GOSlimViewer protocols

View GOSlimViewer computational protocol

GOSlimViewer 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 Ontology annotation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

GOSlimViewer specifications

Information


Unique identifier OMICS_02270
Name GOSlimViewer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for GOSlimViewer

GOSlimViewer in pipelines

 (12)
2018
PMCID: 5879616
PMID: 29619087
DOI: 10.1186/s13068-018-1088-x

[…] 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. specific […]

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

[…] 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 and genomes) databases. […]

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

[…] was returned, goanna was used to retrieve go annotations assigned based on sequence similarity. the resulting annotations were summarized based on the goa and whole proteome goslim set using goslimviewer []., successful rev infection was verified using real-time rt-pcr. the results are presented in figure . virus was not detected in the spleens of chickens in the control group. […]

2016
PMCID: 4992267
PMID: 27542721
DOI: 10.1186/s12864-016-3017-3

[…] s. alterniflora unigenes were assigned on the basis of blast against plant goslim set and compared with oryza sativa goslim terms using goslim viewer (http://agbase.msstate.edu/cgi-bin/tools/goslimviewer_select.pl). the goslim enrichment analysis was performed using bingo tool [] and visualized using cytoscape. the hypergeometric test with false discovery rate (fdr) correction methods [] […]

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

[…] 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 in other species are identified by goanna by a basic local […]


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

GOSlimViewer in publications

 (42)
PMCID: 5936019
PMID: 29728055
DOI: 10.1186/s12870-018-1288-3

[…] 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 and genomes) databases. […]

PMCID: 5595346
PMID: 28854187
DOI: 10.1371/journal.pntd.0005883

[…] iss: inferred by structure/sequence similarity, tas: traceable author statement and ic: inferred by curation., in order to reduce the number of go terms and map them to broader categories, we used goslimviewer from agbase [] to map the set of proteins to go slim terms (broader versions of the go ontologies that provide a summary of results of go annotation)., to identify the go terms enriched […]

PMCID: 5574979
PMID: 28851929
DOI: 10.1038/s41598-017-09260-8

[…] ≤ − 2 (up- and down-regulated) with significance level ‘yes’ were considered for degs., functional categorization of the degs was studied using goslim (http://www.agbase.msstate.edu/cgi-bin/tools/goslimviewer_select.pl) while gene ontology (go) terms were assigned to the expressed genes and assignment of kegg pathways was carried out using blast2go. diffcoex analysis method was used […]

PMCID: 5559503
PMID: 28861098
DOI: 10.3389/fpls.2017.01416

[…] localization of the proteins was assigned using plant-mloc (http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/) and manually translated to gene ontology terms. go terms were summarized using the goslimviewer tool included in agbase based on the plant goslim set (mccarthy et al., )., about 2.5 to 25 μg of the isolated proteins were separated via sds-page and then transferred onto […]

PMCID: 5535294
PMID: 28756775
DOI: 10.1186/s12915-017-0399-x

[…] using a cut-off of 1 × 10–5. the go terms of its closest uniref by e value with documented go terms were assigned to a gene model via a custom perl script, with go slim values derived using goslimviewer []. enrichment of go terms within gene families was ascertained using fisher’s exact test., a genome-scale synteny analysis of the p. tepidariorum scaffolds was conducted using […]


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

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

GOSlimViewer reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GOSlimViewer