Create Expression Browser

The Create Expression Browser tool makes it possible to inspect gene, transcript or miRNA expression level counts, annotations and statistics for many samples at the same time. Further, the plotting functionality helps with visualizing the data in an easy to interpret way.

To run the tool, go to:

Toolbox | RNA-Seq and Small RNA Analysis ()| Create Expression Browser ()

Select some expression tracks (). These can be either Gene level (GE) or Transcript level Expression (TE) tracks, but not a combination of both (see figure 33.2).

Click on the Next button.

Image expressionbrowser_select_tracks
Figure 33.2: Select expression tracks, either GE or TE.

In the second wizard dialog, statistical comparisons and an annotation resource can be selected (see figure 33.3). Information from the selected elements is included in the expression browser.

Image expressionbrowser_select_statcomp_go
Figure 33.3: Information from statistical comparisons and an annotation resource can optionally be included in the expression browser being created.

Statistical comparisons are generated by differential expression tools, described in Differential Expression. The selected statistical comparisons must have been created using the same kind of expression tracks as those selected in the first wizard step. For example, when creating an expression browser using GE expression tracks, statistical comparisons must have been generated using GE tracks.

Annotation resources can come from various sources:

Annotations from the Gene Ontology consortium at http://current.geneontology.org/products/pages/downloads.html. The files downloaded from there can be imported using the Standard Import tool.

Annotations contained in tables. To use such tables as an annotation resource, at least one column must have a header from the list in table 33.4, spelled exactly as shown, and contain identifiers that can be matched with identifier information in the selected expression tracks. Where more than one column has a header from that list, the column with the most matching identifiers is used to determine the row each annotation should be added to.

Excel and CSV format files can be imported as tables using the Standard Import tool. For CSV format files, force the import type to "Table in CSV format (.csv)".

Table 33.4: Column headers for columns containing identifiers.

Accession	GeneName	RefSeq transcript ID
Ensembl	GeneSymbol	RefSeq_ID
EnsemblID	GI	RefSeqAccession
Entrez gene	Gid	RGD name
Entrez_Gene_ID	Identifier	SGD accession number
EntrezGeneID	MGI name	Symbol
Feature ID	Name	Transcript
FlyBase	Primary accession	Transcript ID
GenBank accession	PrimaryAccession	Transcript ID(Array Design)
Genbank identifier	Probe Set ID	transcript_cluster_id
Gene ID	Probe_Id	WormBase
Gene name	ProbeID
Gene symbol	RefSeq accession

Annotations generated by the "Blast2GO PRO" plugin
(see https://digitalinsights.qiagen.com/plugins/blast2go-pro/).
Annotations for human, mouse and rat bundled with Reference Data Sets.

Subsections