About GEO Profiles

Annotation: The gene symbol, full name and aliases as listed in the NCBI Gene, UniGene or Nucleotide databases. At periodic intervals we query Gene, UniGene and Nucleotide with the original sequence Reporter (see below) information extracted from the submitter-supplied Platform record to derive this up-to-date annotation.

Reporter: The original sequence reporter(s) extracted from the submitter-supplied Platform record. Typically, a reporter is a trackable sequence identifier such as a GenBank accession number or Clone ID. It is from these reporters that up-to-date Annotations (see above) are derived.

Experiment: The title of the DataSet from which the Profile is derived, followed by the DataSet Type and Sample Value Type

Profile Neighbors: Connects Profiles that show a similar expression pattern to the chosen Profile within a DataSet. For each DataSet, Pearson correlation coefficients are calculated between pairs of Profiles. The top 200 results are arbitrarily considered to be Profile Neighbors. Pairs with low correlation coefficient values are filtered out using arbitrary thresholds. This feature may help identify functionally-related genes.

Chromosome Neighbors: Connects the 20 physically closest genes on the chromosome from each side of the query gene within a DataSet. This feature may help investigate gene expression neighborhoods.

Sequence Neighbors: Connects Profiles from across all DataSets that are related by nucleotide sequence similarity.

Homologs: Connects genes related by Homologene group across all DataSets.

Links: Reciprocal links to relevant records in other NCBI databases including Gene, UniGene, GenBank, PubMed and OMIM. Neighbors and Links can also be retrieved in batch mode, see Find related data section below.

Clicking on the thumbnail image will enlarge the chart to display the full profile details, expression values, and the DataSet subsets that reflect experimental design. Each chart displays the expression level of one gene across all Samples within a DataSet.

Red column: Each column represents the expression measurement extracted from the VALUE column of one original submitter-supplied Sample record. The original Sample accessions (GSMxxx) are listed in the gray boxes along the bottom of the chart. Sample records are submitted by the scientific community and reflect a wide variety of data types that are processed and normalized using a wide variety of methods. There is no standard unit for gene expression and so expression values should be considered arbitrary units. It can be assumed that the value measurements within a GEO DataSet have been calculated in an equivalent manner, but it is not usually appropriate to make direct comparisons of values between different DataSets. Single channel samples are normalized signal count values, whereas dual channel samples are typically test/reference log ratios. Check the 'Data processing' field or VALUE description in original Sample records for information on how the VALUEs were calculated.

Blue square: Represents rank order of expression measurements. All VALUEs within a Sample are rank ordered, and then placed into percentile 'bins'. In other words, all the values of one hybridization are sorted, then split into 100 groups. Thus, the blue rank squares on charts give an indication of where the expression of that gene falls with respect to all other genes on that array.

It is important to note that the values (red columns) and ranks (blue squares) are charted on different scales - the blue ranks are always on a scale of 1-100% (right Y axis of the chart) while the red value scale slides to fit the values of a particular profile (left Y axis of the chart). This sliding value scale allows subtle differences in values to be more clearly visualized.

Faded columns/squares: These correspond to Affymetrix 'Detection call' = Absent. Detection call is specific to Affymetrix technology. For details of the detection algorithm please refer to Affymetrix literature, e.g., Affymetrix GeneChip Expression Analysis and Affymetrix Statistical Algorithms Description Document. Briefly, a gene may be flagged as absent if expression is not detected or if stray cross-hybridization signals are detected. Extract from Affymetrix literature:

"A detection call answers the question: Is the transcript of a particular gene Present or Absent? In this context, Absent means that the expression level is below the threshold of detection. That is, the expression level is not provably different from zero. In the case of an uncertainty, we can get a Marginal call. It is important to note that some probe-sets are more variable than others, and the minimal expression level provably different from zero may range from a small value to very large value (for a noisy probe-set)."

Some Affymetrix submitters do not consider Detection calls and choose not to supply them, and some Affymetrix transformation algorithms do not generate them, in which cases the calls will not exist in GEO.