Gene Expression: Color-coded rectangular grid representing expression levels for gene vs. sample.

Scatter Plot(s): Scatter plot of genesColor-coded rectangular grid representing expression levels for gene vs. sample.

• Modes: Sample vs. sample, gene by gene, sample group by group (e.g. treatment vs. control), gene cluster by gene cluster, principal component plots, and plots by covariate.
• Optional color coded points, fold-change plot, fitted regression lines, and S.E. bars.
• Multiple (tiled) plots on single display.
• 2-D, or rotating 3-D plots.
• Density or contour mapping of points.
• Automated text or graphical (thumbnail) labeling of points or groups.

Pathways: Displays pathways derived from KEGG or GenMAPP, or custom built.

• Superimpose gene expression data, or data from a selected covariate.
• Click for information on a gene or a metabolic product.
• Annotate with text or thumbnail graphics that summarize key properties of the genes.

Line Graphs: Show changes in expression across time (e.g cell cycle changes)

• Optionally, grouped or with standard errors.
• Find genes with similar patterns.
• Display multiple genes in same or individual (tiled) plots.

Distance Matrix: Presents pairwise measures of distance (or similarity) between samples or genes.

• Any pair can be isolated as a scatterplot.
• The matrix can be used for one-, two- or three-dimensional multidimensional scaling plots.
• The matrix can be used as the basis for hierarchical clustering.

Sequence Analysis: Display and analyze one or more sequences:

• Download: Download genomic sequence for one, or a set of genes, from the Epicenter Software server. Sequence may include user-defined 5' and 3' extensions. Current genomes include human, mouse and rat.
• Display: Selected genomic regions - one or more of the 5' sequence, the exons, the introns and the 3' sequence. Each sequence is shown schematically (indicating exonic regions) and by nucleotide.
• Align: One or more sequence with a primary sequence, with or without gaps. Align Affymetrix probe sequences against the genomic sequence. Highlight mismatches.
• BLAST: Click-and-drag to select a sequence and drop that sequence into a Web-based BLAST engine.
• Find: Find all matches to a motif. The motif can include ambiguous nucleotides, variable length gaps, subregions of fixed sequence and others with a user-speified maximum mismatches. The motif can be a combination of two or more alternatives.
• Motif list: Build a library of nucleotide motifs of interest.
• Compare: Count occurrences of a selected motif in a set of gene sequences, and statistically compare this to a control set. Search can be limited to conserved regions and/or non-repeat regions.
• Conserved: Conserved genomic regions may be highlighted.
• Repeats: Repeat genomic regions can be highlighted.

Distance Matrix: Genes mapped to a chromosomal ideogram are grouped by their proximity in the genome, and the properties of these groups can be statistically evaluated and graphically displayed.

• SNP data can be shown as the location of each SNP (and its genotype, for a given sample). Regions of loss-of-heterozygosity (LOH), based on SNP chip data, can displayed for each sample and averaged over multiple samples. Summary data on a single SNP, with links to the TSC and dbSNP Web site.
• Karyotype description is automatically interpreted to mark up the chromosome ideogram to indicate regions of loss, duplication and sites of translocation.
• Biological data may be compared with expression-related information