Bioinformatics applications for pathway analysis of microarray data

T Werner - Current opinion in biotechnology, 2008 - Elsevier
Changes in transcript levels are assessed by microarray analysis on an individual basis,
essentially resulting in long lists of genes that were found to have significantly changed …

Next generation sequencing in functional genomics

T Werner - Briefings in bioinformatics, 2010 - academic.oup.com
Genome-wide sequencing has enabled modern biomedical research to relate more and
more events in healthy as well as disease-affected cells and tissues to the genomic …

Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data

A Essaghir, F Toffalini, L Knoops, A Kallin… - Nucleic acids …, 2010 - academic.oup.com
Deciphering transcription factor networks from microarray data remains difficult. This study
presents a simple method to infer the regulation of transcription factors from microarray data …

PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation

E Portales-Casamar, S Kirov, J Lim, S Lithwick… - Genome biology, 2007 - Springer
PAZAR is an open-access and open-source database of transcription factor and regulatory
sequence annotation with associated web interface and programming tools for data …

Elevated osteonectin/SPARC expression in primary prostate cancer predicts metastatic progression

CA Derosa, B Furusato, S Shaheduzzaman… - Prostate cancer and …, 2012 - nature.com
Background: The majority of prostate cancers (CaP) are detected in early stages with
uncertain prognosis. Therefore, an intensive effort is underway to define early predictive …

Gene expression profiles of dental follicle cells before and after osteogenic differentiation in vitro

C Morsczeck, G Schmalz, TE Reichert, F Völlner… - Clinical oral …, 2009 - Springer
Recently, osteogenic precursor cells were isolated from human dental follicles, which
differentiate into cementoblast-or osteoblast-like cells under in vitro conditions after the …

Early growth response 1 (Egr1) regulates cholesterol biosynthetic gene expression

NG Gokey, C Lopez-Anido, AL Gillian-Daniel… - Journal of Biological …, 2011 - ASBMB
The early growth response (EGR) family of transcription factors has been implicated in
control of lipid biosynthetic genes. Egr1 is induced by insulin both in vitro and in vivo and is …

Genome-wide expression profiling of the retinoschisin-deficient retina in early postnatal mouse development

A Gehrig, T Langmann, F Horling… - … & visual science, 2007 - iovs.arvojournals.org
purpose. The Rs1h knockout mouse displays retinal features typical for X-linked juvenile
retinoschisis (RS). Consequently, this mouse line represents an excellent model to study …

Induction of lipid oxidation by polyunsaturated fatty acids of marine origin in small intestine of mice fed a high-fat diet

EM van Schothorst, P Flachs, NLW Franssen-van Hal… - BMC genomics, 2009 - Springer
Background Dietary polyunsaturated fatty acids (PUFA), in particular the long chain marine
fatty acids docosahexaenoic (DHA) and eicosapentaenoic (EPA), are linked to many health …

An ecologist's guide to ecogenomics

NJ Ouborg, WH Vriezen - Journal of Ecology, 2007 - JSTOR
1 Currently, plant ecologists are increasingly adopting approaches and techniques from
molecular biology. The new field of ecogenomics aims at understanding the mechanistic …