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IGB can be used to visualize data from Affymetrix showing the locations of GeneChip Expression Array probe sets and target sequences aligned to a genome.

In most Affymetrix arrays, probes are grouped conceptually into probe sets, groups of probes that are expected to measure expression for individual known or computationally-deduced mRNA molecules. 

These target sequences may be identical to known mRNA sequences in GenBank, or they may have been produced computationally by merging ESTs or mRNA sequences into a single sequence, sometimes called a "consensus" sequence.

IGB can display location of design sequences and probes within the genomic sequence. Probe set alignments are available as "link.psl" files from the Affymetrix Web site. Some probe set alignments are also available from Affymetrix and IGBQuickLoad data sources in the Available Data sub-panel of the Data Access planel.

Viewing probe sets from IGB DAS

To view probe sets available from IGB DAS2 data source

  • Open the Data Access panel
  • Open the IGB DAS / affy folder under the Data Sources and Data Sets section of the Data Access tab.
  • Click the checkbox next to the array you would like to examine
  • zoom to a gene or region of interest and click Load Data.

The probe set, including the target sequence and individual probe, will appear in IGB.

Where to find probe set alignment files

Many are available from the Affymetrix customer support Web site.

To obtain these files, go to the Affymetrx site and look for the array you are interested in.

On the array's support page, look for alignment data files in the "NetAffx Annotation Files" section. Look for files labeled as consensus alignment files or something similar. Note that alignment data files may not be available be available for species with well-characterized genomes.

Affymetrix distributes these files in an Affymetrix-specific format called "link.psl" which IGB can read.

These files consist of two sections:

  • Alignments of the target sequences onto the reference genome (ordinary PSL format)
  • Alignments of probe sequence onto the targets

Probes and probe sets on display

Once the data have been loaded, the probes and target sequence alignments will appear in a separate track labeled by chip.  Within the track, probes and their matching target sequences always appear together.  The following figure shows an example from the rat 230 chip. 

Probe set target sequence

The alignment between the probe set target sequence and the genome is represented at the top of the figure as a series of blocks.  Each block represents a block of alignment in which each base in the genome matches a corresponding base in the target sequence.  Gaps between the blocks typically represent areas where the genomic sequence contains inserts relative to the aligned target sequence.  Usually, these gaps are due to introns.

There are some exceptions to this, however.  For example, the sixth and seventh blocks in the figure above are so close together that they almost appear as a single block at this level of zoom. 

Zooming in for a closer view reveals that these two alignment blocks are immediately adjacent to each other.  This indicates that these two blocks of alignment were separated by an insert in the target sequence relative to the genomic sequence.  That is, the target sequence contained some bases that were not present in the genomic sequence.  This may present a problem if this missing region (in the genome, that is) contains some probe sequences.  In this particular case, however, the alignment irregularity occurs in a 5' region, outside the area covered by the probes.  (See the discussion below.)

How can this happen?  There are a number of reasons, but discrepencies between the genomic and target sequences are usually responsible.

Probes and probe sets.

Each target sequence is shown with its corresponding probe set.  Each probe set consists of a group of probes, which are shown superimposed on the alignment blocks of the target sequence.

The figure below shows a close-up view near the 3' end of the target sequence.  The 3' end of the target sequence is annotated with blocks which represent individual probes. 

Two things are important to notice about this image.  First, sometimes individual probes are split across gaps in the alignment, which typically correspond to introns.  When this occurs, the two halves of the probe are connected by a line.

Second, sometimes probes overlap with each other.  This can be seen by clicking on probes.  If a selection outline is visible in the middle of what otherwise looks like a single block, then there is really more than one block.

Probe set labels

Each probe set and probe set target sequence is labeled with the name of the chip (Rat230_2, in this case) and the probe set identifier.

Polyadenylation sites  

For many probe set target sequences, Affymetrix bioinformatics scientists have used computational methods to predict putative polyadenylation sites near the 3' end of the target sequence.  These are shown as dark or light blue boxes riding on top of the terminal alignment span.

If the box is light blue, then the site was deduced from the overlap of multiple expressed sequences (usually 3' ESTs) whose genome alignments all terminate at a common location.  This is sometimes called a "polyA stack."

If the box is dark blue, then the site has been deduced through sequence analysis of an individual, exemplar sequence, such an mRNA sequence record from GenBank.  This is sometimes called a polyA site to distinguish it from a polyA stack.

Recognizing putative probe set targets

It is usually a good idea to load additional tracks of data besides just the probe set information.  For example, in the figure above, the track below the probe set track shows the probe set's likely target, an mRNA from the Rp14 locus.  Based on their relative alignments to the genome sequence, it appears that both sequences overlap in the region that contains the probes.  Thus, it is very reasonable to assume that this probe set does indeed detect the mRNA shown below it. 

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