Inferring tumour purity and stromal and immune cell admixture from expression data

K Yoshihara, M Shahmoradgoli, E Martínez… - Nature …, 2013‏ - nature.com
Infiltrating stromal and immune cells form the major fraction of normal cells in tumour tissue
and not only perturb the tumour signal in molecular studies but also have an important role …

Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells

S Zhao, WP Fung-Leung, A Bittner, K Ngo, X Liu - PloS one, 2014‏ - journals.plos.org
To demonstrate the benefits of RNA-Seq over microarray in transcriptome profiling, both
RNA-Seq and microarray analyses were performed on RNA samples from a human T cell …

Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1

RGW Verhaak, KA Hoadley, E Purdom, V Wang, Y Qi… - Cancer cell, 2010‏ - cell.com
Summary The Cancer Genome Atlas Network recently cataloged recurrent genomic
abnormalities in glioblastoma multiforme (GBM). We describe a robust gene expression …

Prognostically relevant gene signatures of high-grade serous ovarian carcinoma

RGW Verhaak, P Tamayo, JY Yang, D Hubbard… - The Journal of clinical …, 2012‏ - jci.org
Because of the high risk of recurrence in high-grade serous ovarian carcinoma (HGS-OvCa),
the development of outcome predictors could be valuable for patient stratification. Using the …

SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas

AJ Bass, H Watanabe, CH Mermel, S Yu, S Perner… - Nature …, 2009‏ - nature.com
Lineage-survival oncogenes are activated by somatic DNA alterations in cancers arising
from the cell lineages in which these genes play a role in normal development,. Here we …

Suppression of lung adenocarcinoma progression by Nkx2-1

MM Winslow, TL Dayton, RGW Verhaak, C Kim-Kiselak… - Nature, 2011‏ - nature.com
Despite the high prevalence and poor outcome of patients with metastatic lung cancer the
mechanisms of tumour progression and metastasis remain largely uncharacterized. Here we …

Jetset: selecting the optimal microarray probe set to represent a gene

Q Li, NJ Birkbak, B Gyorffy, Z Szallasi, AC Eklund - BMC bioinformatics, 2011‏ - Springer
Background Interpretation of gene expression microarrays requires a map** from probe
set to gene. On many Affymetrix gene expression microarrays, a given gene may be …

Microarray probes and probe sets

H Liu, I Bebu, X Li - Frontiers in bioscience (Elite edition), 2010‏ - pmc.ncbi.nlm.nih.gov
DNA microarrays have gained wide use in biomedical research by simultaneously
monitoring the expression levels of a large number of genes. The successful implementation …

Correlation of mRNA and protein levels: cell type-specific gene expression of cluster designation antigens in the prostate

LE Pascal, LD True, DS Campbell, EW Deutsch, M Risk… - BMC genomics, 2008‏ - Springer
Background: Expression levels of mRNA and protein by cell types exhibit a range of
correlations for different genes. In this study, we compared levels of mRNA abundance for …

Bioinformatics analysis of microarray data

Y Zhang, J Szustakowski, M Schinke - Cardiovascular Genomics: Methods …, 2009‏ - Springer
Gene expression profiling provides unprecedented opportunities to study patterns of gene
expression regulation, for example, in diseases or developmental processes. Bioinformatics …