Glossary of Terms

2SD value. two standard deviation of the spot ratio distribution, 95% of the spots lie within this ratio for normally distributed data.

Abundance. The relative volume among all spots representing a particular protein in a BVA data set. The weakest spot is taken as 1.00 and the others are displayed relative to this.

ANOVA. ANalysis Of VAriance is a family of methods used to perform statistical analysis on experimental results.

ANOVA 1 way. One-way ANOVA test (assigns statistical significance to differences in standardized protein abundance between experimental groups).

ANOVA 2 way. Two-way ANOVA test, (assigns statistical significance to both separate and mutual effects of two experimental conditions on standardized protein abundance)

Appearance Table. Region within a BVA workspace where users can track all information on a particular spot from all the gel images.

Area of Interest. User defined region outside of which any detected protein spots are excluded from analysis.

Artefact Rejection. Filtering out of non proteinaceous signal

Auto Level. The stage in the in the algorithm in which spot are matched.

Bandwidth. The transmission capacity of a communications channel, usually expressed in bits or bytes per second.

Batch Processor. DeCyder module capable of performing fully automated co-detection, quantification and matching of multiple spot maps.

BVA. Biological Variance Analysis DeCyder module

BVA Batch list. The spreadsheet in the batch processor depicting which spot maps are to be matched.

Centre of Volume (CoV). Central tendency of the spot volumes on a spot map.

Co-detection. Simultaneous detection of labelled protein spots from two in-gel images

Comment. User defined text string that can be linked to specific protein or spot map.

DeCyderXML. XML format used to transfer data between the various DeCyder modules

DIA. Differential In-gel Analysis DeCyder module capable of the fully automated co-detection, quantification and matching of an in-gel image pair.

DIA Batch List. Spreadsheet in the batch processor depicting which image pairs are to be detected and quantified.

Exclude Filter. Filter used to remove non proteinaceous artefacts such as dust.

Groups. The collection of spot maps relating to image pairs whose sample images have undergone exactly the same experimental conditions (e.g. 3 spot maps of samples from disease patients treated with drug A at a specific dose is a single group).

Histogram Selections. User adjustable parameters that alter the appearance of the histogram in the DIA module.

Independent Data. Data sets which have no effect on one another.

Master Image. Spot map to which all others are matched to.

Match confirmation. Manual verification by the user of matched spots

Matching. Automatic linking of spots on selected images to the corresponding spot on the master image.

Match table. Area within a BVA workspace where spot match data is displayed

Normalization. Process that allows the direct comparison of spot data derived from different gels.

Null hypothesis. Posits that there is no difference between variables being tested. To reject it is to infer "statistical significance".

Label. Indicates the fluor used to label the protein

Landmarking. Process of manually matching spots to the master image before automated matching to aid the matching algorithm.

Maximum Peak height. Pixel value at the X,Y position of the spot. This is the actual detected peak height value compensated for background level.

Maximum Volume. The highest volume from two co-detected spots.

Paired Data. Data sets with an association between data point in every group.

Pick Filter. Function that enables the user to designate spots for picking based on user defined parametric values.

Primary image. Refers to the left-hand gel image present in the image view of the DIA module and the spot map table, protein table and appearance table modes of the BVA module. In the Match Table mode of BVA module, the primary image is the right hand image as the left-hand image is taken by the master gel.

Protein ID. Unique protein identifier that can be used to search.

Protein Table. Area within a BVA workspace where all the statistical data from the analytical gels is located

Protein Statistics. Function in the BVA module that applies statistical tools to the protein data (providing that an experimental design with an internal standard was used).

Repeated Measures. ANOVA Statistical ANOVA test applied to paired data.

Scatter Parameter. The spot data type used to display the spot ratios in the histogram. This is shown in the right y-axis on the histogram and can be maximum slope, volume, peak height or area.

Secondary image. Refers to the right hand gel image present in the image view in the DIA module and the spot map table, protein table and appearance table mode of the BVA module.

Slope. Maximum gradient associated with the 3 dimensional attributes of a spot map pair.

Spot Controls. Allows user to control, assign or input data to the workspace or individual protein spots.

Spot Map Table. Area within a BVA workspace where all the spot map images and their associated assignments are located.

Spot Number. Unique identifier for a spot in DIA or a spot set in BVA.

Standard Image. Image relating to the internal standard from each gel.

Standardization. Process of quantifying spot map data in relation to the corresponding standard spot map data

Standardized Abundance. Abundance relative to the standard image displayed as a ratio.

Student T-test. Statistical test that assesses differences between two populations.

Threshold Mode. Value above or below which spots are classed as being differentially expressed.

TIFF Image. Flexible image format used to exchange files between platforms and software applications.

Volume. Sum of the detected pixel values above background within a spot boundary.

Volume Ratio. Refers to the ratio of the normalized volumes of a pair of spots from a spot map pair. A value of 2.0 represents a two-fold increase while -2.0 represents a two-fold decrease, whilst a value of 1.00 represents an unchanged spot.

Workspace. Environment where all the experimental data is stored.

XML (Extended Markup Language). Structured universal tagged language.

XML Toolbox. Shell, housing modules used for the extraction of data from DeCyder XML files in the form of tab separated text or web tables.