This package intends to gather information, metadata and relevant scripts in proteogenomic analysis.
1 Collections
As used in several years of proteomic analysis and for future extensions, the collections are in two locations:
-
data/. R datasets. -
inst/.EndNote/,Olink/,scripts/,SomaLogic/, which spread into the package’s root directory after installation.
While library(help=pQTLdata) displays the general information, ? pQTLdata can give a list of data objects in the package.
2 Protein panels
2.1 Caprion
As has been the norm, no snapshot upon data release was provided which consequently requires substantial effort and the notable ones are highlighted here.
| Gene | Gene.orig | Protein | Accession | ensGenes | chr | start | end |
|---|---|---|---|---|---|---|---|
| AMY1 | AMY1A; AMY1B; AMY1C | AMY1_HUMAN | P04745 | ENSG00000174876, ENSG00000187733, ENSG00000237763 | 1 | 103655760 | 103758726 |
| C20orf27 | C20orf27 | CT027_HUMAN | Q9GZN8 | ENSG00000101220 | 20 | 3753508 | 3767781 |
| C4B | C4B; C4B_2 | CO4B_HUMAN | P0C0L5 | ENSG00000224389, ENSG00000236625, ENSG00000228267, ENSG00000233312, ENSG00000228454 | 6 | 3262537 | 32035418 |
| C7orf26 | C7orf26 | CG026_HUMAN | Q96N11 | ENSG00000146576 | 7 | 6590021 | 6608726 |
| CD97 | CD97 | CD97_HUMAN | P48960 | ENSG00000123146 | 19 | 14380501 | 14408725 |
| FAM49B | FAM49B | FA49B_HUMAN | Q9NUQ9 | ENSG00000153310 | 8 | 129839593 | 130017504 |
| GBA | GBA | GLCM_HUMAN | P04062 | ENSG00000177628 | 1 | 155234452 | 155244699 |
| HBA | HBA1; HBA2 | HBA_HUMAN | P69905 | ENSG00000188536, ENSG00000206172 | 16 | 172876 | 177522 |
| HIST | HIST1H4A; HIST1H4B; HIST1H4C; HIST1H4D; HIST1H4E; HIST1H4F; HIST1H4H; HIST1H4I; HIST1H4J; HIST1H4K; HIST1H4L; HIST2H4A; HIST2H4B; HIST4H4 | H4_HUMAN | P62805 | ENSG00000277157, ENSG00000275126, ENSG00000274618, ENSG00000197061, ENSG00000158406, ENSG00000197238, ENSG00000276966, ENSG00000197837, ENSG00000276180, ENSG00000278705, ENSG00000273542, ENSG00000278637, ENSG00000270276, ENSG00000270882 | 6, 12, 1 | 14767999 | 149861159 |
| SLC9A3R1 | SLC9A3R1 | NHRF1_HUMAN | O14745 | ENSG00000109062 | 17 | 74748628 | 74769353 |
| WARS | WARS | SYWC_HUMAN | P23381 | ENSG00000140105 | 14 | 100333790 | 100376805 |
| YARS | YARS | SYYC_HUMAN | P54577 | ENSG00000134684 | 1 | 32775237 | 32818031 |
which again is useful for extracting data from GTEx v8.
3 Published data
This associates with several panels, including SomaScan (SomaScan160410)1, Olink qPCR inflammation
(inf1)2 and Seer (seer1980)3. In particular, inf1 contains updates from the original release by Olink.
