Annotation Dependencies
Annotation data required by certain components
geWorkbench currently can only read in annotation files based on the Affymetrix annotation file format. Following is a list of the column headers for data types required by various geWorkbench components.
- All components require "Probe Set ID".
| Component | Columns required |
|---|---|
| CNKB | Entrez Gene |
| Gene Ontology | Gene Ontology Biological Process, Gene Ontology Cellular Component, Gene Ontology Molecular Function |
| Marker Annotations | |
| Sequence Retrieval (EBI) | |
| Sequence Retrieval (Santa Cruz) |
List of All Affy headers
- Probe Set ID
- GeneChip Array
- Species Scientific Name
- Annotation Date
- Sequence Type
- Sequence Source
- Transcript ID(Array Design)
- Target Description
- Representative Public ID
- Archival UniGene Cluster
- UniGene ID
- Genome Version
- Alignments
- Gene Title
- Gene Symbol
- Chromosomal Location
- Unigene Cluster Type
- Ensembl
- Entrez Gene
- SwissProt
- EC
- OMIM
- RefSeq Protein ID
- RefSeq Transcript ID
- FlyBase
- AGI
- WormBase
- MGI Name
- RGD Name
- SGD accession number
- Gene Ontology Biological Process
- Gene Ontology Cellular Component
- Gene Ontology Molecular Function
- Pathway
- InterPro
- Trans Membrane
- QTL
- Annotation Description
- Annotation Transcript Cluster
- Transcript Assignments
- Annotation Notes
