pCHIPS Patient Cancer Hallmark Integrated Phospho Signature

This is the supplemental site for Patient-Specific Druggable Networks in Lethal Prostate Cancer through Proteome-Guided Multi-Omic Integration

The pCHIPs webserver can be accessed here:

http://disco.soe.ucsc.edu:3000/

This tool allows users to make patient-specific network predictions from their data and visualize the results using the 'pCHIPs' methodology. A diagram of this is shown below:

workflow

You also access the 'TumorMap' resource with these samples loaded. You can access the map at:

http://tumormap.ucsc.edu/?p=evanPaull.pCHIPS

And coming soon, the pCHIPs visualization will be an interactive tool in the UCSC Xena Browser:

http://xena.ucsc.edu/

(Server not up? Email <evan (dot) paull (at) gmail (dot) com> for assistance)

Data:

Gene expression matrices for metastatic prostate cancer can be found on Gene Expression Omnibus.

(Note: sample names on GEO datasets use the 'WA' prefix in place of 'RA')

Contributors:

pCHIPs Tool:

Teo Flemming, Christopher K. Wong and Evan Paull

TumorMap Tool:

Yulia Newton

Xena Browser:

Jing Zhu

Paper Authors:

Justin M. Drake^a,p,*,1, Evan O. Paull^o,*, Nicholas A. Graham^b,c, John K. Lee^d,e, Bryan A. Smith^a, Bjoern Titz^b,c, Tanya Stoyanova^a,q, Claire M. Faltermeier^e, Daniel E. Carlin^o, Teo Flemming^o, Christopher K. Wong^o, Yulia Newton^o, Sud Sudhaⁿ, Ajay A. Vashisht^f, Jiaoti Huang^g,h,l, James A. Wohlschlegel^f, Thomas G. Graeber^b,c,f,i,j, Owen N. Witte^a,c,k,l,1, & Joshua M. Stuart^o,1

aDepartment of Microbiology, Immunology, and Molecular Genetics, bCrump Institute for Molecular Imaging, cDepartment of Molecular and Medical Pharmacology, dDivision of Hematology and Oncology, Department of Medicine, eMolecular Biology Institute, fDepartment of Biological Chemistry,gJonsson Comprehensive Cancer Center, hDepartment of Pathology and Laboratory Medicine, iInstitute for Molecular Medicine, jCalifornia NanoSystems Institute, and kHoward Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095; lEli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095; nDepartment of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109. oDepartment of Biomolecular Engineering, University of California, Santa Cruz, CA 95064. pRutgers Cancer Institute of New Jersey and Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, 08903.qDepartment of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, Palo Alto, CA 94304.

*Authors contributed equally to this work.