Note: The IGB BGN annotation files can be used to load up transcript cluster, probeset, and probe level annotations for the Affymetrix GeneChip® Arrays into IGB. These files allow the user to quickly load a whole chromosome of annotations. For visualizing smaller genic regions the NetAffx IGB links should be used.

Design Time Annotation Files

MoEx-1_0-st-v1 Annotations, Full, Mm5, GFF (285 MB, 3/6/06)

MoEx-1_0-st-v1 Annotations, Full, Mm6, GFF (285 MB, 3/6/06)

MoEx-1_0-st-v1 Annotations, Full, Mm7, GFF (285 MB, 4/19/06)

MoEx-1_0-st-v1 Annotations, Full, Mm8, GFF (275 MB, 6/21/06)

MoEx-1_0-st-v1 Annotations, Full, Mm9, GFF (278 MB, 3/12/08)

MoEx-1_0-st-v1 Annotations, Probeset, Mm5, CSV (42 MB, 10/6/06)

MoEx-1_0-st-v1 Annotations, Probeset, Mm6, CSV (40 MB, 10/6/06)

MoEx-1_0-st-v1 Annotations, Probeset, Mm7, CSV (42 MB, 10/6/06)

MoEx-1_0-st-v1 Annotations, Probeset, Mm8, CSV (40 MB, 10/6/06)

MoEx-1_0-st-v1 Annotations, Probeset, Mm9, CSV (42 MB, 8/22/08)

MoEx-1_0-st-v1 Mappings, TSV (3.3 MB, 8/18/06)

MoEx-1_0-st-v1 Transcript Cluster ID Mappings to Mouse 430 (296 KB, 8/18/06)

Note: For gene level analysis you will need to download one of the probeset level annotation zip files (CSV) to get the meta-probeset lists. None of these files contain textual biological annotations such as gene name or GO annotations; textual biological information can be found in the NetAffx Transcript CSV file. The design time Probeset CSV file provides information about the probeset such as genome coordinate and supporting annotation types. This is a subset of information found in the NetAffx Probeset CSV file. The Probeset CSV file is also a subset of the Full GFF files which contain transcript cluster, exon cluster, probeset, and probe level annotations. The GFF files also contain information about the specific annotations supporting each of the probesets. For example, use the Full GFF files for pulling design time information into a local database. The Mappings TSV file contains mappings between other arrays and annotations. The transcript cluster mapping files provide gene level mappings between 3' IVT probesets and exon array transcript cluster IDs.

Current NetAffx Annotation Files

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (59 MB, 11/9/09)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 30 (18 MB, 11/9/09)

Note: NetAffx Annotation Files are intended for use in automated analysis. Some are not compatible with all spreadsheet applications. Please use the NetAffx Analysis Center to limit download data to your probesets of interest. Annotation CSV files for the exon arrays are split into a probeset level annotation file and a transcript cluster level annotation file; exon array CSV files are compatible with ExACT.

Sequence Files

MoEx-1_0-st-v1 Probe Sequences, FASTA format (154 MB, 3/19/08)

MoEx-1_0-st-v1 Probe Sequences, tabular format (130 MB, 3/19/08)

MoEx-1_0-st-v1 Probeset Sequences FASTA Format (78 MB, 3/19/08)

MoEx-1_0-st-v1 Sequence Files README (11 KB, 3/19/08)

MoEx-1_0-st-v1 Transcript Cluster Sequences, FASTA format (84 MB, 3/19/08)

Archived NetAffx Annotation Files

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 21 (72 MB, 11/27/06)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 22 (72 MB, 3/29/07)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 23 (50 MB, 9/14/07)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 24 (52 MB, 11/12/07)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 25 (54 MB, 3/20/08)