Visualization |
Gene expression |
Color-coded rectangular grid representing expression levels for gene vs. sample. |
Scatter plot(s) |
Scatter plot of genes or samples:
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.
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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.
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Line graphs |
Optionally, grouped or with standard errors.
Find genes with similar patterns.
Display multiple genes in same or individual (tiled) plots.
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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.
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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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Chromosome map |
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
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