BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

Maere, Steven; Heymans, Karel; Kuiper, Martin

doi:10.1093/bioinformatics/bti551

Cited by 3,751 publications

(3,320 citation statements)

References 13 publications

Supporting

Mentioning

3,248

Contrasting

Unclassified

Order By: Relevance

“…To gain further insight into the functions of these hCM differentially expressed genes, we performed Gene Ontology (GO) analyses using the BiNGO (Maere et al, 2005) Cytoscape (Shannon et al, 2003) plugin. Interestingly, hCM upregulated genes were significantly over-represented in cardiac function-related GO terms (complete lists of GO terms are shown in Tables S3-5), including muscle contraction, heart development, and sarcomeric structures.…”

Section: Global Gene Expression Profiling In Hcmsmentioning

confidence: 99%

See 1 more Smart Citation

Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes

Liu

Plongthongkum³

et al. 2013

Protein Cell

View full text Add to dashboard Cite

With defined culture protocol, human embryonic stem cells (hESCs) are able to generate cardiomyocytes in vitro, therefore providing a great model for human heart development, and holding great potential for cardiac disease therapies. In this study, we successfully generated a highly pure population of human cardiomyocytes (hCMs) (>95% cTnT + ) from hESC line, which enabled us to identify and characterize an hCM-specific signature, at both the gene expression and DNA methylation levels. Gene functional association network and gene-disease network analyses of these hCM-enriched genes provide new insights into the mechanisms of hCM transcriptional regulation, and stand as an informative and rich resource for investigating cardiac gene functions and disease mechanisms. Moreover, we show that cardiac-structural genes and cardiac-transcription factors have distinct epigenetic mechanisms to regulate their gene expression, providing a better understanding of how the epigenetic machinery coordinates to regulate gene expression in different cell types.

show abstract

Section: Global Gene Expression Profiling In Hcmsmentioning

confidence: 99%

“…Functional properties of the differentially expressed or methylated genes were categorized using the BiNGO Cytoscape plugin as described previously (Maere et al, 2005). A P-value of less than 0.05 was considered statistically significant.…”

Section: Gene Ontology (Go) Analysismentioning

confidence: 99%

Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes

Liu

Plongthongkum³

et al. 2013

Protein Cell

View full text Add to dashboard Cite

show abstract

“…Entrez Gene IDs were used to do GO enrichment. S-nitrosated proteins were visualized with Cytoscape (Shannon et al, 2003) and used to do GO enrichment using the BiNGO (Maere et al, 2005) plugin with the Gene Ontology (GO) annotation (Ashburner et al, 2000). The Benjamini and Hochberg False Discovery Rate (FDR) correction was chosen as the testing correction, and a p-value threshold of 0.05 was selected for Biological Process categories in the BiNGO settings.…”

Section: Bioinformatic Analysis Of the Results Of S-nitrosationmentioning

confidence: 99%

Quantitative proteomic analysis of S-nitrosated proteins in diabetic mouse liver with ICAT switch method

et al. 2010

View full text Add to dashboard Cite

In this study we developed a quantitative proteomic method named ICAT switch by introducing isotope-coded affinity tag (ICAT) reagents into the biotin-switch method, and used it to investigate S-nitrosation in the liver of normal control C57BL/6J mice and type 2 diabetic KK-Ay mice. We got fifty-eight S-nitrosated peptides with quantitative information in our research, among which thirty-seven had changed S-nitrosation levels in diabetic mouse liver. The S-nitrosated peptides belonged to fortyeight proteins (twenty-eight were new S-nitrosated proteins), some of which were new targets of S-nitrosation and known to be related with diabetes. S-nitrosation patterns were different between diabetic and normal mice. Gene ontology enrichment results suggested that S-nitrosated proteins are more abundant in amino acid metabolic processes. The network constructed for Snitrosated proteins by text-mining technology provided clues about the relationship between S-nitrosation and type 2 diabetes. Our work provides a new approach for quantifying S-nitrosated proteins and suggests that the integrative functions of S-nitrosation may take part in pathophysiological processes of type 2 diabetes.

show abstract

“…Mycoplasma identified proteins were submitted to hierarchical GO overrepresentation tests using the Cytoscape 2.6.3 26 plugin BiNGO 2.3 [67]. Custom M. hyopneumoniae 7448 and J GO annotation files were acquired from Uniprot (http://www.uniprot.org/).…”

Section: Methodsmentioning

confidence: 99%

Comparative proteomics of twoMycoplasma hyopneumoniaestrains andMycoplasma flocculareidentified potential porcine enzootic pneumonia determinants

et al. 2018

View full text Add to dashboard Cite

Mycoplasma hyopneumoniae and Mycoplasma flocculare are genetically similar bacteria, which coinhabit the porcine respiratory tract. These mycoplasmas share most of the known virulence factors, but, while M. hyopneumoniae causes porcine enzootic pneumonia (PEP), M. flocculare is a commensal species. To identify potential PEP determinants and provide novel insights on mycoplasma-host interactions, the whole cell proteomes of two M. hyopneumoniae strains, one pathogenic (7448) and other non-pathogenic (J), and M. flocculare were compared. A cell fractioning approach combined with mass spectrometry (LC-MS/MS) proteomics was used to analyze cytoplasmic and surface-enriched protein fractions. Average detection of ~ 50% of the predicted proteomes of M. hyopneumoniae 7448 and J, and M. flocculare was achieved. Many of the identified proteins were differentially represented in M. hyopneumoniae 7448 in comparison to M. hyopneumoniae J and M. flocculare, including potential PEP determinants, such as adhesins, proteases, and redox-balancing proteins, among others. The LC-MS/MS data also provided experimental validation for several genes previously regarded as hypothetical for all analyzed mycoplasmas, including some coding for proteins bearing virulence-related functional domains. The comprehensive proteome profiling of two M. hyopneumoniae strains and M. flocculare provided tens of novel candidates to PEP determinants or virulence factors, beyond those classically described.

show abstract

BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

Cited by 3,751 publications

References 13 publications

Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes

Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes

Quantitative proteomic analysis of S-nitrosated proteins in diabetic mouse liver with ICAT switch method

Comparative proteomics of twoMycoplasma hyopneumoniaestrains andMycoplasma flocculareidentified potential porcine enzootic pneumonia determinants

Contact Info

Product

Resources

About