GNF Ratio Track Settings
 
GNF Gene Expression Atlas Ratios Using Affymetrix GeneChips   (All Expression tracks)

Display mode:   
Draw intron lines/arrows and exons:
Combine arrays:
Color:
red/green
red/blue
yellow/blue
red/blue on white background
red/blue on yellow background
View table schema
Data last updated at UCSC: 2006-02-01

Description

This track shows expression data from GNF (The Genomics Institute of the Novartis Research Foundation) using Affymetrix GeneChips. The chip types, chip IDs or tissue averages associated with experiments can be displayed by selecting the appropriate option from the Experiment Display menu on the track description page. For more information, see the Track Configuration section.

Methods

For detailed information about the experiments, see Su et al. 2002 in the References section below. Alignments displayed on the track correspond to the target sequences used by Affymetrix to choose probes.

In dense display mode, the track color denotes the average signal over all experiments on a log base 2 scale. Lighter colors correspond to lower signals and darker colors correspond to higher signals. In full display mode, the color of each item represents the log base 2 ratio of the signal of that particular experiment to the median signal of all experiments for that probe.

More information about individual probes and probe sets is available on the Affymetrix website.

Track Configuration

This track may be configured to change the display mode and colors or vary the type of experiment information shown. The configuration controls are located at the top of the track description page, which is accessed via the small button to the left of the track's graphical display or the link on the track's control menu.

  • Display mode: To change the display mode for the track, select the desired display setting from the Display Mode pulldown list.
  • Combine Arrays: All arrays may be displayed with either the chip ID or the tissue type as the label. Replicate arrays may also be combined by expression medians.

When you have finished making changes, click the Submit button to commit your changes and return to the Genome Browser tracks display.

Credits

Thanks to GNF for providing these data.

References

Su, A.I., Cooke, M.P., Ching, K.A., Hakak, Y., Walker, J.R., Wiltshire, T., Orth, A.P., Vega, R.G., Sapinoso, L.M., Moqrich, A. et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA 99(7), 4465-70 (2002).