Bioinformatics Toolbox™

ilmnbslookup

Look up Illumina^® BeadStudio™ target (probe) sequence and annotation information

Syntax

AnnotStruct = ilmnbslookup(AnnotationFile, ID) AnnotStruct = ilmnbslookup(AnnotationFile, ID, 'LookUpField', LookUpFieldValue)

Arguments

AnnotationFile

An Illumina annotation file.

Tip You can download Illumina annotation files, such as HumanRef-8 v2 sequence.csv, from the Illumina Web site. From Support, access the downloads page, then see the section titled gene expression - probe sequences and annotation.

ID

Unique identifier for a target (probe) on an Illumina microarray.

Tip This identifier is returned in the TargetID field in the structure returned by the ilmnbsread function.

LookUpFieldValue Field in AnnotationFile where ilmnbslookup looks for the specified ID. Default is the Search_key field.

Return Values

AnnotStruct Structure containing the probe sequence and annotation information for a target (probe) specified by ID, and by AnnotationFile, an Illumina annotation file.

Description

AnnotStruct = ilmnbslookup(AnnotationFile, ID) returns AnnotStruct, a structure containing probe sequence and annotation information for a target (probe) specified by ID, and by AnnotationFile, an Illumina annotation file.

Tip The ID identifier is returned in the TargetID field in the structure returned by the ilmnbsread function.

AnnotStruct contains the same fields as the annotation file.

Field	Description
`Search_key`	Unique identifier for the target
`Target`	Unique identifier for the target
`ProbeId`	Probe identifier
`Gid`	GenBank^® ID for the gene associated with the target
`Transcript`	GenBank accession number for the transcript
`Accession`	GenBank accession number for the gene associated with the target
`Symbol`	Typically, the gene name
`Type`	Probe type
`Start`	Starting position of the probe sequence in the GenBank record
`Probe_Sequence`	Sequence of the probe
`Definition`	Definition field from the GenBank record
`Ontology`	Gene Ontology terms associated with the gene associated with the target
`Synonym`	Synonyms for the gene (taken from GenBank record)

AnnotStruct = ilmnbslookup(AnnotationFile, ID, 'LookUpField', LookUpFieldValue) looks for ID in the annotation file in the field specified by LookUpFieldValue. Default is the Search_key field.

Examples

Read the contents of a tab-delimited file exported from the Illumina BeadStudio software into a MATLAB^® structure. Note that the example file, GeneProfile.txt, is not provided with the Bioinformatics Toolbox™ software.

ilmnStruct = ilmnbsread('GeneProfile.txt')

ilmnStruct = 

             Header: 'Illumina BeadStudio data from GeneProfile.txt'
           TargetID: {58428x1 cell}
        ColumnNames: {1x29 cell}
               Data: [58428x29 double]
    TextColumnNames: {1x21 cell}
           TextData: {58428x21 cell}

Look up the probe sequence and annotation information for the 100th entry in the annotation file, HumanRef-8 v2 sequence.csv, by using the identifier for the 100th entry from the TargetID field of the structure created with the ilmnbsread function.