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This directory contains the supplementary files for paper: 



Yanjun Qi[1]1, Harpreet K. Dhiman2, Neil Bhola3, Ivan Budyak4, Siddhartha Kar5, David Man2, Arpana Dutta2, Kalyan Tirupula2, Brian I. Carr5, Jennifer Grandis3,  Ziv Bar-Joseph1§ and Judith Klein-Seetharaman1,2,4§

Systematic prediction of human membrane receptor interactions, PROTEOMICS (2009) (In Press)

Supplementary Information see: http://www.cs.cmu.edu/~qyj/HMRI/



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SubDir: ./software



HPPIPM is the name of a software aiming for predicting human protein-protein intearctions by

integrating multiple biological data sources based on "Random Forest" classifier. 

It provides a java based GUI interface and perl based interface from command line.  



Human membrane receptor interactome is provided as a test case for this software. 



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SubDir: ./relatedListGenes



This subdirectory contains various gene list that are useful 

for the analysis. 





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SubDir: ./modules-cutoff2.0



With the cutoff 2.0, we derive a predicted human membrane receptor graph.

Then biclustering was performed on this graph to detect modules. 

This file contains the modules derived from the above precedure. 





Subsubdir:  ./modules-cutoff2.0/subgraphsHMRI4Cytoscape



Subgraphs of the predicted HMRI graph using cutoff 2.0. 



For example, file: score2.0o.ReceptProtein.E1.cytoscape.share.edgeAttrs



With the cutoff 2.0, we derive a predicted human membrane receptor graph.

You can use this file directly in Cytoscape for visualization. 



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SubDir:  ./allresults-eachReceptorOwn



For each human membrane receptor, we predict its potential interaction partners from all human proteins. 

All possible pairs are tested and scores are provided. 



*****  DUE TO THE SERVER SPACE LIMIT, RECEPTOR'S PREDICTION FILES ARE PUT INTO TWO SUBDIR   ******



First half @ http://www.cs.cmu.edu/afs/cs.cmu.edu/project/structure-9/PPI/HMRI/allresults-eachReceptorOwn/

Second half @ http://www.cs.cmu.edu/afs/cs.cmu.edu/project/structure-9/Yanjun/allpredictions/





For each receptor, there exist a separate prediction file which is compressed into *.tar.gz format. 

You can use the gene ID of receptors to locate its prediction file in this subdir. 



Please use "gunzip" then "tar -xvf " to decompress it.  You can OPEN the file using EXCEL. 



In each line, Items are Separated by TAB.

The pairs could be sorted based on the "column E" .



column A, gene ID of gene1 ==> geneID1

column B, gene Symbol of gene1 ==> geneSym1

column C, gene ID of gene2 ==> geneID2

column D, gene Symbol of gene2 ==> geneSym2

column E, predicted score for this pair ==> RFpnScore

column F, the label of HPRD data set : [1 means interact; 2 means not-interact]  ==> hprdLabel

column H, gene description of gene1 ==> GeneID1:Synonyms:description

column J, features we used in the computational method ==> 27features

column L, GDB ID for gene1 ==> GDBID

column M, genetic disorder information for gene1 ==> GeneticDisorder



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