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IT Guy Gets More Mail; Blunt End Gets Smiles

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This is different than what was finally printed

IT Guy Gets More Mail; Blunt End Gets Smiles

Spotfire Gets Serious

In his article, “Microarray Mining Made Easy” (GT 11.00) Nat Goodman described being unable to conduct an analysis on data using Spotfire.net from the published paper, “Molecular portraits of human breast tumours,” Perou, C. M., et al. (2000) Nature 406:747-752. We repeated a bioinformatic analysis comparable to those he described using the same version of Spotfire.net and Array Explorer.

The dataset we used contains 77 experiments, each with 6,178 genes for a total of 475,706 datapoints. Downloading the data, opening and importing the dataset into Spotfire.net, running Array Explorer, hierarchically clustering (only one of the things Array Explorer can do) and rendering the resulting dendrogram for all data was completed in 5 minutes and 36 seconds.

The computer performing this analysis was a dated Compaq Armada 1700 laptop, 266 MHz chip, 160 MB of RAM. The dataset we used is publicly available to all at: http://genome-www. stanford.edu/cellcycle/data/rawdata/combined.txt.

We would hope that anyone interested in serious microarray analysis would contact us for a live demonstration of this. For more information contact us at [email protected]

Bill Ladd, Director of Bioinformatics, Spotfire, Inc.

Back Page KUDOS

How refreshing to see the work of people who can discuss the science of the genome in a cogent manner, without taking themselves so seriously that these same discussions are lost in a sea of self-important bombast. In other words, what a delight it was to finish reading the most recent issue of Genome Technology with the “Blunt End” description of Dysfunctional Genomics, Inc.

[We] hope that your bold experiment — based on the hypothesis that scientists can indeed possess exceptional knowledge, skill, experience, as well as a sense of humor — continues.

Kathleen F. Dunn, President, Vector Communications Division, KF Dunn & Associates

It’s a treat to get each new issue of Genome Technology in the mail. The magazine is a great addition to the heretofore scientific-journal-oriented world of biotechnology. I think you’ve hit on exactly the right mix of serious business and technological coverage, and lightheartedness (e.g., the “Startup is Born” photo-narrative in the November issue is hilarious). Who says biotech is all work and no play?

Janine Sieja Hagerman, Director of Public Affairs & Development, National Center for Genome Resources

Kudos on both the website and the magazine. Both have quickly become favorite reads.

Keep up the great work!

Eric Salmi-Snowdeal, Senior Informatics Software Engineer/New Software Ventures, Motorola

Your new publication looks great. I see it everywhere and people are reading it.

Linda Kirsch, President, Scientific Sales Solutions

Mutated copy

An article in the November issue of Genome Technology contained statements about Akkadix that were misleading. The $250,000 licensing fee cited in the article was a reference not to genes but to the lower limit of fees for research licenses for regulatory elements (or promoters) obtainable from sources other than Akkadix. The genes LEAFY and DET2 were discovered before Akkadix adopted the Menagerie technology. Finally, Akkadix is attempting to create knock-ins with PanGene technology.

 

Email us your comments: [email protected] or mail them to: Editor, GenomeWeb, P.O. Box 998, Peck Slip Station, NY, NY 10272. Include your name, title, company.

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.