ChipInspector

Category Genomics>Gene Expression Analysis/Profiling/Tools

Abstract ChipInspector analyzes raw data files from microarray experiments. It selects those probes from the chip, where the signal is significantly different from the background and puts them in their biological context.

ChipInspector extracts significant information from the expression level of single probes of Affymetrix GeneChip© microarrays, Agilent DNA microarrays and Illumina® whole-genome gene expression arrays.

ChipInspector increases the number of significant features while simultaneously reducing false positive rates by an order of magnitude.

The resulting lists of significantly regulated genes from the experiment are directly usable as input for pathway mining tools such as Genomatix Pathway System (GePS) - (see G6G Abstract Number 20019R).

ChipInspector includes only a rudimentary tool set for quality assessment of microarrays. Low level quality assessment of the hybridization and thus the success of the experiment can be performed with a number of good and cost-free tools such as the Affymetrix TAS software, Agilent’s Feature Extraction, or Illumina’s BeadStudio.

The Genomatix approach puts its focus on the biological knowledge that is accumulated and stored in the annotation. The annotation is made independently of the information and the intention at the time of design of the array.

Thus the data taken from the experiment is reduced to information about hybridization signals, the biological implications are calculated on the basis of the most current state of the genome.

ChipInspector extracts significant information right from the expression level of single probes from microarrays.

Sophisticated analysis techniques and state-of-the-art genomic knowledge dramatically increase the number of significant features while simultaneously reducing false positive rates by an order of magnitude. Start with your existing Affymetrix data (CEL files) to see what is really behind the data.

ChipInspector uses one of the world's largest databases of alternative transcripts and promoters (as stated above...) to achieve superior signal-noise ratios in microarray analysis.

It is unique in removing statistical and gene calling errors right at single probe level. This technology provides the basis for unmatched accuracy in the significance analysis of microarray (SAM) data.

Products features/capabilities include:

1) ChipInspector uses single probe expression levels as input.

2) ChipInspector reduces false positive rates by about an order of magnitude.

3) ChipInspector eliminates normalization/interpolation problems.

4) ChipInspector increases the number of significant features.

5) ChipInspector supports Affymetrix CEL (cell intensity) files (other platforms are possible).

6) ChipInspector assigns probes correctly to transcripts and genes.

7) ChipInspector accounts for alternative transcripts.

8) ChipInspector offers a direct transcript view with probe mapping.

9) ChipInspector applies state-of-the-art genomic knowledge.

10) ChipInspector extracts new information by mining previous microarray experiments.

11) ChipInspector results are directly usable as input to the Genomatix Pathway System (GePS) product.

Note: An Example of a regular SAM analysis vs. ChipInspector --

An example experiment with very good results, based on Affymetrix probe set analysis.

A SAM analysis with a false positive rate of 0.2 % yields an ‘experiment specific network’ with 14 genes linked to four (4) pathways. But some key genes known to be involved remain unconnected to observed pathways.

Re-evaluation of the identical experiment with ChipInspector on a single probe level allows a SAM analysis with a false positive rate of 0.002%.

The identical network analysis yields an ‘experiment specific network’ with 35 significantly regulated genes joined and linked to 31 pathways. All known key genes are included in the network.

System Requirements

Manufacturer

Manufacturer Web Site ChipInspector

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G6G Abstract Number 20133R

G6G Manufacturer Number 101114