Overlap between the genes with REs and Cancer genes
- This script test the overlap signficancy betrween genes with REs and cancer gene sets in particular cancer type.
- The script loads compares the genes with predicted REs and the two cancer gene sets (Sanger and All-Onco).
- The analysis is performed per cancer type.
Loading all Data
## [1] "- Results loaded, with 82205 recordes and 38 cancer types."## [1] "- Sanger cancer gene set loaded: 555 genes."## [1] "- All-Onco cancer gene set loaded: 2129 genes."Loop and create plots for all cancer types
## NULL| Tissue | genes | Mutations | REs |
|---|---|---|---|
| Large Intestine | 3144 | 12387 | 15620 |
| Skin | 2956 | 11587 | 15409 |
| Lung | 2066 | 5743 | 7594 |
| Stomach | 1777 | 4232 | 5213 |
| Haematopoietic And Lymphoid Tissue | 715 | 3933 | 4966 |
| Endometrium | 1710 | 3782 | 4624 |
| Upper Aerodigestive Tract | 625 | 3156 | 4166 |
| Liver | 1136 | 3014 | 3961 |
| Breast | 1018 | 2191 | 2923 |
| Pancreas | 725 | 2357 | 2888 |
| Central Nervous System | 682 | 1682 | 2258 |
| Oesophagus | 819 | 1585 | 2142 |
| Kidney | 813 | 1487 | 1921 |
| Urinary Tract | 551 | 1337 | 1695 |
| Ovary | 524 | 1033 | 1426 |
| Prostate | 565 | 898 | 1131 |
| Thyroid | 343 | 679 | 838 |
| Soft Tissue | 173 | 655 | 813 |
| Cervix | 335 | 508 | 609 |
| Bone | 234 | 346 | 449 |
| Eye | 13 | 106 | 292 |
| Biliary Tract | 71 | 161 | 265 |
| NS | 126 | 195 | 249 |
| Autonomic Ganglia | 106 | 153 | 214 |
| Adrenal Gland | 55 | 121 | 151 |
| Salivary Gland | 24 | 46 | 78 |
| Peritoneum | 21 | 34 | 56 |
| Pleura | 29 | 41 | 48 |
| Genital Tract | 10 | 26 | 45 |
| Vulva | 2 | 16 | 31 |
| Pituitary | 9 | 23 | 30 |
| Meninges | 8 | 16 | 29 |
| Small Intestine | 11 | 16 | 24 |
| Testis | 5 | 14 | 19 |
| Thymus | 2 | 8 | 15 |
| Parathyroid | 7 | 10 | 10 |
| Gastrointestinal Tract (site Indeterminate) | 1 | 2 | 2 |
| Placenta | 1 | 1 | 1 |
Loop and create plots for all cancer types
Table: Overview of the Upper Aerodigestive Tract results.
Item Value
---------------------------------------------- --------------------------
Tissue Upper Aerodigestive Tract
Re Genes 625
Number of REs 4166
Number of random sample 1000
Overlap with Sanger Cancer Genes 60
Overlap with All-Onco Cancer Genes 162
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Thyroid results.
Item Value
---------------------------------------------- ------------------
Tissue Thyroid
Re Genes 343
Number of REs 838
Number of random sample 1000
Overlap with Sanger Cancer Genes 30
Overlap with All-Onco Cancer Genes 79
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Large Intestine results.
Item Value
---------------------------------------------- ------------------
Tissue Large Intestine
Re Genes 3144
Number of REs 15620
Number of random sample 1000
Overlap with Sanger Cancer Genes 197
Overlap with All-Onco Cancer Genes 617
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Skin results.
Item Value
---------------------------------------------- ------------------
Tissue Skin
Re Genes 2956
Number of REs 15409
Number of random sample 1000
Overlap with Sanger Cancer Genes 197
Overlap with All-Onco Cancer Genes 613
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Lung results.
Item Value
---------------------------------------------- ------------------
Tissue Lung
Re Genes 2066
Number of REs 7594
Number of random sample 1000
Overlap with Sanger Cancer Genes 147
Overlap with All-Onco Cancer Genes 429
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Haematopoietic And Lymphoid Tissue results.
Item Value
---------------------------------------------- -----------------------------------
Tissue Haematopoietic And Lymphoid Tissue
Re Genes 715
Number of REs 4966
Number of random sample 1000
Overlap with Sanger Cancer Genes 102
Overlap with All-Onco Cancer Genes 216
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Endometrium results.
