PAICE

PAICE visualizes biological pathways using KEGG-compatible accessions to interpret genomic data from Illumina Solexa next-generation sequencing and Affymetrix microarray experiments.

Key Features:

• Pathway visualization: Maps genes and probes to KEGG pathway diagrams to produce pathway-level visual representations.
• KEGG compatibility: Accepts KEGG (Kyoto Encyclopedia of Genes and Genomes) accessions to align experimental entities with KEGG pathway structures.
• Color-coding: Applies color-coding to pathway nodes to highlight genes or gene sets based on experimental data.
• Integration with experimental data: Incorporates Illumina Solexa next-generation sequencing and Affymetrix microarray data, accounting for detection calls and duplicate gene copies in pathway displays.

Scientific Applications:

• Transcriptomic pathway interpretation: Enables pathway-level interpretation of Illumina Solexa and Affymetrix transcriptomic datasets.
• KEGG pathway overlay: Allows overlay of experimental measurements and annotations onto KEGG pathway diagrams.
• Duplicate-gene assessment: Facilitates assessment of duplicate gene copies within the context of biological pathways.

Methodology:

Uses KEGG-compatible accessions with Illumina Solexa and Affymetrix dataset inputs to generate pathway visualizations and applies color-coding according to detection calls and duplicate gene copies.