Annotations

Annotations Provided in AltAnalyze

Annotations are provided for the various analyses in AltAnalyze at the level of genes, alternative exons, splicing events, microRNA binding sites and proteins. A full description of these annotations can be found in the full online documentation.

Gene Expression Results

AltAnalyze extracts useful gene annotations for determining whether a gene:

• Protein-coding potential
• “Drug-able” targets (e.g. GPCR, kinase)
• Transcriptional and splicing regulator
• Putative microRNA targets
• Associated WikiPathways
• Associated Gene Ontology terms
• UniProt annotated cellular compartment
• Putative housekeeping genes

Alternative Isoform Annotations

Alternative isoform data is obtained through extraction of transcript data from the Ensembl and UCSC databases. This database is primarily built from Ensembl and augmented with unique exons, junctions and transcripts found in the UCSC mRNA table for each species in Ensembl. Novel isoform annotations are included for Affymetrix junction arrays (HJAY, hGlue) and imported RNASeq data. These annotations include:

1. mRNA transcripts
2. associated proteins
3. exons
4. junctions
5. exon/junction aligning protein domains (Ensembl)
6. exon/junction aligning protein motifs (UniProt)
7. exon aligning microRNA binding sites (various)
8. alternative splicing events, promoters and polyadenylation

Pathway Over-representation

See GO-Elite webpage.