Microarrays for an Integrative Genomics 
Isaac S. Kohane  Alvin Kho  Atul J. Butte

MIT Press, August 2002

Software from the Children's Hospital Informatics Program referenced in this book:

Relnet is a software tool written by Atul Butte that allows genomics and bioinformatics researchers to construct relevance networks from their gene expression data. The software comprehensively compares all measured genes and phenotypic measurements against each other, and builds networks from the highest scoring pairs. Advantages of this method over others include: (1) negative associations (e.g. those from tumor suppressing genes) are shown, (2) disparate data types can be included (i.e. clinical, expression, and phenotypic), and (3) multiple connections are allowed (e.g. a transcription factor may be responsible for regulating the expression of multiple other genes).

UNCHIP is a freely available web-based system that takes Affymetrix microarray accession codes and returns the latest information about each probe set, including official gene names, functions, chromosomal positions, and protein domain information.

Errata (please let us know if you find any errors not noted here)

p. 58, Figure 2.10. The figure caption incorrectly refers to a middle panel (which is not shown). The caption above the rightmost panel should read "Label variance" rather than "Sample variance". On page 55, the text refers to red points in this figure which is printed black and white. The red points are those which appear outside the twofold increase/decrease lines in the figure (Thanks to Frederique Galisson for pointing this out)

pg. 137 Fig. 3.25. An extra point was inadvertently added to the bottom right graphic grid.

Relevant Links

Data models/data exchange

The MicroArray Gene Expression Data Society (MGED) officially become a Society registered in California on May 29, 2002. An article on MAGE-ML and a web site on this emerging standard are now available.