Item Value
---------------------------------------------- ------------------
Tissue Endometrium
Re Genes 1710
Number of REs 4624
Number of random sample 1000
Overlap with Sanger Cancer Genes 114
Overlap with All-Onco Cancer Genes 376
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Prostate results.
Item Value
---------------------------------------------- ------------------
Tissue Prostate
Re Genes 565
Number of REs 1131
Number of random sample 1000
Overlap with Sanger Cancer Genes 50
Overlap with All-Onco Cancer Genes 154
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Stomach results.
Item Value
---------------------------------------------- ------------------
Tissue Stomach
Re Genes 1777
Number of REs 5213
Number of random sample 1000
Overlap with Sanger Cancer Genes 128
Overlap with All-Onco Cancer Genes 385
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Breast results.
Item Value
---------------------------------------------- ------------------
Tissue Breast
Re Genes 1018
Number of REs 2923
Number of random sample 1000
Overlap with Sanger Cancer Genes 79
Overlap with All-Onco Cancer Genes 252
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Central Nervous System results.
Item Value
---------------------------------------------- -----------------------
Tissue Central Nervous System
Re Genes 682
Number of REs 2258
Number of random sample 1000
Overlap with Sanger Cancer Genes 64
Overlap with All-Onco Cancer Genes 170
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Liver results.
Item Value
---------------------------------------------- ------------------
Tissue Liver
Re Genes 1136
Number of REs 3961
Number of random sample 1000
Overlap with Sanger Cancer Genes 99
Overlap with All-Onco Cancer Genes 278
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Urinary Tract results.
Item Value
---------------------------------------------- ------------------
Tissue Urinary Tract
Re Genes 551
Number of REs 1695
Number of random sample 1000
Overlap with Sanger Cancer Genes 54
Overlap with All-Onco Cancer Genes 130
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Kidney results.
Item Value
---------------------------------------------- ------------------
Tissue Kidney
Re Genes 813
Number of REs 1921
Number of random sample 1000
Overlap with Sanger Cancer Genes 69
Overlap with All-Onco Cancer Genes 190
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Autonomic Ganglia results.
Item Value
---------------------------------------------- ------------------
Tissue Autonomic Ganglia
Re Genes 106
Number of REs 214
Number of random sample 1000
Overlap with Sanger Cancer Genes 10
Overlap with All-Onco Cancer Genes 24
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Pancreas results.
Item Value
---------------------------------------------- ------------------
Tissue Pancreas
Re Genes 725
Number of REs 2888
Number of random sample 1000
Overlap with Sanger Cancer Genes 65
Overlap with All-Onco Cancer Genes 183
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Soft Tissue results.
Item Value
---------------------------------------------- ------------------
Tissue Soft Tissue
Re Genes 173
Number of REs 813
Number of random sample 1000
Overlap with Sanger Cancer Genes 29
Overlap with All-Onco Cancer Genes 48
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Oesophagus results.
Item Value
---------------------------------------------- ------------------
Tissue Oesophagus
Re Genes 819
Number of REs 2142
Number of random sample 1000
Overlap with Sanger Cancer Genes 63
Overlap with All-Onco Cancer Genes 186
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Ovary results.
Item Value
---------------------------------------------- ------------------
Tissue Ovary
Re Genes 524
Number of REs 1426
Number of random sample 1000
Overlap with Sanger Cancer Genes 43
Overlap with All-Onco Cancer Genes 126
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Cervix results.
Item Value
---------------------------------------------- ------------------
Tissue Cervix
Re Genes 335
Number of REs 609
Number of random sample 1000
Overlap with Sanger Cancer Genes 33
Overlap with All-Onco Cancer Genes 76
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Bone results.
Item Value
---------------------------------------------- ------------------
Tissue Bone
Re Genes 234
Number of REs 449
Number of random sample 1000
Overlap with Sanger Cancer Genes 27
Overlap with All-Onco Cancer Genes 59
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Pleura results.
Item Value
---------------------------------------------- ------------------
Tissue Pleura
Re Genes 29
Number of REs 48
Number of random sample 1000
Overlap with Sanger Cancer Genes 3
Overlap with All-Onco Cancer Genes 10
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Adrenal Gland results.
