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ISOpure specifications

Information


Unique identifier OMICS_21892
Name ISOpure
Alternative name ISOpureR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A tumour mRNA abundance profiles of the same cancer sub-type; and normal mRNA abundance profiles, from the same tissue as the tumour.
Output data A purified gene expression profiles, an estimation of the percentage of cancer content of each tumor sample, a log of the final model and a purified cancer profile.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, MATLAB, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.21
Stability Stable
Source code URL https://codeload.github.com/gquon/ISOpure/zip/1.0
Maintained Yes

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Versioning


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Documentation


Maintainers


  • person_outline Paul Boutros
  • person_outline Quaid Morris

Publication for ISOpure

ISOpure citations

 (5)
library_books

Immunological landscape of consensus clusters in colorectal cancer

2017
Oncotarget
PMCID: 5739639
PMID: 29285252
DOI: 10.18632/oncotarget.22169

[…] imal number of K = 5 clusters was deduced based on integrative analysis of 5 clustering algorithms and 11 cluster validity metrics across the increasing variable subsets (from 1000 to 10000).We used “ISOpureR” package to estimate normal tissue content in each sample (in each CRC cluster separately) [, ]. Consequently, we eliminated samples that matched low-purity Cluster 1 (see results section). I […]

library_books

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

2017
eLife
PMCID: 5718706
PMID: 29130882
DOI: 10.7554/eLife.26476.049

[…] gene signatures obtained from the TCGA data for melanoma or colorectal cancer depending on the origin of cancer.ESTIMATE () was run with their R package version 1.0.11.For CIBERSORT, DeconRNASeq and ISOpure, when run based on our gene expression reference profiles, we used the reference profiles from peripheral blood immune cells for the predictions in blood and the reference profiles from tumor- […]

library_books

Topic model based mass spectrometric data analysis in cancer biomarker discovery studies

2016
BMC Genomics
PMCID: 5001243
PMID: 27535232
DOI: 10.1186/s12864-016-2796-x

[…] {βm}) each ion originates from. We infer the latent variables γ′,{γd}d=1,⋯,D,{θd}d=1,⋯,D, and estimate the parameters using the two-step learning approach developed based on variational EM algorithm (ISOpure package [], version 1.4). The graphical model representing the above topic model is shown in Fig. . This three-level model allows a single profile to be associated with multiple topics (i.e., […]

library_books

Gene Expression Deconvolution for Uncovering Molecular Signatures in Response to Therapy in Juvenile Idiopathic Arthritis

2016
PLoS One
PMCID: 4887077
PMID: 27244050
DOI: 10.1371/journal.pone.0156055

[…] rofiles from a group of individuals with similar conditions to uncover the commonality in the course of treatment.To identify common molecular signatures in a group of subjects, Quon et al. developed ISOpure-S1, a computational gene expression deconvolution method, to characterize a single, common cancer expression profile from heterogeneous tumor profiles [, ]. The method utilizes probabilistic a […]

library_books

Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction

2013
Genome Med
PMCID: 3706990
PMID: 23537167
DOI: 10.1186/gm433

[…] (the predominant histological subtype, and the same subtype represented in all other patient cohorts used here). This dataset included 17 healthy samples, of which 14 were used for purification with ISOpure and three were treated as blind control samples (NL1179, NL1675, and NL1698). Of the 127 lung adenocarcinoma samples, 32 were annotated with tumor cellularity estimates made by two pathologist […]

Citations

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ISOpure institution(s)
Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Department of Oncology, University of Oxford, Oxford, UK; Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; The Donnelly Centre, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
ISOpure funding source(s)
Supported by the Government of Ontario; a Terry Fox Research Institute New Investigator Award; a Terry Fox Research Institute Program Project; a CIHR New Investigator Award; by Prostate Cancer Canada; and the Movember Foundation – Grant #RS2014-01.

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