| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Goat Polyclonal IgG Human Osteoactivin/GPNMB antibody | R&D Systems | Catalog: AF2550, RRID: AB_416615 |
| Rabbit Polyclonal IgG Human MAPRE3 antibody | Atlas Antibodies | Catalog: HPA009263 RRID: AB_1078716 |
| Mouse Monoclonal IgG Human FOXI1 antibody | Origene Technologies | Catalog: TA800146 RRID: AB_2625262 |
| Rabbit Monoclonal IgG Human Cyclin D1 | Cell Marque | Catalog: 241R-18 RRID: AB_1158233 |
| Mouse Monoclonal IgG Human PIGR antibody | Santa Cruz | Catalog: SC-374343, RRID: AB_10989564 |
| Rabbit Polyclonal IgG Human PYCR1 antibody | Cell Signaling Technology | Catalog: 47935 |
| Rabbit Polyclonal IgG Human AKT antibody | Cell Signaling Technology | Catalog: 9272 |
| Rabbit Polyclonal IgG Human Phospho-AKT (Ser473) Antibody | Cell Signaling Technology | Catalog: 9271 |
| Rabbit Polyclonal IgG Human p44/42 MAPK (Erk1/2) Antibody | Cell Signaling Technology | Catalog: 9102 |
| Rabbit Monoclonal IgG Human Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) antibody | Cell Signaling Technology | Catalog: 4376 |
| Rabbit Polyclonal IgG Human Vinculin Antibody | Cell Signaling Technology | Catalog: 4650 |
| Biological samples | ||
| Primary tumor and normal adjacent tissue samples | See experimental model and study participant details | See Table S1 |
| Critical commercial assays | ||
| Discovery CC1 | Roche-Ventana Medical System | Catalog: 950-500 |
| Discovery CC2 | Roche-Ventana Medical System | Catalog: 950-123 |
| OptiView Universal DAB Detection Kit | Roche-Ventana Medical System | Catalog: 760-700 |
| UltraView Universal DAB Detection Kit | Roche-Ventana Medical System | Catalog: 760-500 |
| Discovery mRNA DAB Detection RUO | Roche-Ventana Medical System | Catalog: 760-224 |
| RNAscope® 2.5 HD Reagent Kit -BROWN | Advanced Cell Diagnostics, Inc | Catalog: 322300 |
| RNAscope® VS Universal HRP Reagent Kit | Advanced Cell Diagnostics, Inc | Catalog: 323200 |
| RNAscope Target Probe - Hs-PIGR | Advanced Cell Diagnostics, Inc | Catalog: 472681 |
| RNAscope Target Probe - Hs-PYCR1 | Advanced Cell Diagnostics, Inc | Catalog: 509259 |
| RNAscope Target Probe - Hs-SOSTDC1 | Advanced Cell Diagnostics, Inc | Catalog: 469929 |
| RNAscope PositiveProbe - Hs-PPIB | Advanced Cell Diagnostics, Inc | Catalog: 313901/313909 |
| RNAscope Negative Probe – DapB | Advanced Cell Diagnostics, Inc | Catalog: 310043/312039 |
| Rabbit Polyclonal IgG Human IGF2BP3 | Proteintech | Catalog: 14642-1-AP, RRID: AB_2122782 |
| Rabbit Polyclonal IgG Human ADGRF5 (GPR116) | Proteintech | Catalog: 14047-1-AP, RRID: AB_2113095 |
| Deposited data | ||
| CPTAC non-ccRCC clinical data and proteomic data | This manuscript | https://pdc.cancer.gov/ |
| CPTAC ccRCC genomic, transcriptomic, and snRNA-seq data | This manuscript | https://portal.gdc.cancer.gov/projects/CPTAC-3 |
| CPTAC non-ccRCC pathology and radiology images | This manuscript | https://portal.imaging.datacommons.cancer.gov/ |
| TCGA KIRC | Cancer Genome Atlas Research Network108 |
https://portal.gdc.cancer.gov/ |
| TCGA KIRP | Cancer Genome Atlas Research Network75 |
https://portal.gdc.cancer.gov/ |
| Software and algorithms | ||
| CNVEX | https://github.com/mctp/cnvex | |
| R v4.1 | R Development Core Team | https://www.R-project.org |
| Python | Python Software Foundation | https://www.python.org/ |
| Philosopher | da Veiga Leprevost et al.109 | https://philosopher.nesvilab.org/ |
| MSFragger | Kong et al.110 | https://msfragger.nesvilab.org/ |
| PTM-Shepherd | Geiszler et al.111 | https://ptmshepherd.nesvilab.org/ |
| TMT-Integrator | Djomehri et al.112 | https://github.com/Nesvilab/TMT-Integrator |
| ARD-NMF | Tan et al.30 | https://github.com/getzlab/getzlab-SignatureAnalyzer |
| CancerSubtypes | Xu et al.113 | https://www.bioconductor.org/packages/release/bioc/html/CancerSubtypes.html |
| Limma | Ritchie et al.90 | https://bioconductor.org/packages/release/bioc/html/limma.html |
| PTM-SEA | Krug et al.114 | https://github.com/broadinstitute/ssGSEA2.0 |
| KSA-2D | Han et al.115 | https://github.com/ginnyintifa/KSA2D |
| CLUMPS-PTM | Geffen et al.53 | https://github.com/getzlab/CLUMPS-PTM |
| IMPaLA | Kamburov et al.116 | http://impala.molgen.mpg.de/ |
| ClusterProfiler | Yu et al.117 | https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html |
| pySCENIC | Van de Sande et al.118 | https://github.com/aertslab/pySCENIC |
| BayesDeBulk | Petralia et al.119 | http://www.bayesdebulk.com/ |
| DreamAI | Ma et al.120 | https://github.com/WangLab-MSSM/DreamAI |
| OmniPathR | D Turei et al.99,121 | https://www.bioconductor.org/packages/release/bioc/html/OmnipathR.html |
| Survival | Therneau et al.122 | https://cran.r-project.org/web/packages/survival/index.html |
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