Filters








4 Hits in 1.6 sec

HDTD: analyzing multi-tissue gene expression data

Anestis Touloumis, John C. Marioni, Simon Tavaré
2016 Bioinformatics  
We illustrate the utility of HDTD by applying it to analyze data generated by the Genotype-Tissue Expression consortium. Availability and Implementation: The R package HDTD is part of Bioconductor.  ...  For each subject, the data measurements can be written as a matrix with the different subsamples (e.g. multiple tissues) indexing the columns and the genes indexing the rows.  ...  Summary Although HDTD was motivated by and illustrated using multitissue gene expression data, we emphasize that HDTD is suitable for analyzing other types of high-dimensional transposable data including  ... 
doi:10.1093/bioinformatics/btw224 pmid:27266441 pmcid:PMC4937203 fatcat:6pggpxm725gb5lvlkackeuxp6u

HDTD: Analyzing multi-tissue gene expression data

Anestis Touloumis, John Marioni, Simon Tavaré, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository
2016
We illustrate the utility of HDTD by applying it to analyze data generated by the Genotype-Tissue Expression consortium.  ...  For each subject, the data measurements can be written as a matrix with the different subsamples (e.g., multiple tissues) indexing the columns and the genes indexing the rows.  ...  SUMMARY Although HDTD was motivated by and illustrated using multitissue gene expression data, we emphasize that HDTD is suitable for analyzing other types of high-dimensional transposable data including  ... 
doi:10.17863/cam.67 fatcat:qgegbhfnsnao3ojx3mqby6yboy

Contributions to Drug Resistance in Glioblastoma Derived from Malignant Cells in the Sub-Ependymal Zone

S. G. M. Piccirillo, I. Spiteri, A. Sottoriva, A. Touloumis, S. Ber, S. J. Price, R. Heywood, N.-J. Francis, K. D. Howarth, V. P. Collins, A. R. Venkitaraman, C. Curtis (+3 others)
2014 Cancer Research  
Through fluorescence-guided resection, we identified fluorescent tissue in the sub-ependymal zone (SEZ) of patients with glioblastoma.  ...  Acknowledgments We thank Amy Frary for tissue collection, Andy Lynch for help with the design of the expression array  ...  We next used the R package HDTD to identify gene ontology (GO) terms whose genes are differentially expressed (Supplementary Table S3 ).  ... 
doi:10.1158/0008-5472.can-13-3131 pmid:25406193 pmcid:PMC4286248 fatcat:tcozycltqberbc52wwgvrqr7ni

Analysis, integration and applications of the human interactome [article]

Gautam Chaurasia, Humboldt-Universität Zu Berlin, Humboldt-Universität Zu Berlin
2017
To find the modifiers, a network-based modeling approach was implemented by integrating huntingtin-specific protein interaction network with gene expression data from HD patients in multiple steps.  ...  Several new tools were included for querying, analyzing and visualizing human PPI networks.  ...  As tissue expression data set, the Human Gene Expression Atlas was utilized (Su et al., 2004) .  ... 
doi:10.18452/16635 fatcat:z227vy6lsje6jhtanzwwo5xik4