TMA Navigator: network inference, patient stratification and survival analysis with tissue microarray data
Abstract
Tissue microarrays (TMAs) allow multiplexed analysis of tissue samples and are frequently used to estimate biomarker protein expression in tumour biopsies. TMA Navigator (www.tmanavigator.org) is an open access web application for analysis of TMA data and related information, accommodating categorical, semi-continuous and continuous expression scores. Non-biological variation, or batch effects, can hinder data analysis and may be mitigated using the ComBat algorithm, which is incorporated with enhancements for automated application to TMA data. Unsupervised grouping of samples (patients) is provided according to Gaussian mixture modelling of marker scores, with cardinality selected by Bayesian information criterion regularization. Kaplan-Meier survival analysis is available, including comparison of groups identified by mixture modelling using the Mantel-Cox log-rank test. TMA Navigator also supports network inference approaches useful for TMA datasets, which often constitute comparatively few markers. Tissue and cell-type specific networks derived from TMA expression data offer insights into the molecular logic underlying pathophenotypes, towards more effective and personalized medicine. Output is interactive, and results may be exported for use with external programs. Private anonymous access is available, and user accounts may be generated for easier data management.
Citation
Lubbock , A L R , Katz , E , Harrison , D J & Overton , I M 2013 , ' TMA Navigator: network inference, patient stratification and survival analysis with tissue microarray data ' , Nucleic Acids Research , vol. 41 , no. W1 , pp. W562-W568 . https://doi.org/10.1093/nar/gkt529
Publication
Nucleic Acids Research
Status
Peer reviewed
ISSN
0305-1048Type
Journal article
Description
Scottish Funding Council (SFC) and the Chief Scientist’s Office (CSO) (to D.H.); Royal Society of Edinburgh Scottish Government Fellowship co-funded by Marie Curie Actions and the UK Medical Research Council (MRC) (to I.O.). Funding for open access charge: Royal Society of Edinburgh.Collections
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