10.1002/cam4.1315

[…] NAs in the ceRNA network, there were three mRNAs that were statistically significant in the survival analysis and directly linked with hsa‐miR‐33a‐3p (CCR5, CXCL11, and ADAMDEC1) and hsa‐miR‐106b‐5p (AMIGO2, IL21R, and MSR1), of which hsa‐miR‐33a‐3p was the risk factor from the survival analysis. This may hint that perhaps the dysregulation of mRNAs has more consequential effects on the developmen […]

Citations

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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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