agriGO statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Gene set enrichment analysis Gene Ontology annotation Differential expression chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

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 No
Maintained No

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


This tool is not available anymore.

Additional information


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

Publications for agriGO

agriGO in pipelines

 (95)
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) [], based on available phaseolus vulgaris annotations. the differentially expressed genes (deg) were compared with candidate genes found in the qtl regions., […]

2018
PMCID: 5787291
PMID: 29373953
DOI: 10.1186/s12864-017-4397-8

[…] 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 []., 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 ts […]

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

[…] calculated the expression in fragments per kilobase of transcript per million mapped reads (fpkm) using cufflinks v2.2.1()., all enrichment and go terms reported in this paper were calculated using agrigo (). the go annotation file was retrieved through the rice genome annotation project (). enrichment was determined using the fisher’s exact test with correction for multiple testing. results […]

2018
PMCID: 5826930
PMID: 29483511
DOI: 10.1038/s41467-018-03238-4

[…] in at least sample were subjected to differential expression analysis. the cutoff for differential expression was adjusted false discovery rate p < 0.05. go term analysis was performed with agrigo singular enrichment analysis using the hypergeometric statistical test method, with significance level set to 0.01., five samples of young panicle (0.2–0.9 cm) were collected from wt btx623 […]

2018
PMCID: 5859661
PMID: 29554982
DOI: 10.1186/s40168-018-0434-3

[…] sequences (refseq) []: plant-refseq release 71 [], protozoa-refseq release 71 [] and fungal-refseq release 72 []. brachypodium distachyon and arabidopsis thaliana databases were downloaded from agrigo []. the following protein databases, including kog (eukaryotic orthologous group) annotation files for functional annotation, were downloaded from jgi [, ]: arabidopsis lyrata [], rhizophagus […]


To access a full list of citations, you will need to upgrade to our premium service.

agriGO in publications

 (674)
PMCID: 5958073
PMID: 29773913
DOI: 10.1038/s41598-018-25963-y

[…] chemiluminescence, the membrane was stained with colloidal gold solution., statistical analyses were performed using r (v3.2.0) open software. gene ontology (go) analysis was performed using agrigo (http://bioinfo.cau.edu.cn/agrigo/)., , junko hasegawa and takuya sakamoto contributed equally to this work., electronic supplementary material , supplementary information accompanies […]

PMCID: 5954142
PMID: 29765069
DOI: 10.1038/s41598-018-25845-3

[…] contigs followed by pediculus humanus corporis, nasonia vitripennis, and aspergillus oryzae rib40 (table ).figure 1table 3figure 2, the go mapping was performed using a. pisum data available at agrigo database. a total of 102 biological processes, 68 molecular functions, and 27 cellular components were mapped. cellular process (2167 genes), metabolic process (2348 genes), primary metabolic […]

PMCID: 5945678
PMID: 29748645
DOI: 10.1038/s41598-018-25826-6

[…] (rsem; https://deweylab.github.io/rsem). fold change was calculated and transcripts that exhibited two fold or above differential expression were considered as differentially expressed. agrigo’s singular enrichment analysis (sea) module was used to identify the enriched gene ontology terms (http://bioinfo.cau.edu.cn/agrigo/analysis.php). the enrichment analysis was performed […]

PMCID: 5943562
PMID: 29774046
DOI: 10.3389/fpls.2018.00601

[…] in ubi:dacbf4 under normal and cold-stress conditions (supplementary table ). to identify enriched gene ontology (go) terms for these genes, over-represented go categories were analyzed using agrigo (fisher's exact test p < 0.05) (tian et al., )., in the biological process category, the go terms photosynthesis, generation of precursor metabolites and energy, and translation […]

PMCID: 5930771
PMID: 29720087
DOI: 10.1186/s12864-018-4700-3

[…] of dtgs common to all of the dehydrated cg rhizome segments. over-represented functional gene categories within each cluster were determined using go enrichment analysis (http://bioinfo.cau.edu.cn/agrigo/). dtg annotation was achieved using the plexdb tool (www.plexdb.org). consensus sequences of selected probes were subjected to blast search against uniref90 (www.uniprot.org) using blastx, […]


To access a full list of publications, you will need to upgrade to our premium service.

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

star_border star_border star_border star_border star_border
star star star star star

Peter Scott

star_border star_border star_border star_border star_border
star star star star star
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.