molecular genetic analyses

Analysis of Microarray Data

General Information

Affymetrix or Agilent expression experiments produce large amounts of data. We facilitate the analysis of microarray data by generating tables and graphical representations that help understanding relations between experimental conditions. We offer a standardized analysis of microarray data and help to control the quality of the experiments using well established and tested statistical methods and clustering algorithms. A comprehensive up-to-date annotation from publicly available data sources is included, too.

Analysis of microarray data: Top 100 Annotations Click on the image to see an example of a comprehensive annotation of microarray data. Currently, the standard output from Affymetrix' GeneChip Operating Software, GCOS, and other software (providing a probeset Id in the first column) is annotated with up-to-date versions of identifiers and is directly linked to the following data sources: Ensembl, Entrez Gene, Unigene, Uniprot, and GeneOntology. We provide to our customers two MS Excel™ files with annotation for the statistically most relevant genes, which replaces the original GCOS annotation.

Analysis of microarray data: Heatmap of top regulated genes Click on the image to see an excerpt from the PDF Report: The heat map shows a two-dimensional clustering of the top one hundred genes. Genes that fall into one cluster (vertical axis) have similar behaviors in the experiments. From the clustering of the categories (horizontal axis). Expression intensities are represented by red and green, for high and low intensities, respectively. Black indicates medium intensities.

Applications

  • Analysis of Affymetrix Gene Expression experiments
  • Analysis of Agilent Gene Expression experiments

Service Range

  • Standard statistical methods ranging from
  1. M versus A analysis
  2. Principal Component analysis
  3. Clustering
  4. t-test, ANOVA
  5. False Discovery Rate
  • The statistically most promising genes are determined and
  1. Annotated and linked with information from
  2. Metabolic Pathways, and
  3. GeneOntology

Data Delivery

  • Detailed report with annotations for the top genes, i.e. ranked by absolute fold change value
  • Detailed annotations with hyperlinks for top genes: Unigene, Uniprot, Ensembl, and Entrez Gene, where possible
  • Detailed annotations with hyperlinks for top genes: GeneOntology, where possible
  • Fold change und log(fold change) and intensity values
  • Absent/present values for the Affymetrix probesets
microarrays
 
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