Absolute Analysis: The qualitative analysis of
a single array to determine if a transcript is Present,
Absent or Marginal.
Affymetrix tab-delimited format of the
probe sequence download file:
The probe sequence download file in the Download
Center is a tab-delimited file containing the following
Probe Set Name: For example, 1007_s_at
Probe X: The X coordinate of the probe sequence
on the GeneChip® probe array.
Probe Y: The Y coordinate of the probe sequence
on the GeneChip probe array.
Probe Interrogation Position: The position of
the 13th ("middle") nucleotide of the probe
sequence as it aligns on the consensus/exemplar
Probe Sequence: The 25-base perfect match
Target Strandedness: The sense/antisense
orientation of the target sequence that can
hybridize with the probe sequence.
Note: Probe Sequence databanks in the NetAffx™
Analysis Center have an additional column called, "Serial
Order". This column provides the relative order of probe
sequences as they align with the consensus/exemplar
Array: A collection of probes on glass encased
in a plastic cartridge.
Average Difference: A quantitative relative
indicator of the level of expression of a transcript.
Background: A measurement of signal intensity
caused by autofluoresence of array surface and
non-specific binding of target/stain molecules
Base: Nucleic acids are biological
macromolecules. Sugar and phosphate groups form an
uniform backbone (the phosphate groups are actually the
acids). Variable side chains are attached to each sugar.
The side chains of DNA are either of four nitrogenous
bases: two purines (adenine and guanine) and two
pyrimidines (cytosine and thymine). RNA comprises uracil
instead of thymine.
Baseline Array: An array designated as the
baseline when being analyzed in comparison analysis with
which the experimental array is compared to detect
changes in expression. For example, if the baseline file
is derived from a treated sample and the experiment from
an untreated sample, all genes activated by the treatment
will have decrease calls.
Chip: See Array
Clone: A colony of cells that are hosting a
piece of foreign DNA. Breading one cell from a clone is a
common technique to amplify the foreign DNA. (In general,
a clone is a colony of genetically identical cells that
are all descendents from a single anchestor cell.)
Comparative Analysis: The analysis of an
experimental array compared to a baseline array.
Decision Matrix: An algorithm that examines a
collection of metrics used to determine the status of a
Detection: A quantitative measurement
indicating if the transcript is detected (Present), not
detected (Absent), or marginally detected (Marginal).
Empirical Algorithms: The algorithms contained in
GeneChip Analysis Suite and Microarray Suite 4.0 based on
empirical data generated by Affymetrix.
Experimental Array: An array that is used in
comparison analysis to be compared to the baseline array
to detect changes in expression. For example, if the
baseline file is derived from an untreated sample and the
experiment from a treated sample, all genes activated by
the treatment will have increase calls.
A sequence in FASTA format begins with a single-line
description, followed by lines of sequence data. The
description line is distinguished from the sequence data
by a greater-than (">") symbol in the first column. It
is recommended that all lines of text be shorter than 80
characters in length. An example sequence in FASTA format
>exemplar:AtGenome1:16876_at; gb|AL023094; AL023094
/FEATURE=cds-2 /GENE=T4L20.20 /LABEL= /PRODUCT= putative
serine/threonine protein kinase /STRAND=forward
/DEFINITION=Arabidopsis thaliana DNA chromosome 4, BAC
clone T4L20 (ESSA project).
Feature: A single square-shaped probe cell on
an array (another term for probe cell). A feature ranges
in size from 18 to 50 microns depending on the array
Gene: Genes are composed of deoxyribonucleic
acid (DNA), except in some viruses, which have genes
consisting of a closely related compound called
ribonucleic acid (RNA). A DNA molecule is composed of two
chains of nucleotides that wind about each other
resembling a twisted ladder.
GeneChip Unit Type/Probe Set Name
- _at : antisense target
- _st : sense target
- _s_at : similarity constraint
- _g_at: common groups
- _r_at: rules dropped
- _i_at : incomplete
- _b_at : ambiguous probe set
- _l_at : long probe s
Hybridization Controls: Controls added to the
sample before hybridization to the array.
Labeling: Coupling a marker to a bio molecule.
Markers are organic dyes or naoparticles (beads) that are
chemically (covalently) bound to a bio molecule. Pure bio
molecules are hard to detect by optical methods, but
labeled molecules can be detected with customary
Mask: Filter used during synthesis of a
GeneChip array that exposed discreet areas of a wafer to
Mismatch Probe (MM): A 25-mer oligonucleotide
designed to be complementary to a reference sequence
except for a single, homomeric (nucleotide mismatch that
contains the complementary base to the original) base
change at the 13th position. Mismatch probes serve as
specificity controls when compared to their corresponding
Perfect Match probes.
Normalization: Adjusting an average value of an
experimental array equal to that of the baseline array so
that the arrays can be compared.
Photolithography: The process used to
manufacture probe arrays in conjunction with
combinatorial chemistry through a series of cycles. Using
light, photolabile protection groups are removed from
linkers bound to the glass substrate (wafer) to enable
nucleotide phosphoramidite addition in specific
deprotected locations. Each light exposure and subsequent
phosphoramidite addition is equal to one cycle.
Typically, probe arrays are synthesized in about 80
Probe: A 25-mer oligonucleotide designed to be
complementary to a reference sequence. The probe sequence
that is complementary to the sequence to be
Probe Array Tiling: The spatial organization of
probe array features into probe paires and sets.
Probe Cell: A single square-shaped feature on
an array containing probes with a unique sequence. A
probe cell ranges in size from 18 to 50 microns per side
depending on the array type.
Probe Pair: Two features within a probe set.
Each probe of a probe pair is designed to differ only at
the nucleotide base interrogation position. The probe
pair is designed to detect a Perfect Match (PM) and a
Probe Set: A collection of probe pairs which
interrogates the same sequence, or set of sequences. A
probe set typically contains between 11 to 20 probe
SAPE: Streptavidin-phycoerythin dye used to
bind the biotin. In the GeneChip Expression Assay, the
biotinylated nucleotides are incorporated into the cRNA
during the in vitro transcription (IVT) reaction.
Scaling: Adjusting the average intensity or
signal value of every array to a common value (target
intensity) in order to make the arrays comparable.
Spike Controls: Controls that are added to the
sample before cDNA synthesis.
Target: The sample applied as labeled
(biotinylated), fragmented cRNA to a GeneChip probe array
Wafer: the glass substrate onto which probes
are synthesized during the manufacturing of probe