Getting Started

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Home Page

Each component in the Home page corresponds to the specific tasks. You can initiate each step by clicking on the relevant steps. You cannot directly navigate to some steps without going through the previous steps. In any instance, the steps you can perform will be shown in a dark color mode. The steps you cannot yet perform will appear in a lighter color.

Tour around GeNet

• Click on the “START TOUR” to get simple tips and instructions.
• Click on the bell icon at the bottom right corner of the page to mute/ unmute the tour.

Upload Files

• If you want to upload a new data set, you can do so by clicking on the “Choose File”. You can choose the data set from your system. The file should be in comma-separated value (.csv) format.
• If you just want to get hands-on experience with GeNet, you can just select a sample file by clicking on the “SELECT SAMPLE FILE” button.
• You can view the sample file by downloading it through the “DOWNLOAD SAMPLE FILE” button.
• After choosing your data set (.csv file) click on the “SUBMIT” button to continue.
• Click on the “info” icon to get more information on the input format of the data file.

Click here for more info on the input format

Pre-processing

• Choose your data set by clicking on the drop-down menu in the “Available Files” tab. The drop-down will show you the list of already uploaded data sets.
• Choose the corresponding annotation table by clicking on the drop-down menu of the “Annotation Table” tab.
• Select any Probe Selection method from the drop-down menu of the Probe Selection method. You can choose 'other' option and upload a custom annotation table also.
• If you want to proceed without mapping to gene symbols, click “SKIP MAPPING” button.
• If you want to map the probe_IDs to gene symbols click “SUBMIT”.
• If you want to get a quick glance at your data set, you can do so by clicking on the “View” button.
• Interquartile Range: You can choose the interquartile range of all the values corresponding to a particular gene symbol for each sample.

Click here for more info on annotation tables and probe selection methods

Viewing the Data Set

• You can download the selected data set by clicking on the download icon.
• GeNet by default shows you 10 entries by page, you can change this number by changing the values at the “Show” icon.
• Use the search bar to type in any value you want to search in the data set.

Data Set with Probe_IDs mapped to Gene Symbols

• This page shows your data set after the probe_IDs have been mapped into the gene symbols.
• Click “CONTINUE” to proceed.

Normalization and Imputation

• Select the normalization method by clicking on the drop-down menu in the scaling tab.
• Select how you wish to handle the missing values by choosing a method from the Imputation tab.
• If you are all set, click on “PRE_PROCESS”.

Data Set after Pre-processing

• This page shows how your data set looks after scaling and imputation methods have been performed.
• Click “CONTINUE” to proceed.

Setting the Range of Fold Change and P-Values

• You can select the most impactful genes by setting up boundary values for Fold Change and P-Value.
• After you select the appropriate values click on “CALCULATE” to filter out relevant genes.

Feature Reduction

• Input the number of genes that you like to proceed with. The tip is to get the number of genes corresponding to the knee point of the graph.
• After this step, your pre-processed file is automatically saved on your profile.

Feature Selection

• Pick the pre-processed file you want to proceed with.
• Select methods(minimum three methods) out of the options to further narrow down the number of genes.
• Change the number of genes you want to apply these methods by dragging the pointer along the line.
• Click “CONTINUE” to proceed.

Results

• Click on each part of the Venn diagram to get the details of the genes found by each method.
• Click on each gene symbol to get more details on the functionality of the gene.
• Click "MORE DETAILS" to view more details on the specific gene
• View the list of genes by choosing either the “GRID” option or the “LIST” option.
• Click “Analyze” to proceed.

Analysis

• If you are proceeding from the beginning, the pre-processed file is automatically added to the Selected File tab. Click on the “Change File” icon if you want to analyze results for a different file.
• Select one method to proceed with the analysis.

Analysis of Results by Correlation Values

• The first section of this page shows the variation of correlation coefficients with regard to the 3 feature selection methods.
• The second section shows the behavior of the genes selected by considering correlation values obtained for the genes selected by the method specified in the previous step.
• Click “CONTINUE” to proceed.

Selected features

• The infobox at the top of the page shows the number of genes selected by each method. Click on “more” to view their gene symbols.
• To compare your results with already available data, select the type of disease you want to check with.
• Click “VALIDATE” to proceed.

Validation

• This page shows the relationship of genes selected by GeNet and the genes validated by biological sources.
• Click on “Modeling” to proceed to modeling steps.

Modeling

• Choose the file you want to use for the modeling.
• Choose a classifier to do the modeling.
• Click on “SUBMIT”.
• It shows the accuracy of the model created.
• Click on “Let’s try” to try and predict the results of a new data set.

Prediction

• If you want to build a different model, click on “CUSTOMIZE MODEL”. There, you can repeat the same steps and build a new model.
• Choose the data set you want to predict the results for by selecting the file under “Choose File”.
• Turn on “Normalize” if you want to normalize the selected data set.
• Turn on “Annotation Table Mapping” and select the relevant annotation table if you want to map the probe_IDS to gene symbols.
• Click on submit to see the predicted results.

Prediction results

• This page shows the prediction results of each sample.
• Download the prediction results by clicking on the download icon.

Visualization

• Choose a data set from “Available Files”.
• Input the gene symbol you want to visualize.
• Click on “UPDATE” to visualize different plots.

CLUSTERING

• Choose a file you want to visualize gene regulatory network.
• You can visualize a specific cluster by choosing the particular cluster on the drop down menu of “Select Cluster”.
• You can also zoom in and out the cluster to get a better view.
• Click on “Change File” to visualize gene network patterns of a different file.