snowball_bio_hairball

Web-Based Visualization and Analysis Tool for
High-Dimensional Biological Data

Nicolas Fernandez
Ma'ayan Lab
Icahn School of Medicine at Mount Sinai
BD2K-LINCS Data Coordination and Integration Center
Data Blitz 2016
bit.ly/clustergram-blitz

Biological Data is Difficult to Visualize

Biological data can be very high dimensional
 
This can lead to hairballs



bit.ly/clustergram-blitz

snowball_bio_hairball
adapted from @drob and kittentoob.com

Heatmap/Clustergram Visualizations

Heatmaps enable direct visualization of high-dimensional data
 
It is currently difficult to share interactive heatmaps


sky
adapted from www2.warwick.ac.uk

Clustergrammer Web App

Web built Clustergrammer to address these problems

Features

  • Easily generate interactive and shareable heatmaps
  • User friendly data exploration
  • Free and open source

Lung Cancer Post-Translational Modification Signaling

Collaborators at Cell Signaling Technology measured phosphorylation levels in 42 lung cancer cell lines

We are using Clustergrammer to analyze their data

Lung Cancer Gene Expression

Gene expression data was also obtained from the Cancer Cell Line Encyclopedia

Cell lines cluster similarly based on phosphorylation and expression

Conclusions

Clustergrammer can visualize a wide variety of data

Provides visualizations for several Ma'ayan lab apps

Also available as an IPython/Jupyter Notebook Widget

Acknowledgments

Avi Ma'ayan
Greg Gundersen
Michael McDermott
Matthew Jones
Andrew Rouillard
Qiaonan Duan
Zichen Wang
Alexander Lachmann
Maxim Kuleshov
Neil Clark
Caroline Monteiro
Simon Koplev
Anders Dohlman
Troy Goff
Edward He