Below are a variety of datasets that can be used to explore Graphia’s functionality. To learn more about creating your own supported file visit the Wiki
Mouse tissue expression atlas – Comma Seperated Value (.csv)
This is the data set that started it all off. It is a microarray analysis of gene expression across a range of different mouse tissues. It consists of over 36,000 measurements taken across 122 samples (61 tissue and cells types) of embryonic and adult mouse samples. It represents one of the first ‘big’ gene expression data sets in biology and was originally published by Su et al. back in 1994 (PNAS, 101: 6062); the study has now been cited nearly 3,000 times. It was the frustrations of trying to analyse these data using conventional bioinformatics approaches that drove us to develop the network analysis approach incorporated into Graphia
Nutritional Food Data – Comma Seperated Value (.csv)
The figures included in tables on the side of food packaging contain only a fraction of the available nutrients that are commonly tested for. It is not uncommon for laboratories to test for over a 100 different nutrients in a given food product. This is a rich source of information, but when tested across many foodstuffs the amount of data becomes significant challenge to understand. Here we provide nutritional data from a wide variety of foods in a format ready for network analysis. The data comes from the UK Government’s Food Standards Agency website. After some data cleaning we have taken nutritional values for 948 foods and where available the results of 104 nutritional value scores. An analysis ready copy of these data are provided here.
2008-2009 NASDAQ Shares – Comma Seperated Value (.csv)
Share prices rise and fall based on the performance of the company, but their value is also subject to the vagaries of the market and external forces. 2008 witnessed the now famous crash of the stock market. Sept 15th was named ‘Black Monday’ after Lehman Brothers declared bankruptcy and the Dow dropped over 500 points. Following this, market uncertainty increased and bottomed on March 5th 2009.
This data set from the NASDAQ Stock Market covers the period from the beginning of 2008 until then end of 2009. It lists the end of day prices (505 in total) of 2,615 companies and therefore covers the peak period of this bear market. Visualisation of correlation networks these data provide a unique interface to explore the events of a catastrophic market meltdown.
Finance256 – BioLayout File (.layout)
This is an example graph file provided by the University of Florida sparse matrix collection. This collection is used to test the layout capabilities of a variety of graph layout algorithms. The collection is designed to be particularly difficult for a stable optimum layout to be found. This graph is particularly large, however Graphia effortlessly provides an appealing layout
London Tube map – Simple Pairwise Two Column Text File (.txt)
This is an example of a simple Pairwise text file using two columns to represent connected tube stations in the London underground. The London tube map was originally the brainchild of electrical draughtsman, Harry Beck, who produced his imaginative and beautifully simple design back in 1933. It is now one of the most famous network diagrams in the world. Here we present the data used for it a connectivity map of stations and lines, as a simple node-edge relationship file for visualisation within Graphia.
Mouse Gene Clusters – Weighted Pairwise Example (.txt)
A sub graph derived from Dataset 1 and saved as a simple weighted edge file format consisting of node-edge relationships and edge weight (3 column format). It is graph of mouse genes and their coexpression relationships to each other. The underlying data is however not saved with the graph.
Cylinder graph – (.gml)
A Cylinder shape provided in .gml format with a random series of “holes” within the structure, specifically to make optimum layout difficult
Blackhole – Simple Pairwise Two Column Text File (.txt)
A “Black hole” shape provided by a simple pairwise connection of nodes in a text file
Flower – (.gml)
A complex flower shape created in the .gml format provided by the Hachul graph set