NEW   An open-access, high-quality whole genome sequenced dataset of post-mortem tissue samples from Target ALS

  • The dataset currently includes 132 samples and will be continuously updated in real time going forward.
  • The samples are being RNA sequenced and are clinically annotated, with zero embargo on use. Check back soon for updates.

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MetroNome

Visual data exploration for a genomic data warehouse

MetroNome allows researchers to explore data visually with the goal to correlate genotypes with phenotypes. The system accepts genomic sequence and clinical data from any research project.

Participating researchers can explore their data in an interactive visual interface and organize data along many dimensions.

 
 

How to get started

If you want to follow along step by step (and you have a larger monitor), click here to open MetroNome in a new window.

MetroNome is designed to help you find samples with specific variants, or find variants that appear in samples from subjects that fit specific criteria.
Currently all data is aligned to build GRCh37.

1. Accept Terms

Please read and accept our terms before continuing.

2. Select a Dataset

Type a few letters to reduce the options, or scroll down the list.

3. Optional: Select Subject/Sample Criteria

Here you can narrow your search by specifying subject- or sample-specific attributes. Again, type or scroll down the list. You can combine mutliple criteria by clicking the "Add Rule" button.

If you don't want to narrow your search:

4. Select Genomic Criteria

Pick Genomic Criteria

You can search for variants in specific genes, genomic regions, or samples with specific variants. Again, you can combine as many rules as you wish. Just click the "Add Rule" button.

Gene Attribute Explorer

As an alternative, you can start with a matrix of the most frequently mutated genes and samples in the chosen dataset. Each dot represents a summary of a gene/sample combination — move your pointer over a dot to see details.

Make a selection by clicking and dragging across the matrix.

5. Launch Your Query!

Scroll down to the bottom and click the "Run Query" button.

 

Search Results

Overview: Patient Metadata and Gene Summary

This view shows the result set in a large number of dimensions, along with a summary of variants per gene. The diagrams are all interactively linked, so that selections you make in one place update all contents.

Numerical Dimensions

This parallel coordinates plot represents each subject as one line. That line traverses the dimensions at the points corresponding to each value.

You can click and drag along any dimension to constrain the selection of samples to the red range — here above 65 years at diagnosis — now only 13 samples are selected. The new selection will be reflected in the other components on the page. Click outside the range on that axis to release the selection.

Donut Gauges

Keep an eye on them: when you make a selection in any of the diagrams, these counters update to show how many samples, variants, and genes are now actively selected.

Categorical Dimensions

This parallel sets plot illustrates percentages of subjects in various categories, and how they combine to form subgroups.

Hover over any band to see specific information.

You can click on the grey bar for any category to constrain the selection of samples to that category. Click the category again to release the selection.

Gene Summary

Shows how many variants are present in each gene. Click on any row in this table to open a gene diagram.

Gene Diagram

Shows the location and frequency for each variant in this gene, mapped to genomic coordinates (bottom). Exons are drawn as grey blocks. At the top you see the protein transcript with functional domains. The height of each "lollipop" indicates the number of samples with this variant.

Click on any circle to open a pop-up with detailed information. This action also updates the sample table below, showing only the samples with this particular variant.

Sample Table

At the bottom of the page, this table updates dynamically whenever the selection above is changed. Click "Download data: CSV" (top right) to receive its contents as a comma-separated file.

Variants Table

While a gene diagram is displayed, this table shows the variants present in this gene, for the result set or active selection. Click "Download data: CSV" (top right) to receive its contents as a comma-separated file.

Tutorials

This is where we plan to have a few specific, task-oriented video tutorials - we will keep you posted when they become available.