Item Value
---------------------------------------------- ------------------
Tissue Adrenal Gland
Re Genes 55
Number of REs 151
Number of random sample 1000
Overlap with Sanger Cancer Genes 9
Overlap with All-Onco Cancer Genes 21
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Peritoneum results.
Item Value
---------------------------------------------- ------------------
Tissue Peritoneum
Re Genes 21
Number of REs 56
Number of random sample 1000
Overlap with Sanger Cancer Genes 6
Overlap with All-Onco Cancer Genes 10
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Biliary Tract results.
Item Value
---------------------------------------------- ------------------
Tissue Biliary Tract
Re Genes 71
Number of REs 265
Number of random sample 1000
Overlap with Sanger Cancer Genes 10
Overlap with All-Onco Cancer Genes 21
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the NS results.
Item Value
---------------------------------------------- ------------------
Tissue NS
Re Genes 126
Number of REs 249
Number of random sample 1000
Overlap with Sanger Cancer Genes 15
Overlap with All-Onco Cancer Genes 39
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Pituitary results.
Item Value
---------------------------------------------- ------------------
Tissue Pituitary
Re Genes 9
Number of REs 30
Number of random sample 1000
Overlap with Sanger Cancer Genes 2
Overlap with All-Onco Cancer Genes 4
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Genital Tract results.
Item Value
---------------------------------------------- ------------------
Tissue Genital Tract
Re Genes 10
Number of REs 45
Number of random sample 1000
Overlap with Sanger Cancer Genes 5
Overlap with All-Onco Cancer Genes 7
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Meninges results.
Item Value
---------------------------------------------- ------------------
Tissue Meninges
Re Genes 8
Number of REs 29
Number of random sample 1000
Overlap with Sanger Cancer Genes 4
Overlap with All-Onco Cancer Genes 6
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Parathyroid results.
Item Value
---------------------------------------------- ------------------
Tissue Parathyroid
Re Genes 7
Number of REs 10
Number of random sample 1000
Overlap with Sanger Cancer Genes 1
Overlap with All-Onco Cancer Genes 2
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Small Intestine results.
Item Value
---------------------------------------------- ------------------
Tissue Small Intestine
Re Genes 11
Number of REs 24
Number of random sample 1000
Overlap with Sanger Cancer Genes 5
Overlap with All-Onco Cancer Genes 5
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Salivary Gland results.
Item Value
---------------------------------------------- ------------------
Tissue Salivary Gland
Re Genes 24
Number of REs 78
Number of random sample 1000
Overlap with Sanger Cancer Genes 7
Overlap with All-Onco Cancer Genes 10
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Eye results.
Item Value
---------------------------------------------- ------------------
Tissue Eye
Re Genes 13
Number of REs 292
Number of random sample 1000
Overlap with Sanger Cancer Genes 5
Overlap with All-Onco Cancer Genes 8
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Testis results.
Item Value
---------------------------------------------- ------------------
Tissue Testis
Re Genes 5
Number of REs 19
Number of random sample 1000
Overlap with Sanger Cancer Genes 4
Overlap with All-Onco Cancer Genes 4
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Thymus results.
Item Value
---------------------------------------------- ------------------
Tissue Thymus
Re Genes 2
Number of REs 15
Number of random sample 1000
Overlap with Sanger Cancer Genes 2
Overlap with All-Onco Cancer Genes 2
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Vulva results.
Item Value
---------------------------------------------- ------------------
Tissue Vulva
Re Genes 2
Number of REs 31
Number of random sample 1000
Overlap with Sanger Cancer Genes 2
Overlap with All-Onco Cancer Genes 2
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Gastrointestinal Tract (site Indeterminate) results.
Item Value
---------------------------------------------- --------------------------------------------
Tissue Gastrointestinal Tract (site Indeterminate)
Re Genes 1
Number of REs 2
Number of random sample 1000
Overlap with Sanger Cancer Genes 1
Overlap with All-Onco Cancer Genes 1
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 
Table: Overview of the Placenta results.
Item Value
---------------------------------------------- ------------------
Tissue Placenta
Re Genes 1
Number of REs 1
Number of random sample 1000
Overlap with Sanger Cancer Genes 1
Overlap with All-Onco Cancer Genes 1
p-value of overlap with Sancer cancer genes 0.002997002997003
p-value of overlap with All-Onco cancer genes 0.002997002997003 