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Biological Interpretation
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Gene information |
Text description |
Function summary from LocusLink, symbol, chromosomal localization, gene identifiers. |
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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).
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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.
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Web links |
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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. |
Gene list interpretation |
Attribute analysis |
Attributes are gene classifications that include GO codes (Molecular Function, Biological Process and Cellular Component) and pathway membership, in tree structure. Genes in a list are compared to all genes to determine the Attributes 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. |
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