PROBE_ID
headers (that is: 'Probe Set ID', 'Feature ID', 'ProbeID' or 'Probe_Id').
Note that some column headers are alternatives so that only one of the alternative columns headers should be used.
Also note that when adding annotations from an annotation file onto an experiment the file contents are merged onto the experiment by matching the entries in a user specified annotation column in the annotation file to the entries in the feature id column of the experiment. It will thus typically be useful to include a column in your annotation file in which the entries are a subset of, or identical to, the entries in the Feature Id column of the experiment you want to annotate.
A simple example of an annotation file is shown here:
"Probe Set ID","Gene Symbol","Gene Ontology Biological Process" "1367452_at","Sumo2","0006464 // protein modification process // not recorded" "1367453_at","Cdc37","0051726 // regulation of cell cycle // not recorded" "1367454_at","Copb2","0006810 // transport // /// 0016044 // membrane organization // "Download this example plus a more elaborate one here:
To meet requirements imposed by special functionalities in the workbench, there are a number of further restrictions on the contents in the entries of the columns:
PUBLIC_ID
column, so this column must be present for the action to work
and should contain the NCBI accession number.
///
and it interprets all that appears
before //
as the actual entry and all that appears after //
within an entry as comments. Example:
/// 0000001 // comment1 /// 0000008 // comment2 /// 0003746 // comment3The annotation tests will interpret this as three entries (0000001, 0000008, and 0003746) with the according comments.
Column header in imported file (alternatives separated by commas) | Label in experiment table | Description (tool tip) |
Probe Set ID, Feature ID, ProbeID, Probe_Id, transcript_cluster_id | Feature ID | Probe identifier tag |
Representative Public ID, Public identifier tag, GenbankAccession | Public identifier tag | Representative public ID |
Gene Symbol, GeneSymbol | Gene symbol | Gene symbol |
Gene Ontology Biological Process, Ontology_Process, GO_biological_process | GO biological process | Gene Ontology biological process |
Gene Ontology Cellular Component, Ontology_Component, GO_cellular_component | GO cellular component | Gene Ontology cellular component |
Gene Ontology Molecular Function, Ontology_Function, GO_molecular_function | GO molecular function | Gene Ontology molecular function |
Pathway | Pathway | Pathway |
The full list of possible column headers:
Column header in imported file (alternatives separated by commas) | Label in experiment table | Description (tool tip) |
Species Scientific Name, Species Name, Species | Species name | Scientific species name |
GeneChip Array | Gene chip array | Gene Chip Array name |
Annotation Date | Annotation date | Date of annotation |
Sequence Type | Sequence type | Type of sequence |
Sequence Source | Sequence source | Source from which sequence was obtained |
Transcript ID(Array Design), Transcript | Transcript ID | Transcript identifier tag |
Target Description | Target description | Target description |
Archival UniGene Cluster | Archival UniGene cluster | Archival UniGene cluster |
UniGene ID, UniGeneID, Unigene_ID, unigene | UniGene ID | UniGene identifier tag |
Genome Version | Genome version | Version of genome on which annotation is based |
Alignments | Alignments | Alignments |
Gene Title | Gene title | Gene title |
geng_assignments | Gene assignments | Gene assignments |
Chromosomal Location | Chromosomal location | Chromosomal location |
Unigene Cluster Type | UniGene cluster type | UniGene cluster type |
Ensemble Ensembl | Ensembl | |
Entrez Gene, EntrezGeneID, Entrez_Gene_ID | Entrez gene | Entrez gene |
SwissProt | SwissProt | SwissProt |
EC | EC | EC |
OMIM | OMIM | Online Mendelian Inheritance in Man |
RefSeq Protein ID | RefSeq protein ID | RefSeq protein identifier tag |
RefSeq Transcript ID | RefSeq transcript ID | RefSeq transcript identifier tag |
FlyBase | FlyBase | FlyBase |
AGI | AGI | AGI |
WormBase | WormBase | WormBase |
MGI Name | MGI name | MGI name |
RGD Name | RGD name | RGD name |
SGD accession number | SGD accession number | SGD accession number |
InterPro | InterPro | InterPro |
Trans Membrane | Trans membrane | Trans membrane |
QTL | QTL | QTL |
Annotation Description | Annotation description | Annotation description |
Annotation Transcript Cluster | Annotation transcript cluster | Annotation transcript cluster |
Transcript Assignments | Transcript assignments | Trancript assignments |
mrna_assignments | mRNA assignments | mRNA assignments |
Annotation Notes | Annotation notes | Annotation notes |
GO, Ontology | Go annotations | Go annotations |
Cytoband | Cytoband | Cytoband |
PrimaryAccession | Primary accession | Primary accession |
RefSeqAccession | RefSeq accession | RefSeq accession |
GeneName | Gene name | Gene name |
TIGRID | TIGR Id | TIGR Id |
Description | Description | Description |
GenomicCoordinates | Genomic coordinates | Genomic coordinates |
Search_key | Search key | Search key |
Target | Target | Target |
Gid, GI | Genbank identifier | Genbank identifier |
Accession | GenBank accession | GenBank accession |
Symbol | Gene symbol | Gene symbol |
Probe_Type | Probe type | Probe type |
crosshyb_type | Crosshyb type | Crosshyb type |
category | category | category |
Start, Probe_Start | Start | Start |
Stop | Stop | Stop |
Definition | Definition | Definition |
Synonym, Synonyms | Synonym | Synonym |
Source | Source | Source |
Source_Reference_ID | Source reference id | Source reference id |
RefSeq_ID | Reference sequence id | Reference sequence id |
ILMN_Gene | Illumina Gene | Illumina Gene |
Protein_Product | Protein product | Protein product |
protein_domains | Protein domains | Protein domains |
Array_Address_Id | Array adress id | Array adress id |
Probe_Sequence | Sequence | Sequence |
seqname | Seqname | Seqname |
Chromosome | Chromosome | Chromosome |
strand | Strand | Strand |
Probe_Chr_Orientation | Probe chr orientation | Probe chr orientation |
Probe_Coordinates | Probe coordinates | Probe coordinates |
Obsolete_Probe_Id | Obsolete probe id | Obsolete probe id |