• Data importing, supporting flat files with delimited columns.
• An optional GUI for users to specify and/or select data fields, optional use of standard and user-defined filters specific for chips and experiments.

• Genome overview/summary plots to allow user to quickly identify interesting genomic regions for detailed analysis.
• Detailed analysis for individual chromosomes: two-way zooming with coverage resolution from chromosome to individual data points.
• Choice of different plot types including bar plot, point plot, frequency plot, and heat map.
• The default plot is a bar-type point plot similar to point plot but with a bar to indicate the minimal and maximal values of all data points within each of the represented genomic region units. This allows users to have visualization of the outliers at any resolution level. Users can also access the raw data (the IDs and their values) of the individual data points within the area by right click on the bar. At the highest level of resolution at which all individual data points are displayed, the plot is the same as a point plot.
• Access to UCSC, NCBI, ENSEMBL, and SOURCE for gene annotation for the selected regions or data points according to user’s preference through hyperlink by right mouse click on any bar or data points.
• Input of threshold for defining outliers; cytogenetic Ideogram alongside the chromosome location; search and locate any specific data IDs.
• Printing plot images and exporting in standard image formats including jpeg, png, and tiff.

The aCGHview will import data from tab delimited text files. The data file is required to contain a column of BAC IDs, optionally a corresponding column of genomic locations, and columns of experimental values. These data columns may represent various normalization or statistical analytical results. The program displays a genomic summary plot allowing the user to select a particular chromosome for further examination. The user can also choose one particular column of values to plot. Upon selection of a chromosome, the program displays the values for the BACs from that chromosome as a bar graph. This allows the user to select chromosomal regions containing amplification or deletions. The user can then select a particular data point of interest and have the application launch a web browser to NCBI or UCSC with the ID, such as BAC ID, as a parameter.

We provide image analysis as a separate service for microarray slides not made in this facility. The hybridized slides are scanned using an Axon GenePix 4200AL Scanner to generate high-resolution images for both cy3 and cy5 channels. Image analysis is performed on the raw image files using the ImaGene (current version 8.0.1) software from BioDiscovery, Inc. The spots are identified using an optimized segmentation algorithm. The spots of poor quality, as well as spots with signal levels indistinguishable from the background, are labeled as bad spots. The image data are extracted and used for data analysis. This service is charged based on number of slides and hourly for additional for image analysis. For details, please contact Devin McQuaid at 716-845-8805.