Universität zu Köln

Crispatzu, Giuliano, Schrader, Alexandra, Nothnagel, Michael ORCID: 0000-0001-8305-7114, Herling, Marco and Herling, Carmen Diana (2016). A Critical Evaluation of Analytic Aspects of Gene Expression Profiling in Lymphoid Leukemias with Broad Applications to Cancer Genomics. AIMS Med. Sci., 3 (3). S. 248 - 272. SPRINGFIELD: AMER INST MATHEMATICAL SCIENCES-AIMS. ISSN 2375-1576

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Abstract

In cancer research, transcriptional aberrations are often deduced from mRNA-based gene expression profiling (GEP). Although transcriptome sequencing (RNA-seq) has gained ground in the recent past, mRNA-based microarrays remain a useful asset for high-throughput experiments in many laboratories. Possible reasons are the lower per-sample costs and the opportunity to analyze obtained GEP data in association with published data sets. There are established and widely used methods for the analysis of microarray data, which increase the comparability of different GEP data sets and facilitate data-mining approaches. However, analytic pitfalls, such as batch effects and issues of sample purity, e.g. by complex tissue composition, are often not properly addressed by these standard approaches. Moreover, most of these tools do not capitalize on the full range of public data sources or do not take advantage of the analytic possibilities for functional interpretation or of comprehensive meta-analyses. We present an overview of the most critical steps in the analysis of microarray-based GEP data. We discuss software and database query solutions that may be useful for each step and for generally overcoming analytic challenges. Aside from machine-learning applications to classify and cluster samples, we describe clinical applications of GEP, including a novel exploratory algorithm to identify potential biomarkers of prognosis in small sample cohorts as demonstrated by exemplary data from lymphatic leukemias. Overall, this review and the attached source code provide guidance to both molecular biologists and bioinformaticians / biostatisticians to properly conduct GEP analyses as well as to evaluate the clinical / biological relevance of obtained results.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Crispatzu, Giuliano UNSPECIFIED UNSPECIFIED UNSPECIFIED Schrader, Alexandra UNSPECIFIED UNSPECIFIED UNSPECIFIED Nothnagel, Michael UNSPECIFIED orcid.org/0000-0001-8305-7114 UNSPECIFIED Herling, Marco UNSPECIFIED UNSPECIFIED UNSPECIFIED Herling, Carmen Diana UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-288279
DOI:	10.3934/medsci.2016.3.248
Journal or Publication Title:	AIMS Med. Sci.
Volume:	3
Number:	3
Page Range:	S. 248 - 272
Date:	2016
Publisher:	AMER INST MATHEMATICAL SCIENCES-AIMS
Place of Publication:	SPRINGFIELD
ISSN:	2375-1576
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Biology > Institute for Genetics
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language MICROARRAY DATA; CHEMOIMMUNOTHERAPY; CYCLOPHOSPHAMIDE; BIOCONDUCTOR; FLUDARABINE; NETWORKS; DATABASE; SINGLE Multiple languages Medicine, Research & Experimental Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/28827