Wildcards:

“_” is the single character wildcard (i.e. “TK_”)

“%” is the multiple character wildcard (i.e. “thymidine%”)

Report Parameters:

• “Produce heatmap”: Check to view expression heatmap of genes found by query.
• “Limit to X results per page”: Choose how many genes to show per page.
• Check which annotations to display on the report page.
• “Threshold for heatmap colors”: Set the contrast for the heatmap here. A value of sets the colormap such that expression ratios of >=2 will be assigned the brightest red color, and expression ratios of <=-2 will be assigned the brightest green values.
• “Use these values for heatmap”: 3 choices of row-wise (i.e. per gene) data normalization exist:
• Log2 Ratios
• Median-centered Log2 Ratios
• Z-score of Log2 Ratios (Median-centered Log2 divided by the standard deviation for each gene)
• “Order results by”: Choose any of the listed annotations to order the genes on the results page by.

Two Query Types exist:

1) Select “Full Text Annotation Searches” to query on:

• Annotation
• Gene Symbol & Aliases (i.e. “TK1”)
• Cytoband (i.e. “17q23%”)
• Chromosome (i.e. “17”)
• Gene Name (i.e. “Thymidine kinase 1, soluble ”)
• Locuslink (i.e. “7083”)
• Unigene (i.e. “Hs.164457”)

• IMAGE Clone (i.e. “379920”)

• GO Term (i.e. “apoptosis”)

• GO ID (i.e. “GO:0006915”)

2) Select "Chromosome Location Search" to query for genes on a particular chromosome within a specified basepair range on that chromosome. On the next page, select the chromosome you are interested in and type in the basepair range that you would like to search in.