GAAS - Download

Downloadable packages

• GAAS.zip (966 KB): software application package containing all files necessary to run GAAS.
  

  Content:

  • GeneArrayAssembler.exe: the Gene Array Assembler Software program. It performs data pre-processing converting MS-Excel data file format in MS-Access file format with a built-in structure suitable for GAAS analyses.

  • GeneArrayAnalyzer.exe: the Gene Array Analyzer Software program. It performs: data processing and analysis, result visualization, and storage.

  • SysInfo.dll: utility dynamic link library. It is used by both GeneArrayAssembler and GeneArrayAnalyzer programs.

  • Gauss.txt: text ASCII file containing values of standardized Gaussian density function.

  • MasterDB.mdb: the GAAS system database. This relational MS-Access 2000 database stores specific input data formats, user settings, and values of data analysis, visualization, and storing variables.

 

• FilterData.zip (12118 KB) and MicroData.zip (3719 KB): testing data packages containing gene expression data from a three replica experiment using Genome Systems nylon filter arrays (Gene Discovery Arrays v1.2 - Genome Systems) and from a three replica experiments using cDNA microarrays spotted on glass slides, respectively. These packages also contain the corresponding label databases necessary to analyze the data.
  

  The datasets contained in the testing data packages derive from experiments performed on NB4 or U937 cells treated with Retinoic Acid or Vitamin D. These results derive form pilot experiments, performed with the aim of optimizing dosage and duration of treatments, and the biological significance of results has not been evaluated.
  
  

  Nylon filter array data (FilterData.zip):

  • LabelFilter.mdb: label database for GDAv1.2 Genome System nylon filter cDNA arrays spotted with 192 x 192 spots organized in 48 x 48 primary spot structures of 4 x 4 spots each and quantified with Gene Discovery Software (Genome Systems).
    
    

  • FilterControl1.xls: gene expression data from a nylon filter array hybridized with a control RNA (first experimental replica).

  • FilterControl2.xls: gene expression data from a nylon filter array hybridized with a control RNA (second experimental replica).

  • FilterControl3.xls: gene expression data from a nylon filter array hybridized with a control RNA (third experimental replica).

  • FilterTest1.xls: gene expression data from a nylon filter array hybridized with a test RNA (first experimental replica).

  • FilterTest2.xls: gene expression data from a nylon filter array hybridized with a test RNA (second experimental replica).

  • FilterTest3.xls: gene expression data from a nylon filter array hybridized with a test RNA (third experimental replica).

  • Filter.mdb: database containing gene expression data of a complete experiment with nylon filter arrays (three experimental replica of test vs. control condition).

  
  cDNA Microarray data (MicroData.zip):

  • PlateList.xls: list of 384-well plates containing the cDNA clones spotted on the microarrays used for the experiment. The list of the whole clone plate library, with the information of all clones contained, is in the label database (LabelMicro.mdb) associated with the experiment.

  • LabelMicro.mdb: label database for glass slide cDNA microarrays spotted with 32 x 144 spots from 384 well plates and quantified with ArrayVision v.5 software.

  • MicroControl1_L.xls: gene expression data from a microarray hybridized with a control RNA stained with Cy3 and a neutral RNA stained with Cy5 (first experimental replica). These data refer to the left half-side of the microarray slide with the first of the two spots of each clone spotted on the slide.

  • MicroControl1_R.xls: gene expression data from a microarray hybridized with a control RNA stained with Cy3 and a neutral RNA stained with Cy5 (first experimental replica). These data refer to the right half-side of the microarray slide with the second of the two spots of each clone spotted on the slide.

  • MicroControl2_L.xls: gene expression data from a microarray hybridized with a control RNA stained with Cy3 and a neutral RNA stained with Cy5 (second experimental replica). These data refer to the left half-side of the microarray slide with the first of the two spots of each clone spotted on the slide.

  • MicroControl2_R.xls: gene expression data from a microarray hybridized with a control RNA stained with Cy3 and a neutral RNA stained with Cy5 (second experimental replica). These data refer to the right half-side of the microarray slide with the second of the two spots of each clone spotted on the slide.

  • MicroControl3_L.xls: gene expression data from a microarray hybridized with a control RNA stained with Cy3 and a neutral RNA stained with Cy5 (third experimental replica). These data refer to the left half-side of the microarray slide with the first of the two spots of each clone spotted on the slide.

  • MicroControl3_R.xls: gene expression data from a microarray hybridized with a control RNA stained with Cy3 and a neutral RNA stained with Cy5 (third experimental replica). These data refer to the right half-side of the microarray slide with the second of the two spots of each clone spotted on the slide.

  • MicroTest1_L.xls: gene expression data from a microarray hybridized with a test RNA stained with Cy3 and a neutral RNA stained with Cy5 (first experimental replica). These data refer to the left half-side of the microarray slide with the first of the two spots of each clone spotted on the slide.

  • MicroTest1_R.xls: gene expression data from a microarray hybridized with a test RNA stained with Cy3 and a neutral RNA stained with Cy5 (first experimental replica). These data refer to the right half-side of the microarray slide with the second of the two spots of each clone spotted on the slide.

  • MicroTest2_L.xls: gene expression data from a microarray hybridized with a test RNA stained with Cy3 and a neutral RNA stained with Cy5 (second experimental replica). These data refer to the left half-side of the microarray slide with the first of the two spots of each clone spotted on the slide.

  • MicroTest2_R.xls: gene expression data from a microarray hybridized with a test RNA stained with Cy3 and a neutral RNA stained with Cy5 (second experimental replica). These data refer to the right half-side of the microarray slide with the second of the two spots of each clone spotted on the slide.

  • MicroTest3_L.xls: gene expression data from a microarray hybridized with a test RNA stained with Cy3 and a neutral RNA stained with Cy5 (third experimental replica). These data refer to the left half-side of the microarray slide with the first of the two spots of each clone spotted on the slide.

  • MicroTest3_R.xls: gene expression data from a microarray hybridized with a test RNA stained with Cy3 and a neutral RNA stained with Cy5 (third experimental replica). These data refer to the right half-side of the microarray slide with the second of the two spots of each clone spotted on the slide.

  • Micro_ARM-SE.mdb: database containing gene expression data of a complete experiment with microarrays hybridized with a control and a test RNA stained with Cy3 and a neutral RNA stained with Cy5 (three experimental replica of test vs. control condition). Intensity of each spot was quantified with an Artifact-Removed Density (ARM) value representing the average of the spot pixel intensities remaining after first removing those spot pixel intensities exceeding four median absolute deviations above the median intensity of all spot pixels.

 

Required software utilities

The GAAS management framework uses Microsoft Data Access Object (DAO) technology for managing database communications. This technology requires the Microsoft Data Access Component utility MDAC 2.6 installed on the user PC.

This utility can be installed from the MS-Office installation disk. Conversely, MDAC 2.6 utility can be downloaded from the Microsoft web site choosing the appropriate language version among the Install Option selections. The language version must correspond to that of the MS-Office installed on the user PC or, if MS-Office is not installed, to that of the user PC MS-Windows operating system.
After saving to disk the downloaded MDAC 2.6 file, double clicking on it to unpack and run the installation program.