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BayGO: Bayesian analysis of ontology term enrichment in microarray data

Ricardo Z N Vêncio, Tie Koide, Suely L Gomes, Carlos A de B Pereira
2006 BMC Bioinformatics  
BayGO implements a Bayesian approach to search for enriched terms from microarray data.  ...  The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis.  ...  Venancio for several suggestions and critical reading of the manuscript. TK is supported by a doctoral fellowship from Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP).  ... 
doi:10.1186/1471-2105-7-86 pmid:16504085 pmcid:PMC1440873 fatcat:jqjkhmvinrg3rmikksuucan3u4

LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data

Maureen A. Sartor, George D. Leikauf, Mario Medvedovic
2008 Computer applications in the biosciences : CABIOS  
Motivation: The elucidation of biological pathways enriched with differentially expressed genes has become an integral part of the analysis and interpretation of microarray data.  ...  Results: We present a logistic regression based method (LRpath) for identifying predefined sets of biologically related genes enriched with (or depleted of) differentially expressed transcripts in microarray  ...  ACKNOWLEDGEMENTS Comments provided by Michael Newton and an anonymous reviewer helped us significantly improve upon the initial version of this mansuscript.  ... 
doi:10.1093/bioinformatics/btn592 pmid:19038984 pmcid:PMC2639007 fatcat:4gakcfhd7ra7nllrda3wywrga4

Bayesian assignment of gene ontology terms to gene expression experiments

P. Sykacek
2012 Bioinformatics  
State-of-the-art data analysis provides lists of involved genes, either by calculating significance levels of mRNA abundance or by Bayesian assessments of gene activity.  ...  Such probability measures result from many Bayesian approaches for expression data analysis.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bts405 pmid:22962488 pmcid:PMC3436832 fatcat:3yd3olpe6ff7jiedcvdsl4l2mu

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

Da Wei Huang, Brad T. Sherman, Richard A. Lempicki
2008 Nucleic Acids Research  
Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task.  ...  Approximately 68 bioinformatics enrichment tools that are currently available in the community are collected in this survey.  ...  ACKNOWLEDGEMENTS Thanks go to Dr Xin Zheng and Ms Jun Yang in the Laboratory of Immunopathogenesis and Bioinformatics (LIB) group for biological and bioinformatics discussion.  ... 
doi:10.1093/nar/gkn923 pmid:19033363 pmcid:PMC2615629 fatcat:gwatxne6hng23gtydhc4puem6a

Markov Chain Ontology Analysis (MCOA)

H Frost, Alexa T McCray
2012 BMC Bioinformatics  
Of particular relevance are methods, such as enrichment analysis, that quantify the importance of ontology classes relative to a collection of domain data.  ...  Results: In this paper, we describe a methodology called Markov Chain Ontology Analysis (MCOA) and illustrate its use through a MCOA-based enrichment analysis application based on a generative model of  ...  Bayesian methods that perform enrichment analysis using a prior probability distribution include MGSA and the BayGO framework [26] .  ... 
doi:10.1186/1471-2105-13-23 pmid:22300537 pmcid:PMC3329418 fatcat:a5kgiwsou5ciraqowhm3ggdtly

Transcriptional profiling of Neurospora crassa Δmak-2 reveals that mitogen-activated protein kinase MAK-2 participates in the phosphate signaling pathway

Diana E. Gras, Gabriela F. Persinoti, Nalu T.A. Peres, Nilce M. Martinez-Rossi, Ana C. Tahira, Eduardo M. Reis, Rolf A. Prade, Antonio Rossi
2013 Fungal Genetics and Biology  
A high Pearson correlation between microarray and quantitative Real-time PCR data was observed.  ...  Quantitative Real-time PCR gene expression analysis of 18 selected genes, using independent RNA samples, validated our microarray results.  ...  Gene Ontology term enrichment was performed using the BayGO algorithm , and the significantly enriched terms (p-value < 0.05) were further analyzed.  ... 
doi:10.1016/j.fgb.2013.05.007 pmid:23733042 fatcat:4xg4hlsrzvh6bhgh6sa77i4yei

Integrative Visual Data Mining of Biomedical Data: Investigating Cases in Chronic Fatigue Syndrome and Acute Lymphoblastic Leukaemia [chapter]

Paul Kennedy, Simeon J. Simoff, Daniel R. Catchpoole, David B. Skillicorn, Franco Ubaudi, Ahmad Al-Oqaily
Lecture Notes in Computer Science  
They combine in a consistent manner a set of visualisation and data mining techniques that operate over an integrated data set of several diverse components, including medical (clinical) data, patient  ...  outcome and interview data, corresponding gene expression and SNP data, domain ontologies and health management data.  ...  The research work presented in this chapter has been supported by the Children's Hospital at Westmead (Sydney, Australia), the University of Technology, Sydney and Silicon Graphics.  ... 
doi:10.1007/978-3-540-71080-6_21 fatcat:kcoxsqvnrbaf5dvahheo3nd3pi