Text Description: Function summary, symbol, chromosomal localization, gene identifiers and aliases from LocusLink/Entrez.

Attribute:

• Gene Ontology (GO) categories and pathway membership.
• Histogram of expression values, by sample.
• Find genes with similar patterns of expression or common GO/pathway membership(s).

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 and can easily be expanded to fit the user base.
• Display: Selected genomic regions - one or more of the 5' sequence, exons, 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, conserved regions repeats and other regions of interest.
• 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, sub-regions of fixed sequence and others with a user-specified 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.

Web Links: Web links to Internet resources is customizable by the user.

Probe Level Data: View data from each of the perfect match (PM) and mis-match (MM) probes for a gene. Plots show the signal level for each probe, and the PM-MM differences. Examine sample-to-sample consistency in probe patterns by cycling through each sample.

Attribute Analysis: Attributes are gene classifications that include GO codes (Molecular Function, Biological Process and Cellular Component) and pathway membership, in a tree structure. Genes in a list are compared to all genes to determine the which attributes are over-represented (with odds ratio and statistical significance)

Pathways: Displays pathways (derived from KEGG, GenMAPP or custom built), with gene expression, or covariate data superimposed. Click for information on a gene or a metabolic product. Annotated with text or thumbnail graphics that summarize key properties of the genes.

Chromosome Map: Map of gene expression (and related data, including karyotype) to gene locations; by cytogenetic band, by fixed chromosomal length, or gene-by-gene.