A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
BayGO: Bayesian analysis of ontology term enrichment in microarray data
2006
BMC Bioinformatics
Preserved Fulltext
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
2008
Computer applications in the biosciences : CABIOS
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2010; you can also visit the original URL.
The file type is application/pdf.
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
2012
Bioinformatics
Preserved Fulltext
The Internet Archive has a preservation copy of this work in our general collections.
The file type is application/pdf.
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
2008
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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)
2012
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2013
Fungal Genetics and Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
Lecture Notes in Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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