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AgBase specifications


Unique identifier OMICS_03223
Name AgBase
Restrictions to use None
Maintained Yes


  • person_outline AgBase Team

Publication for AgBase

AgBase citations


Long non coding RNAs of switchgrass (Panicum virgatum L.) in multiple dehydration stresses

BMC Plant Biol
PMCID: 5936019
PMID: 29728055
DOI: 10.1186/s12870-018-1288-3

[…] maize B73 RefGen_v3 database, and the Rice Genome Annotation Project (RGAP) release 7. All target genes and differentially expressed target genes were analyzed. Gene ontology (GO) was analyzed using AgBase GORetriever and GOSlimViewer [], and enriched pathways were identified using NCBI Flink ( based on KEGG (Kyoto Encyclopedia of Genes and G […]


RNA Seq transcriptome analysis of Amaranthus palmeri with differential tolerance to glufosinate herbicide

PLoS One
PMCID: 5908165
PMID: 29672568
DOI: 10.1371/journal.pone.0195488

[…] re [] and transmembrane regions predicted with tmHMM ( Gene ontology terms were derived from the best BLAST match [] and clustered to determine enrichment using the Agbase tool [].The entire dataset was submitted as NCBI BioProject (PRJNA390774), which is a part of the U.S. National Library of Medicine of the National Institutes of Health. The 12 samples that wer […]


Transcriptional and physiological data reveal the dehydration memory behavior in switchgrass (Panicum virgatum L.)

Biotechnol Biofuels
PMCID: 5879616
PMID: 29619087
DOI: 10.1186/s13068-018-1088-x

[…] sis Information Resource Proteins database (release TAIR10), the maize B73 RefGen_v3 database, and the Rice Genome Annotation Project (RGAP) release 7. Gene Ontology (GO) analysis was performed using AgBase GORetriever and GOSlimViewer [], and pathways were enriched using the NCBI Flink ( and KEGG (Kyoto Encyclopedia of Genes and Genomes) data […]


In depth proteomic analysis of boar spermatozoa through shotgun and gel based methods

BMC Genomics
PMCID: 5774113
PMID: 29347914
DOI: 10.1186/s12864-018-4442-2
call_split See protocol

[…] EMBL) for resulting peptide masses and matching peptide spectra. Proteins identified with shotgun were functionally annotated (Gene ontology or GO, Enrichment, and KEGG pathway) using online tools of Agbase (; []) and DAVID (Database for Annotation, Visualization and Integrated Discovery; DAVID Bioinformatics Resources 6.7;; []). […]


Using Human iPSC Derived Neurons to Uncover Activity Dependent Non Coding RNAs

PMCID: 5748719
PMID: 29261115
DOI: 10.3390/genes8120401
call_split See protocol

[…] Functional analyses of differentially expressed genes were carried out using two different approaches. First, we used tools available at the Mississippi State University AgBase portal (version 2.0) [] to assign ontologies to the transcripts of interest. GoAnna annotates genes by transferring ontologies based on sequence homology, and GoSlim further summarizes the resu […]


Aspergillus flavus infection triggered immune responses and host pathogen cross talks in groundnut during in vitro seed colonization

Sci Rep
PMCID: 5574979
PMID: 28851929
DOI: 10.1038/s41598-017-09260-8
call_split See protocol

[…] e log2 fold change values of ≥ + 2 and ≤ − 2 (up- and down-regulated) with significance level ‘yes’ were considered for DEGs.Functional categorization of the DEGs was studied using GoSlim ( while gene ontology (GO) terms were assigned to the expressed genes and assignment of KEGG pathways was carried out using Blast2GO. DiffCoEx an […]


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AgBase institution(s)
Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, MS, USA

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