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Citations per year

Number of citations per year for the bioinformatics software tool BayGO
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Tool usage distribution map

This map represents all the scientific publications referring to BayGO per scientific context
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Associated diseases

This word cloud represents BayGO usage per disease context
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Protocols

BayGO specifications

Information


Unique identifier OMICS_18896
Name BayGO
Interface Web user interface
Restrictions to use None
Input data A list of genes.
Programming languages Perl, R
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Ricardo Vencio
  • person_outline Carlos Pereira
  • person_outline Tie Koide
  • person_outline Suely Gomes

Publication for BayGO

BayGO citations

 (7)
call_split

mus 52 disruption and metabolic regulation in Neurospora crassa: Transcriptional responses to extracellular phosphate availability

2018
PLoS One
PMCID: 5905970
PMID: 29668735
DOI: 10.1371/journal.pone.0195871
call_split See protocol

[…] hange ≥ 1.5 or ≤−1.5) was applied as an expression threshold. Functional annotation of the DEGs was performed according to GO [], using Bast2GO software []. GO term enrichment was performed using the BayGO algorithm []. To identify metabolic pathways in which genes could be modulated in response to phosphate availability, annotation was performed using Kegg Orthology [], using the Kegg Automatic A […]

library_books

Transcriptome wide survey of gene expression changes and alternative splicing in Trichophyton rubrum in response to undecanoic acid

2018
Sci Rep
PMCID: 5802734
PMID: 29410524
DOI: 10.1038/s41598-018-20738-x

[…] improves our understanding of the molecular mechanisms responsive to UDA. Considering the physiological context, we examined the functional distributions of the modulated genes using the Blast2GO and BayGO software programs. The categories of genes that were differentially expressed at 3 h vs. 0 h, and 12 h vs. 0 h are shown in Fig. , with only the over-represented genes shown. This analysis indic […]

library_books

The Secreted Protease PrtA Controls Cell Growth, Biofilm Formation and Pathogenicity in Xylella fastidiosa

2016
Sci Rep
PMCID: 4974619
PMID: 27492542
DOI: 10.1038/srep31098

[…] fic RNA-seq libraries were generated and sequenced on one lane of an Illumina HighSeq 2500 (Illumina, CA). Enrichment of gene ontology terms of differentially expressed transcripts was performed with BayGO using 500 simulations and a P-value cutoff of 0.05. […]

call_split

Trichoderma reesei CRE1 mediated Carbon Catabolite Repression in Re sponse to Sophorose Through RNA Sequencing Analysis

2016
Curr Genomics
PMCID: 4864841
PMID: 27226768
DOI: 10.2174/1389202917666151116212901
call_split See protocol

[…] ≤ 0.05 were established as thresholds. Samples were normalized using median log deviation implemented in the DESeq package. Functional categorization was performed with Gene Ontology (GO) terms using BayGO software [], adopting a p-value of ≤ 0.05 as the criterion for significantly enriched categories. Raw sequence data and count data for all samples are available at Gene Expression Omnibus (GEO; […]

library_books

RNA sequencing analysis of Trichophyton rubrum transcriptome in response to sublethal doses of acriflavine

2014
BMC Genomics
PMCID: 4243288
PMID: 25573029
DOI: 10.1186/1471-2164-15-S7-S1

[…] greater than 1.5 or lower than −1.5 (i.e, at least 2.8-fold difference) were functionally categorized according to the GO using the Blast2GO [] algorithm. Enrichment analysis was performed using the BayGO algorithm []. Mapping results were visualized using both the Gaggle Genome Browser [] and Genome View []. Pileup coverage files were uploaded to the Gaggle Genome Browser to inspect the read cov […]

library_books

Investigating the concordance of Gene Ontology terms reveals the intra and inter platform reproducibility of enrichment analysis

2013
BMC Bioinformatics
PMCID: 3644270
PMID: 23627640
DOI: 10.1186/1471-2105-14-143

[…] l. used z-statistics and permutation test to identify significantly enriched gene sets []. In addition, other statistical methods including significance analysis of function and expression (SAFE) [], BayGO [], ProbCD [], EasyGO [], ProfCom [], GlobalANCOVA [], GOEAST [] and LRpath [] were also developed for enrichment analysis.Based on the methods mentioned above, researchers can subsequently reve […]


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BayGO institution(s)
BIOINFO-USP Núcleo de Pesquisas em Bioinformática, Universidade de São Paulo, São Paulo, Brazil; Instituto Israelita de Ensino e Pesquisa Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, Brazil; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil; Departamento de Estatística, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil
BayGO funding source(s)
Supported by a doctoral fellowship from Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) and by Conselho Nacional de Desenvolvimento Cientí- fico e Tecnológico (CNPq).

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