Eva Comperat's session at the 2021 GUASCO described several new Kidney cancer subtypes including a thyroid-like variant dubbed TLFRCC. Ko describes this variant in her paper "Whole-genome and transcriptome profiling of a metastatic thyroid-like follicular renal cell carcinoma". Since my p1RCC might be related to thyroid cancer, I decided to investigate. I created two tables by
- Selecting Genes listed in the Abstract and Table1 of Ko's paper.
- From the 18,368 row Supplemental Table S5- TSPG Perturbations for all 5 TCGA Patients and for BP Towards a Normal Target Tissue.csv fromTargonski and Bender's TSPG paper, using my 2020 RNA-seq Hackathon data
- and sorted by BP-Tumor differential.
Based on the tables below, I suspect that my cancer is not of this variant.
Abstract
| Gene | BP-Tumor | TCGA-BQ-5884 | TCGA-BQ-7051 | TCGA-DZ-6131 | TCGA-GL-7966 | TCGA-Y8-A8RY | |
|---|---|---|---|---|---|---|---|
| 871 | AR | -0.211614 | -0.017011 | -0.364995 | -0.123798 | -0.121868 | -0.231878 |
| 9983 | MYC | -0.106763 | -0.061247 | -0.102986 | -0.262828 | -0.315389 | 0.021576 |
| 9137 | MAP2K2 | -0.054956 | -0.015010 | 0.050954 | -0.182945 | -0.047145 | -0.104429 |
| 2933 | CDK6 | -0.051317 | -0.021210 | -0.123691 | -0.074179 | -0.078184 | -0.044222 |
| 11452 | PDGFRB | 0.238150 | 0.167966 | 0.319553 | 0.036347 | 0.027004 | 0.242385 |
| 11451 | PDGFRA | 0.367115 | 0.315557 | 0.380796 | 0.229878 | 0.234411 | 0.358568 |
Table1
| Gene | BP-Tumor | TCGA-BQ-5884 | TCGA-BQ-7051 | TCGA-DZ-6131 | TCGA-GL-7966 | TCGA-Y8-A8RY | |
|---|---|---|---|---|---|---|---|
| 4710 | E2F1 | -0.268096 | -0.210663 | -0.312030 | -0.380435 | -0.442005 | -0.215067 |
| 4711 | E2F2 | -0.266385 | -0.258009 | -0.400997 | -0.443134 | -0.571322 | -0.224849 |
| 2690 | CCNA2 | -0.228158 | -0.201702 | -0.313020 | -0.347024 | -0.591778 | -0.227453 |
| 9323 | MDM4 | -0.209965 | -0.095992 | -0.143609 | -0.031123 | -0.286186 | -0.142436 |
| 16373 | TOP2A | -0.205414 | -0.211388 | -0.262869 | -0.294304 | -0.538290 | -0.194491 |
| 9983 | MYC | -0.106763 | -0.061247 | -0.102986 | -0.262828 | -0.315389 | 0.021576 |
| 16390 | TP53 | -0.100091 | -0.071941 | -0.260981 | -0.117477 | -0.383892 | -0.103676 |
| 12815 | RAD51 | -0.092361 | -0.119231 | -0.211125 | -0.210738 | -0.433904 | -0.143697 |
| 4712 | E2F3 | -0.073424 | -0.138427 | -0.197478 | -0.131264 | -0.292214 | -0.016827 |
| 9137 | MAP2K2 | -0.054956 | -0.015010 | 0.050954 | -0.182945 | -0.047145 | -0.104429 |
| 2933 | CDK6 | -0.051317 | -0.021210 | -0.123691 | -0.074179 | -0.078184 | -0.044222 |
| 3503 | COL1A1 | -0.016258 | -0.044517 | -0.010810 | -0.159825 | -0.277542 | 0.010240 |
| 2774 | CD274 | -0.003547 | -0.247358 | 0.062292 | -0.167837 | -0.096958 | 0.074009 |
| 5781 | FHIT | 0.009491 | -0.020224 | 0.003310 | 0.062299 | 0.178956 | -0.003514 |
| 1576 | BRD4 | 0.025710 | -0.005122 | 0.033947 | -0.066529 | -0.162211 | 0.042427 |
| 5083 | ERBB2 | 0.026003 | 0.170631 | 0.005395 | 0.187722 | 0.178390 | 0.010045 |
| 12447 | PRSS8 | 0.033081 | 0.105601 | 0.064322 | 0.122759 | 0.594064 | 0.041250 |
| 12554 | PTEN | 0.125224 | -0.081410 | 0.075240 | -0.038048 | -0.064603 | 0.100576 |
| 3856 | CTNNB1 | 0.128816 | 0.019109 | -0.035645 | 0.121470 | 0.147212 | 0.220156 |
| 11452 | PDGFRB | 0.238150 | 0.167966 | 0.319553 | 0.036347 | 0.027004 | 0.242385 |
| 11451 | PDGFRA | 0.367115 | 0.315557 | 0.380796 | 0.229878 | 0.234411 | 0.358568 |
| 8759 | LMO1 | 0.421346 | 0.370964 | 0.425843 | 0.262508 | -0.028689 | 0.436359 |
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