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README.md

Datasets

This directory contains example datasets. It can also be used to store new input data files. There are currently very small toy datasets and one real dataset.

File formats

Node file

Node files include a header row and rows providing attributes for each node. One column is for the node identifier and must have the header value NODEID. All other columns specify additional node attributes such as prizes. Any nodes that are listed in a node file but are not present in one or more edges in the edge file will be removed. For example:

NODEID	prize	sources	targets	active dummy
A	1.0		True	True	True
B	3.3	True		True
C	2.5		True	True
D	1.9	True	True	True

A secondary format provides only a list of node identifiers and uses the filename as the node attribute, as in the example sources.txt. This format may be deprecated.

Edge file

Edge files do not include a header row. Each row lists the two nodes that are connected with an edge, the weight for that edge, and, optionally, a directionality column to indicate whether the edge is directed or undirected. The directionality values are either a 'U' for an undirected edge or a 'D' for a directed edge. If the directionality column is not included, SPRAS will assume that the file's edges are entirely undirected. The weights are typically in the range [0,1] with 1 being the highest confidence for the edge.

For example:

A	B	0.98    U
B	C	0.77    D

or

A	B	0.98
B	C	0.77

Toy datasets

The following files are very small toy datasets used to illustrate the supported file formats

  • alternative-network.txt
  • alternative-targets.txt
  • network.txt
  • node-prizes.txt
  • sources.txt
  • targets.txt

Epidermal growth factor receptor (EGFR)

This dataset represents protein phosphorylation changes in response to epidermal growth factor (EGF) treatment. The network includes protein-protein interactions from iRefIndex and kinase-substrate interactions from PhosphoSitePlus. The files are originally from the Temporal Pathway Synthesizer (TPS) repository. They have been lightly modified for SPRAS by lowering one edge weight that was greater than 1, removing 182 self-edges, removing a PSEUDONODE prize, and adding a prize of 10.0 to EGF_HUMAN. The only source is EGF_HUMAN. All proteins with phosphorylation-based prizes are also labeled as targets. All nodes are considered active.

If you use any of the input files tps-egfr-prizes.txt or phosphosite-irefindex13.0-uniprot.txt, reference the publication

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data. Ali Sinan Köksal, Kirsten Beck, Dylan R. Cronin, Aaron McKenna, Nathan D. Camp, Saurabh Srivastava, Matthew E. MacGilvray, Rastislav Bodík, Alejandro Wolf-Yadlin, Ernest Fraenkel, Jasmin Fisher, Anthony Gitter. Cell Reports 24(13):3607-3618 2018.

If you use the network file phosphosite-irefindex13.0-uniprot.txt, also reference iRefIndex and PhosphoSitePlus.

iRefIndex: a consolidated protein interaction database with provenance. Sabry Razick, George Magklaras, Ian M Donaldson. BMC Bioinformatics 9(405) 2008.

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Peter V Hornbeck, Bin Zhang, Beth Murray, Jon M Kornhauser, Vaughan Latham, Elzbieta Skrzypek. Nucleic Acids Research 43(D1):D512-520 2015.

The TPS publication describes how the network data and protein prizes were prepared.