| Category | Tool | Icon | Function | How to Access | Help Page |
|---|---|---|---|---|---|
Quality Assessment |
Assess Array Quality for an Array List | Calculate a "Q-score" (quality score) for a set of experiments based on a genelist | from "Lists" -> "All programs" -> "Tools" | YES | |
| Compare replicate arrays | Compare the measured data between two replicate experiments | from "Search" -> "Advanced Results Search"-> "Display Data" -> "View Array Details" icon -> "Compare measurements with an experiment from the same Print" | YES | ||
| Get Ratios on Array | Investigate spatial location or plate bias on an array | from "Search" -> "Advanced Results Search" -> "Display Data" -> "View Array Details" icon -> "Ratios on Array" | |||
| Data Plotter |  |
Plot data from a selected array (scatter plot or histogram). Can select any two parameters to plot. | from "Search" -> "Advanced Results Search" (or "Basic Search" -> "Display Data") -> "Display Data" -> "Plot Array Data" icon or "View Array Details" icon -> "Plot Data" or "Signal Intensities" | ||
| Plot Data Distribution | Make a histogram of log2(RAT2N) for one experiment | from "Search" -> "Advanced Results Search" -> "Display Data" -> "View Array Details" icon or "Edit" icon -> "(View) Data Distribution" | |||
Clustering and other Data Analysis |
Cluster Data |  |
Filter and organize data using hierarchical clustering or self organizing maps | from "Search" -> "Advanced Results Search" ->"Data Retrieval and Analysis" -> select experiments -> "Data Retrieval and Analysis" | YES |
| Reenter Data Clustering Pipeline |  |
Reenter the data clustering pipeline starting with a repository file | from "My Repository" -> click on icon | YES | |
| Synthetic Genes |  |
Add annotations or combine expression data from a group of reporters (e.g. for clustering) | from "My Data" -> "My Repository" -> click on icon (input is a .pcl file) | YES | |
| KNNimpute |  |
Impute values for missing data | from "My Data" -> "My Repository" -> click on icon | ||
| GeneXplorer |  |
Interactively view clustered data | from "My Data" -> "My Repository" -> click on icon | ||
| TreeView | Graphically browse results of clustering and other analyses from Cluster | Download software from Eisen Lab (requires .cdt and .gpr files) |
YES(intrinsic) | ||
| Singular Value Decomposition (SVD) |  |
Identify patterns (real experimental results or artifacts) in a data set | from "My Data" -> "My Repository" -> click on icon | YES | |
| Merge PCL files | Merge PCL files (e.g. for co-clustering data or for adding clinical values to gene expression data) | from "List all Programs" -> "Tools" | YES | ||
Data Viewing / Visualization |
GeneXplorer | |
Interactively view clustered data | from "My Data" -> "My Repository" -> click on icon | |
| Ontology Term Finder (GO::TermFinder) | Identify Gene Ontology terms for a group of genes that annotate that group in a statistically significant manner. This can help one discover what biological processes, cellular localizations or molecular functions are shared by members of groups of genes. | from Main Tool Menu Bar or from "Lists" -> "All programs" -> "Tools" | YES | ||
| Data Plotter | |
Plot data from a selected array (scatter plot or histogram). Can select any two parameters to plot. | from "Search" -> "Advanced Results Search" (or "Basic Search" -> "Display Data") -> "Display Data" -> "Plot Array Data" icon or "View Array Details" icon -> "Plot Data" or "Signal Intensities" | ||
| Plot Data Distribution | Make a histogram of log2(RAT2N) for one experiment | from "Search" -> "Advanced Results Search" -> "Display Data" -> "View Array Details" icon or "Edit" icon -> "(View) Data Distribution" | |||
| TreeView | Graphically browse results of clustering and other analyses from Cluster | Download software from Eisen Lab (requires .cdt and .gpr files) |
YES(intrinsic) | ||
| View Array Images and Grids |  |
Select various criteria for filtering; then display the array image with selected spots boxed. Can also click on spots to get spot data | from "Search" -> "Advanced Results Search" -> "Display Data" -> click on icon | ||
| Get Spot Data (= View Array Images) |
 |
Obtain biological information and data from hybridization for a particular spot in one experiment. Can use to change flagging of spot. Similar to "View Array Images and Grids", but can select only one spot | from "Search" -> "Advanced Results Search" -> "Display Data" -> ("View and Sort Array Data" icon -> "Display Data" -> "Zoom") or from Grids icon | ||
| View Array Details |  |
Display Metadata about one experiment | from "Search" ->"Advanced Results Search" -> "Display Data" -> click on icon | ||
| View and Sort Array Data |  |
Sort data from one experiment by a selection of criteria. After sorting, can view individual spots in array context. | from "Search" -> "Advanced Results Search" -> "Display Data" -> click on icon | ||
Data Transformation |
Synthetic Genes | |
Add annotations or combine expression data from a group of reporters (e.g. for clustering) | from "My Data" -> "My Repository" -> click on icon (input is a .pcl file) | YES |
| KNNimpute | |
Impute values for missing data | from "My Data" -> "My Repository" -> click on icon | Renormalize an Experiment or all Experiments using a Result Set List | Renormalize one or several results sets (arrays) with a variety of algorithms. | from "Search" -> "Advanced Results Search" -> "Display Data" -> "Edit" icon -> "Select normalization options" or ("Lists" -> "All Programs" -> "Edit/Delete Data" -> "Batch Renormalize Data") | YES |
