In addition to updating selected existing data sets, we have introduced several new annotations to various assemblies. High-confidence gene annotations from the Consensus Coding DNA Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) have been added to more human assemblies and to the mouse. The Affymetrix Transcriptome Phase 3 data set (human) (27) displays transcriptome data from tiling Affymetrix GeneChips. The ORegAnno (Open Regulatory Annotation) track (several species) shows literature-curated regulatory regions, transcription factor binding sites and regulatory polymorphisms from the ORegAnno database (28). The ACEScan annotation (human) identifies predicted alternative human-mouse conserved exons from ACEScan (29). The CGAP SAGE track (human, mouse) displays genomic mappings for human LongSAGE tags from the Cancer Genome Anatomy Project (CGAP) (30), using the Serial Analysis of Gene Expression (SAGE) quantitative technique (31). The MGI QTL track (mouse) shows approximate positions of quantitative trait loci based on reported peak LOD scores from the Jackson Laboratory Mouse Genome Informatics group. The zebrafish genome now provides expression data using the Affymetrix Zebrafish GeneChip Genome Array (32).
