agriGO pipeline

agriGO specifications

Information


Unique identifier OMICS_28869
Name agriGO
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Bombyx mori
  • Mammals
    • Bos taurus
  • Plants and Fungi
    • Arabidopsis thaliana
    • Glycine max
    • Medicago truncatula
    • Oryza sativa
    • Populus trichocarpa
    • Vitis vinifera
    • Zea mays
  • Rodents
    • Mus musculus
  • Vertebrates
    • Gallus gallus

Maintainers


  • person_outline Zhen Su <>
  • person_outline Wenying Xu <>

Additional information


http://systemsbiology.cau.edu.cn/agriGOv2/FAQ.php

Publications for agriGO

agriGO IN pipelines

 (54)
2018
PMCID: 5754085
PMID: 29300744
DOI: 10.1371/journal.pone.0189185

[…] treatment. a false discovery rate (fdr) ≤ 0.1 and log2fc ≥ ±1 was used as the threshold to judge the significance of each gene expression difference. go analysis was performed using a web-based tool agrigo (http://bioinfo.cau.edu.cn/agrigo) [25], based on available phaseolus vulgaris annotations. the differentially expressed genes (deg) were compared with candidate genes found in the qtl […]

2018
PMCID: 5767312
PMID: 29375595
DOI: 10.3389/fpls.2017.02212

[…] proost et al., 2015) annotation data were used to annotate mapped sequences. gene ontology enrichment analysis was carried out using singular enrichment analysis (sea) available through agrigo toolkit (http://bioinfo.cau.edu.cn/agrigo/analysis.php). customized analysis was performed using hypergeometric statistical test, at significance level of p = 0.01 and minimum mapping entries […]

2018
PMCID: 5767312
PMID: 29375595
DOI: 10.3389/fpls.2017.02212

[…] data were used to annotate mapped sequences. gene ontology enrichment analysis was carried out using singular enrichment analysis (sea) available through agrigo toolkit (http://bioinfo.cau.edu.cn/agrigo/analysis.php). customized analysis was performed using hypergeometric statistical test, at significance level of p = 0.01 and minimum mapping entries of 5. the go data for the whole set […]

2018
PMCID: 5798027
PMID: 29378032
DOI: 10.1093/gbe/evy006

[…] in fragments per kilobase of transcript per million mapped reads (fpkm) using cufflinks v2.2.1(trapnell et al. 2010)., all enrichment and go terms reported in this paper were calculated using agrigo (du et al. 2010). the go annotation file was retrieved through the rice genome annotation project (kawahara et al. 2013). enrichment was determined using the fisher’s exact test […]

2018
PMCID: 5812550
PMID: 29444085
DOI: 10.1371/journal.pgen.1007234

[…] between b73 and mo17. the go enrichments and the pathway enrichments of the regulated genes by hotspots were conducted using bingo plugin in cytoscape based on the annotation information from agrigo and maizecyc database, respectively. the results of go enrichments and pathway enrichments are in table s5 and table s6, respectively., in the legend for fig 3, the phrase “the additive […]

agriGO institution(s)
State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
agriGO funding source(s)
Supported by the National Natural Science Foundation of China [31371291, 31571360].

agriGO review

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Peter Scott

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Web
It gives better annotations for plants that PANTHER. For example Panther will asign arabidopsis proteins labels like "alzhimers related protein" while AgriGo won't.