GenePlus™
is a software tool for analyzing gene expression data, a paradigm technology
shift from cluster analysis. It facilitates an objective analysis of complex
genomic expression data and enables researchers to test specific hypotheses.
Version 1.2 is a major upgrade from version 1.1, and includes many significant
improvements over the previous version. Here are major highlights:
| Application |
| Time-Course (single series & two series) |
| Dose-Response |
| Multiple Group Comparison (two- & multi-groups) |
| Clinical Studies with Multiple Covariates |
| Repeated Measurements (Replicates) |
| Longitudinal Studies with Time-Varying
Covariates |
| Analysis of Two Chips |
| Analysis of Multiple Pairs of Chips |
| Technologies |
| Oligonucleotide Data |
Differences of PM and MM obtained by GeneChip Techology |
| Ratio data with common reference in Microarray
Chip technology |
| Intensity data obtained by Microarray Chip technology |
| cDNA Array Data |
Assembled array data from multiple cDNA array data obtained by microarray
technology |
| Array data obtained from user-chosen image analysis
programs |
| Normalization of array data between two channels |
| Statistical
Techniques |
| Estimating Equations |
| Bootstrap |
| Permutations |
| Use of Standard Statistics (Signals,
Standard Deviations, Z-scores and P-values) |
| Use of NFD(Number of False Discoveries) to measure the
significance of discovered gene list |
| Use of genomewide rankscores |
| Efficiency and Robustness |
| Heterogeneity
Adjustment |
| Adjustment by correcting means and standard deviations |
| Parametric Adjustment |
Additive adjustment |
| Multiplicative adjustment |
| Both additive and multiplicative adjustment |
| Nonparmatric adjustments |
Additive adjustment |
| Multiplicative adjustment |
| Both additive and multiplicative adjustment |
| Normalization of two chips |
| Normalization of multiple chips |
| Missing
Data |
| User-defined missing data |
| Permutations for missing data |
| Finding and replacing missing values |
| Incorporating missing values in the
analysis |
| Database
Management and I/O |
| Management of users |
| Management of data and results |
| Representation in Spreadsheets |
| User-Friendly I/O |
| Versatile interactions with Excel |
| No limitations in number of genes
or number of samples |
| Import data stored in multiple files |
| Connections
with Public Databases |
| Established connections with |
Locuslink |
| OMIN |
| PubMed |
| User-specified connections
with |
Any public databases |
| Any private databases |
| Report
Generator |
| Generating summary reports |
| Generating reports with discovered
information from web |
| Miscellaneous
Tools |
| Transformation |
Logarithm with a specified base |
| Exponentiation with a specified base |
| Box-Cox transformations |
| Many other functions |
| Sorting Capacity |
Sort rows or columns |
| Sort and save order |
| Sort by an established order |
| Editing Function |
Finding |
| Copying |
| Pasting |
| Interactions with Excel |
Import from Excel & ASCII Text |
| Export to Excel & ASCII Text |
| Cut and paste between GenePlus and Excel &
ASCII Text |
| Manipulating variables |
Filtering data |
| Re-coding data |
| Creating dummy variables |
| Creating cross-products |
| Selecting resulting data
of interest |
Selecting a subset of data for further analysis |
| Identifying candidate gene lists |
| Comparing candidate gene lists |
X-Y plots