| Renormalize Experiments using a Genelist | Calculate a normalization constant based on a restricted list of genes. Does not actually alter data | from "Lists" -> "All programs" -> "Tools" | YES | ||
Data Organization |
Create an Experiment Set | Compile selected experiments into a set that can be easily shared or published. | from "Search" -> "Advanced Search" -> "Data Retrieval and Analysis" -> "Create Experiment Set" | YES | |
| Create a Result Set | Compile selected arrays into a set. The results from one set of arrays can be processed into different result sets. | from "Search" -> "Advanced Search" -> "Data Retrieval and Analysis" -> "Create Result Set List" | YES | ||
| Convert an Arraylist to an Experiment Set | Convert an Array list to an Experiment set | from Main Tool Menu Bar or from "Lists" -> "All programs" -> "Tools" | YES | ||
| Delete Experiment |  |
Remove experiment from the database | from "Search" -> "Advanced Results Search" -> "Display Data" ->click on icon | YES | |
| Edit Experimental Data |  |
Edit MetaData about experiments | from "Search" -> "Advanced Results Search" ->"Display Data"->click on icon | ||
| Associate Patient Information | Associate clinical(patient and sample) information with an experiment | from "Search" -> "Advanced Results Search" -> "Display Data" ->"Edit" icon -> "Associate Patient Information" or "Associate Clinical Information" | |||
| Enter Protocol | Enter a new protocol and its details | from "My Data" -> "Add Protocol" | YES | ||
| Enter Experiment Annotation by Batch | Add Experiment annotation to multiple experiments at once via a batch file | from "My Data"->"Procedural Information" | YES | ||
| View Array Details | |
Display Metadata about one experiment | from "Search" ->"Advanced Results Search" -> "Display Data" -> click on icon | ||
| Merge PCL files | Merge PCL files (e.g. for co-clustering data or for adding clinical values to gene expression data) | from "List all Programs" -> "Tools" | YES | ||
Entering Microarray |
Enter an Experiment | Upload (from loader account)results from an experiment. Can also be uploaded in batch | from "My Data" -> "Enter my Data" | YES | |
| Create a Result Set | Compile selected arrays into a set. The results from one set of arrays can be processed into different result sets. | from "Search" -> "Advanced Search" -> "Data Retrieval and Analysis" -> "Create Result Set List" | YES | ||
| Replace Proxy Image | Upload (from loader account) a proxy image for a particular experiment | from "Lists" -> "All Programs" -> "Enter Data" -> "Replace Proxy Image" | YES | ||
| Enter Protocol | Enter a new protocol and its details | from "My Data" -> "Add Protocol" | YES | ||
| Associate Patient Information | Associate clinical(patient and sample) information with an experiment | from "Search" -> "Advanced Results Search" -> "Display Data" ->"Edit" icon -> "Associate Patient Information" or "Associate Clinical Information" | |||
| Enter Experiment Annotation by Batch | Add Experiment annotation to multiple experiments at once via a batch file | from "My Data"->"Procedural Information" | YES | ||
| Validate a list of Plate Samples | Format a list of plate samples in proper format for print entry into the database. | from "Lists" -> "All programs" -> "Tools" | YES | ||
Data Download |
Download Raw Data |  |
Obtain all raw data from one experiment | from "Search" -> "Advanced Results Search" -> "Display Data" -> click on icon | |
| Generate Chromosome-Aligned Data for Caryoscope |  |
Generate chromosome-aligned representation of data for use with Caryoscope | from "Search" -> "Advanced Results Search" -> "Display Data" ->click on icon | Caryoscope home | |
| Download Raw Data for a Result Set List | Retrieve raw data for a set of experiments(up to 50). Results go to an archive and are retrieved in compressed form. | from "Lists" -> "All programs" -> "Tools" | |||
| Get Gal File | Obtain a gal file for a particular print. | from "Search" -> "Advanced Results Search" -> "Display Data" -> "View Array Details" icon -> "GAL file" | |||
| Get Spot History | Obtain a compilation of the expression level of the clone specified in all microarray experiments to which you have access | from "Search" -> "Advanced Results Search" -> "Display Data" -> "View and Sort Array Data" icon -> "Display Data" -> "Spot History" or starting from Gene Search -> search for name-> "View Expression History" | YES | ||
| Gene Search | Find data on a particular entity by gene name. View data on the entity for all experiments to which you have access. Can link to expression history. | from "Search" -> "Gene Search" | YES | ||
| Retrieve all public data for an organism | Retrieve all public data for an organism | from "Lists"->"All programs"->"Search"->"Get Public Data By Organism" | YES | ||
| Retrieve Experiment Meta Data for an Arraylist | Retrieve and print to a downloadable file some Meta Data for each experiment in an Arraylist | from "Lists"->"All programs" -> "Tools" | |||
| Genomic Alignment | Enter cloneID, gene name, accession number, gene symbol or cytoband position and find the genomic alignment as given by goldenPath at UCSC | from "Lists"->"All programs" -> "Tools" | YES | ||
Data Access |
Edit Experimental Data | |
Edit MetaData about experiments (including Access privileges) | from "Search" -> "Advanced Results Search" ->"Display Data"->click on icon | |
| Add Data Access by Batch | Give user or group access to a batch of experiments via an array list | from list of all programs | |||
| Change Password | Change your PUMAdb/Loader Password | from Main Tool Menu Bar or from "Lists" -> "All programs" -> "Tools" |