Remove self-edges from EGFR data

Reed-CompBio · Dec 3, 2023 · cd625d4 · cd625d4
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diff --git a/input/README.md b/input/README.md
@@ -35,6 +35,7 @@ For example:
 A	B	0.98    U
 B	C	0.77    D
 ```
+or
 ```
 A	B	0.98
 B	C	0.77 
@@ -53,15 +54,15 @@ The following files are very small toy datasets used to illustrate the supported
 This dataset represents protein phosphorylation changes in response to epidermal growth factor (EGF) treatment.
 The network includes protein-protein interactions from [iRefIndex](http://irefindex.org/) and kinase-substrate interactions from [PhosphoSitePlus](http://www.phosphosite.org/).
 The files are originally from the [Temporal Pathway Synthesizer (TPS)](https://github.com/koksal/tps) repository.
-They have been lightly modified for SPRAS by lowering one edge weight that was greater than 1, removing a PSEUDONODE prize, and adding a prize of 10.0 to EGF_HUMAN.
+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](https://doi.org/10.1016/j.celrep.2018.08.085).
-Ali Sinan K�ksal, Kirsten Beck, Dylan R. Cronin, Aaron McKenna, Nathan D. Camp, Saurabh Srivastava, Matthew E. MacGilvray, Rastislav Bod�k, Alejandro Wolf-Yadlin, Ernest Fraenkel, Jasmin Fisher, Anthony Gitter.
+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.
@@ -75,3 +76,4 @@ Peter V Hornbeck, Bin Zhang, Beth Murray, Jon M Kornhauser, Vaughan Latham, Elzb
 *Nucleic Acids Research* 43(D1):D512-520 2015.
 
 The TPS [publication](https://doi.org/10.1016/j.celrep.2018.08.085) describes how the network data and protein prizes were prepared.
+