| gene | prot | uniprot | target | target.short | chr | start | end | ensembl_gene_id | alt_name | ensGene | chromosome | start38 | end38 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ADA | ADA | P00813 | Adenosine Deaminase (ADA) | ADA | 20 | 43248163 | 43280874 | ENSG00000196839 | NA | NA | NA | NA | NA |
| ARTN | ARTN | Q5T4W7 | Artemin (ARTN) | ARTN | 1 | 44398992 | 44402913 | ENSG00000117407 | NA | NA | NA | NA | NA |
| AXIN1 | AXIN1 | O15169 | Axin-1 (AXIN1) | AXIN1 | 16 | 337440 | 402673 | ENSG00000103126 | NA | NA | NA | NA | NA |
| BDNF | BDNF | P23560 | Brain-derived neutrophic factor (BDNF) | BDNF | 11 | 27676440 | 27743605 | ENSG00000176697 | NA | NA | NA | NA | NA |
| CASP8 | CASP.8 | Q14790 | Caspase 8 (CASP-8) | CASP-8 | 2 | 202098166 | 202152434 | ENSG00000064012 | NA | NA | NA | NA | NA |
| CCL11 | CCL11 | P51671 | Eotaxin-1 (CCL11) | CCL11 | 17 | 32612687 | 32615353 | ENSG00000172156 | CCL11 | NA | NA | NA | NA |
| CCL13 | MCP.4 | Q99616 | Monocyte chemotactic protein 4 (MCP-4) | MCP-4 | 17 | 32683471 | 32685629 | ENSG00000181374 | CCL13 | NA | NA | NA | NA |
| CCL19 | CCL19 | Q99731 | C-C motif chemokine 19 (CCL19) | CCL19 | 9 | 34689564 | 34691274 | ENSG00000172724 | NA | NA | NA | NA | NA |
| CCL2 | MCP.1 | P13500 | Monocyte chemotactic protein 1 (MCP-1) | MCP-1 | 17 | 32582304 | 32584222 | ENSG00000108691 | CCL2 | NA | NA | NA | NA |
| CCL20 | CCL20 | P78556 | C-C motif chemokine 20 (CCL20) | CCL20 | 2 | 228678558 | 228682272 | ENSG00000115009 | NA | NA | NA | NA | NA |
| CCL23 | CCL23 | P55773 | C-C motif chemokine 23 (CCL23) | CCL23 | 17 | 34340096 | 34345005 | ENSG00000167236 | NA | ENSG00000274736 | 17 | 36013056 | 36017972 |
| CCL25 | CCL25 | O15444 | C-C motif chemokine 25 (CCL25) | CCL25 | 19 | 8117651 | 8127534 | ENSG00000131142 | NA | ENSG00000131142 | 19 | 8052318 | 8062660 |
| CCL28 | CCL28 | Q9NRJ3 | C-C motif chemokine 28 (CCL28) | CCL28 | 5 | 43376747 | 43412493 | ENSG00000151882 | NA | NA | NA | NA | NA |
| CCL3 | MIP.1.alpha | P10147 | Macrophage inflammatory protein 1-alpha (MIP-1 alpha) | MIP-1 alpha | 17 | 34415602 | 34417515 | ENSG00000006075 | NA | ENSG00000277632 | 17 | 36088256 | 36090169 |
| CCL4 | CCL4 | P13236 | C-C motif chemokine 4 (CCL4) | CCL4 | 17 | 34430983 | 34433014 | ENSG00000129277 | NA | ENSG00000275302 | 17 | 36103827 | 36105621 |
| CCL7 | MCP.3 | P80098 | Monocyte chemotactic protein 3 (MCP-3) | MCP-3 | 17 | 32597240 | 32599261 | ENSG00000108688 | CCL7 | NA | NA | NA | NA |
| CCL8 | MCP.2 | P80075 | Monocyte chemotactic protein 2 (MCP-2) | MCP-2 | 17 | 32646055 | 32648421 | ENSG00000108700 | CCL8 | NA | NA | NA | NA |
| CD244 | CD244 | Q9BZW8 | Natural killer cell receptor 2B4 (CD244) | CD244 | 1 | 160799950 | 160832692 | ENSG00000122223 | NA | NA | NA | NA | NA |
| CD274 | PD.L1 | Q9NZQ7 | Programmed cell death 1 ligand 1 (PD-L1) | PD-L1 | 9 | 5450503 | 5470566 | ENSG00000120217 | NA | NA | NA | NA | NA |
| CD40 | CD40 | P25942 | CD40L receptor (CD40) | CD40 | 20 | 44746911 | 44758502 | ENSG00000101017 | NA | NA | NA | NA | NA |
| CD5 | CD5 | P06127 | T-cell surface glycoprotein CD5 (CD5) | CD5 | 11 | 60869867 | 60895324 | ENSG00000110448 | NA | NA | NA | NA | NA |
| CD6 | CD6 | P30203 | T-cell surface glycoprotein CD6 isoform (CD6) | CD6 | 11 | 60739115 | 60787849 | ENSG00000138675 | NA | ENSG00000013725 | 11 | 60971680 | 61020377 |
