GORetriever protocols

View GORetriever computational protocol

GORetriever statistics

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Associated diseases

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GORetriever specifications

Information


Unique identifier OMICS_22589
Name GORetriever
Interface Web user interface
Restrictions to use None
Input data Some protein accessions.
Input format TXT
Computer skills Basic
Stability Stable
Maintained Yes

Additional information


http://www.agbase.msstate.edu/help/retrieverhelp.htm http://www.agbase.msstate.edu/Education/NABDAWorkshop/tutorial_3/tutorial_3.htm

GORetriever in pipelines

 (8)
2018
PMCID: 5879616
PMID: 29619087
DOI: 10.1186/s13068-018-1088-x

[…] 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 (https://www.ncbi.nlm.nih.gov/structure/flink/flink.cgi) and kegg (kyoto encyclopedia of genes and genomes) databases. […]

2018
PMCID: 5936019
PMID: 29728055
DOI: 10.1186/s12870-018-1288-3

[…] 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 (https://www.ncbi.nlm.nih.gov/structure/flink/flink.cgi) based on kegg (kyoto encyclopedia of genes […]

2017
PMCID: 5387025
PMID: 28097424
DOI: 10.1007/s00705-016-3180-5

[…] set at 100 ppm, fragment tolerance set at 0.8 da. the criterion for successful identification of a protein was a protein score confidence interval (c.i. %) ≥95%., spot identities were submitted to goretriever (http://www.agbase.msstate.edu/) to obtain the go annotations. if no annotation was returned, goanna was used to retrieve go annotations assigned based on sequence similarity. […]

2015
PMCID: 4620937
PMID: 26526746
DOI: 10.4137/BBI.S30525

[…] out functional analysis of agricultural plant and animal gene products. agbase provides go for bovine gene products and also has tools for functional genomics data analysis. agbase tools like goretriever fetch available go for an input gene list and goslimviewer summarizes go annotations at a higher level. for bovine gene products that lack go, functional domains with go annotations […]

2015
PMCID: 4620937
PMID: 26526746
DOI: 10.4137/BBI.S30525

[…] allow rapid analysis of functional genomics data for biological interpretation. given a list of bovine genes, it is possible to retrieve the available functional go information using the agbase tool goretriever and summarize the go using goslimviewer. for a set of bovine genes that lack functional annotation, goanna at agbase can add gos based on sequence homology. pathways resources […]


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GORetriever in publications

 (25)
PMCID: 5936019
PMID: 29728055
DOI: 10.1186/s12870-018-1288-3

[…] 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 (https://www.ncbi.nlm.nih.gov/structure/flink/flink.cgi) based on kegg (kyoto encyclopedia of genes […]

PMCID: 5774113
PMID: 29347914
DOI: 10.1186/s12864-018-4442-2

[…] data with p (benjamini-hocheberg) ≤ 0.05 and fdr ≤ 10% were retained for interpretations. a systematic search for compatible pig protein identifiers resulted in 2236 successful conversions (using goretriever from agbase), corresponding to 82% of the total sperm proteome being used for functional classification of all go terms (fig. ). detailed distributions of the biological functions […]

PMCID: 5387025
PMID: 28097424
DOI: 10.1007/s00705-016-3180-5

[…] set at 100 ppm, fragment tolerance set at 0.8 da. the criterion for successful identification of a protein was a protein score confidence interval (c.i. %) ≥95%., spot identities were submitted to goretriever (http://www.agbase.msstate.edu/) to obtain the go annotations. if no annotation was returned, goanna was used to retrieve go annotations assigned based on sequence similarity. […]

PMCID: 5177929
PMID: 28004741
DOI: 10.1038/srep39373

[…] and predicted protein(s) were used to generate regulatory networks underlying stress response. putative target proteins and their associated go terms and functions were identified using agbase goretriever (http://www.agbase.msstate.edu/cgi-bin/tools/goretriever_select.pl). gene regulatory networks were constructed using cytoscape. mirna targets were used as query to search annotated […]

PMCID: 4620937
PMID: 26526746
DOI: 10.4137/BBI.S30525

[…] allow rapid analysis of functional genomics data for biological interpretation. given a list of bovine genes, it is possible to retrieve the available functional go information using the agbase tool goretriever and summarize the go using goslimviewer. for a set of bovine genes that lack functional annotation, goanna at agbase can add gos based on sequence homology. pathways resources […]


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