Data Analysis

Since the bioinformatic data analysis plays a key role in every project, the GTL offers support for data anylsis.

Data analysis support is divided into three different levels:

Level 1: Generation of raw per-sample FastQ files and basic QC statistics, data delivery
Level 2: Standard semi-automated analysis generating the baseline for experiment specific result evaluation, basic sanity check
Level 3: Experiment specific result evaluation requiring manual custom analysis including expert knowledge and platforms enabling the same.

Data analysis level 1 is a compulsory part of every NGS-Project, while Level 2 ans level 3 data anlysis support are optional.

Analysis of Microarray-Data

We have established and optimized data analysis pipelines for the analysis and interpretation of DNA microarray data. Depending on the particular experimental design used and the microarray platform used, various software packages are used for statistical data analysis (GeneSpring GX, Partek Genomic Suite, Bioconductor-R packages). In this way, we are able to generate specific gene expression profiles and carry out various cluster analyses (hierarchical clustering, Principal Component Analysis PCA). The identification of differentially expressed genes then happens via various statistical methods up to analysis of variance (ANOVA) including error correction in multiple tests. For functional analysis of differentially expressed genes, we can perform both GeneOntology analysis and detailed network and pathway analysis.

Analysis of NGS-Data

For the analysis of extensive NGS datasets we have various commercial and open source software packages as well as the corresponding IT resources available.

During primary data analysis, the quality of the generated raw data (sequence reads in fastq / xsq format) is checked and documented.

For the evaluation of the sequence data the following parameters are used:

  •      Correct recognition of barcodes / demultiplexing
  •      Read numbers per run / lane / chip / sample etc.
  •      Read length distribution
  •      Average quality of reads

The detailed secondary data analysis (read mapping, DeNovo assembly, miRNA detection, etc.) or the analysis of the differential gene expression is carried out with the appropriate software packages (CLCbio Genomics Workbench, Partek Genomics Suite, etc.).

Upon request, tertiary data analyses on a functional level (Ingenuity Pathway Analysis) can be carried out.

Head of GTL

Prof. Dr. Karl Köhrer

Biologisch-Medizinisches Forschungszentrum (BMFZ) Heinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf
Phone +49 211 81-13165
Fax +49 211 81-11922
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