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Centre for Gene Regulation & Expression
School of Life Sciences
University of Dundee
DD1 5EH Dundee
Scotland, United Kingdom
Angus' PA Carol Urquhart:
c.a.urquhart@dundee.ac.uk
College of Life Sciences, University of Dundee



Who we are


Professor Angus I. Lamond's Laboratory is part of the Centre for Gene Regulation & Expression,

in the School of Life Sciences University of Dundee


News


September 8th 2017

A new manuscript from the Lamond group, published in Nucleic Acids Research (Brenes et al., 2017), reviews the creation and functionality of the Encyclopedia of Proteome Dynamics (EPD), (https://peptracker.com/epd/).

The EPD is a searchable, open access online database, designed to provide a convenient, interactive interface for exploration of proteomics and polyomics data. The EPD was first introduced in 2013. Based on user feedback and to meet the challenges of growing data volumes and complexity, a major redesign of the EPD was undertaken to provide improved scalability and additional interactive features.

This new version of the EPD, which was first released in March 2015, makes use of scalable noSQL (not only Structured Query Language) solutions combined with a client side JS (Java Script) library, used to visualise and analyse data interactively. The EPD includes data from many different types of proteomics experiments, performed using human cells and model organisms. The EPD currently has >100 different interactive visualizations, ranging from volcano plots to parallel coordinate plots. The type of visualization is selected to be the most appropriate for the class of information provided by each respective dataset. During the past year, the EPD has had a median of >18,450 hits and 698 unique users per day.

The EPD is part of the PepTracker software suite, which includes also tools designed for convenient laboratory data management, metadata tracking and data analysis. The new manuscript in NAR describes the functionality provided by the EPD, with examples of each type of plot and their respective interactive features.

August 18th 2017


In addition to the below mentioned HipSci paper, the Lamond lab has had several collaborative publications released this summer. These include Comparative genetic, proteomic and phosphoproteomic analysis of C. elegans embryos with a focus on ham-1/STOX and pig-1/MELK in dopaminergic neuron development., The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription., Multi-omics Analyses of Starvation Responses Reveal a Central Role for Lipoprotein Metabolism in Acute Starvation Survival in C. elegans. and Brd4-Brd2 isoform switching coordinates pluripotent exit and Smad2-dependent lineage specification


PepTracker
PepTracker provides management and mining capabilities for data generated during mass spectrometry studies.
Data Shop
Visualisation and statistical analysis tool for quantitative datasets
Proteomics Support
The Proteomics Support team have created a website that provides useful resources for proteomics studies.
Encyclopedia of Proteome Dynamics
A collection of multi-dimensional proteome properties from large-scale mass spectrometry experiments
Cell Biologist's Guide
The Cell Biologist's Guide to Proteomics provides information about mass spectrometry and experimentation.