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


  • Animals
    • Bombyx mori
    • Bos taurus
    • Gallus gallus
    • Mus musculus
  • Plants
    • Arabidopsis thaliana
    • Glycine max
    • Medicago truncatula
    • Oryza sativa
    • Populus trichocarpa
    • Vitis vinifera
    • Zea mays

Maintainers


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

Additional information


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

agriGO articles

agriGO citations

 (14)
2018
PMCID: 5787291

[…] dj) < 0.05, and then genes with positive log2_fc were determined as up-regulated, and genes with negative values were determined as down-regulated. go term enrichment analysis were performed using agrigo with default settings [42]., statistical methods were used as previously reported: we used k-means clustering as the clustering method to classify genes based on nucleosome patterns across the […]

2018
PMCID: 5767312

[…] 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 […]

2017
PMCID: 5662759

[…] levels compared to dmso control values, which was in turn log2-transformed and computed for spearman correlation coefficients between samples. gene ontology analysis was performed using the online “agrigo” tool (http://bioinfo.cau.edu.cn/agrigo/), and a heat map was created using the r “pheatmap” package., one-week-old col-0 plants grown on half-strength ms agar media were transferred […]

2017
PMCID: 5787830

[…] expressed genes showing significant enrichment in response to control and induced treatments and comparisons were analysed using tair (http://www.arabidopsis.org/tools/bulk/go/index.jsp), agrigo (du et al., 2010), genesis (sturn et al., 2002) and kegg databases., quantitative real‐time pcr (qrt‐pcr) was performed on cdna obtained from one of the biological replicates belonging […]

2017
PMCID: 5527001

[…] with fold change ≥2, fdr ≤ 0.01 and read number ≥20 in at least one of the two comparison samples were considered to be differentially expressed. gene ontology (go) analyses were performed using agrigo61., three biological replicates of total rna were used for qrt-pcr analysis. total rna was extracted as described above. after dnase i treatment, approximately 4 μg of total rna was reverse […]

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.