Pathway Analysis Service
Service description Finding the biological meaning for gene clusters The Pathway Analysis Service converts primary microarray data into biologically significant results; thus, evaluating expression profiles based on biological criteria. Based on various service modules, i.e. Data Pre-processing, Discriminatory Genes Analysis or Cluster Analysis, the Pathway Analysis Service consists of biological annotation analysis and signaling network analysis. This service includes also a functional grouping of the gene lists and provides the results in an extensive service report plus data CD/DVD-ROM. Annotation enrichment analysis Based on cluster or discriminatory genes analysis, the annotation enrichment analysis using the proprietary TreeRanker software finds significantly enriched annotations within groups of co-regulated genes. Examples for such biological functions or characteristics are: • Involvement in the same pathways • Neighboring chromosome location • Correlation with the same disease or cellular process • Sharing common protein motifs The respective genes can be further analyzed with signaling network analysis. Signaling network analysis Signaling network analysis visualizes if and how the genes of interest or their protein products could interact. Common direct regulators or downstream targets can be detected, and activation or inhibition is distinguished. This analysis is based on biomedical literature using the PathwayArchitect™ Software, Agilent Technologies, for pathway analysis and visualization. Next to algorithmic aspects, the available data sources are crucial for successful pathway analysis. Partly, data are imported from commercially and publicly available databases. Further proprietary data sources have been created by Miltenyi Biotec´s bioinformatics specialists. All data sources are continually updated. Please supply the expression data in compliance with the requirements described in the Bioinformatics Services, “File formats for data analysis” (PDF). Minimum requirement of datasets depends on previous analysis: with prior Clustering Analysis, three datasets, and with previous DGA, six datasets, respectively. All data will be delivered either a written report detailing procedures including most significant findings on CD-ROM. Package Further information File formats for Bioinformatics Service.pdf [PDF; 83,6 KB]		Figure 1 Signaling network analysis The network analysis shows known interactions and biological processes for the genes of interest. In addition, this method can find regulators or targets that were not present on the microarray. Figure 2 Signaling network analysis The example shows the genes of interest (green circle) and their interacting molecules. The mode of interaction is illustrated by the connecting lines between the molecules. A blue line depicts binding, while a blue arrow stands for the regulation of gene expression. Grey arrows with green boxes represent regulation in general and grey arrows with orange circles indicate protein modifications.

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