| CDCP1 | CDCP1 | Q9H5V8 | CUB domain-containing protein 1 (CDCP1) | CDCP1 | 3 | 45123770 | 45187914 | ENSG00000163814 | NA | NA | NA | NA | NA |
| CSF1 | CSF.1 | P09603 | Macrophage colony-stimulating factor 1 (CSF-1) | CSF-1 | 1 | 110452864 | 110473614 | ENSG00000184371 | NA | NA | NA | NA | NA |
| CST5 | CST5 | P28325 | Cystatin D (CST5) | CST5 | 20 | 23856572 | 23860387 | ENSG00000170367 | NA | NA | NA | NA | NA |
| CX3CL1 | CX3CL1 | P78423 | Fractalkine (CX3CL1) | CX3CL1 | 16 | 57406370 | 57418960 | ENSG00000006210 | NA | NA | NA | NA | NA |
| CXCL1 | CXCL1 | P09341 | C-X-C motif chemokine 1 (CXCL1) | CXCL1 | 4 | 74735110 | 74736959 | ENSG00000163739 | NA | NA | NA | NA | NA |
| CXCL10 | CXCL10 | P02778 | C-X-C motif chemokine 10 (CXCL10) | CXCL10 | 4 | 76942273 | 76944650 | ENSG00000169245 | NA | NA | NA | NA | NA |
| CXCL11 | CXCL11 | O14625 | C-X-C motif chemokine 11 (CXCL11) | CXCL11 | 4 | 76954835 | 76962568 | ENSG00000169248 | NA | NA | NA | NA | NA |
| CXCL5 | CXCL5 | P42830 | C-X-C motif chemokine 5 (CXCL5) | CXCL5 | 4 | 74861359 | 74864496 | ENSG00000163735 | NA | NA | NA | NA | NA |
| CXCL6 | CXCL6 | P80162 | C-X-C motif chemokine 6 (CXCL6) | CXCL6 | 4 | 74702214 | 74714781 | ENSG00000124875 | CXCL6 | NA | NA | NA | NA |
| CXCL9 | CXCL9 | Q07325 | C-X-C motif chemokine 9 (CXCL9) | CXCL9 | 4 | 76922428 | 76928641 | ENSG00000138755 | NA | NA | NA | NA | NA |
| DNER | DNER | Q8NFT8 | Delta and Notch-like epidermal growth factor related receptor (DNER) | DNER | 2 | 230222345 | 230579274 | ENSG00000187957 | NA | NA | NA | NA | NA |
| EIF4EBP1 | 4E.BP1 | Q13541 | Eukaryotic translation initiation factor 4E-binding protein 1 (4EBP1) | 4EBP1 | 8 | 37887859 | 37917883 | ENSG00000187840 | NA | NA | NA | NA | NA |
| FGF19 | FGF.19 | O95750 | Fibroblast growth factor 19 (FGF-19) | FGF-19 | 11 | 69513000 | 69519410 | ENSG00000162344 | NA | NA | NA | NA | NA |
| FGF21 | FGF.21 | Q9NSA1 | Fibroblast growth factor 21 (FGF-21) | FGF-21 | 19 | 49258816 | 49261587 | ENSG00000105550 | NA | NA | NA | NA | NA |
| FGF23 | FGF.23 | Q9GZV9 | Fibroblast growth factor 23 (FGF-23) | FGF-23 | 12 | 4477393 | 4488894 | ENSG00000118972 | NA | NA | NA | NA | NA |
| FGF5 | FGF.5 | P12034 | Fibroblast growth factor 5 (FGF-5) | FGF-5 | 4 | 81187753 | 81257834 | ENSG00000013725 | NA | ENSG00000138675 | 4 | 80266639 | 80336680 |
| FLT3LG | Flt3L | P49771 | Fms-related tyrosine kinase 3 ligand (FIt3L) | FIt3L | 19 | 49977464 | 49989488 | ENSG00000090554 | NA | NA | NA | NA | NA |
| GDNF | GDNF | P39905 | Glial cell line-derived neutrophic factor (hGDNF) | hGDNF | 5 | 37812779 | 37839788 | ENSG00000168621 | NA | NA | NA | NA | NA |
| HGF | HGF | P14210 | Hepatocyte growth factor (HGF) | HGF | 7 | 81328322 | 81399754 | ENSG00000019991 | NA | NA | NA | NA | NA |
| IFNG | IFN.gamma | P01579 | Interferon gamma (IFN-gamma) | IFN-gamma | 12 | 68548548 | 68553527 | ENSG00000111537 | NA | NA | NA | NA | NA |
| IL10 | IL.10 | P22301 | Interleukin-10 (IL-10) | IL-10 | 1 | 206940947 | 206945839 | ENSG00000136634 | NA | NA | NA | NA | NA |
| IL10RA | IL.10RA | Q13651 | Interleukin-10 receptor subunit alpha (IL-10RA) | IL-10RA | 11 | 117857063 | 117872196 | ENSG00000110324 | NA | NA | NA | NA | NA |
| IL10RB | IL.10RB | Q08334 | Interleukin-10 receptor subunit beta (IL10RB) | IL10RB | 21 | 34638663 | 34669539 | ENSG00000243646 | NA | NA | NA | NA | NA |
| IL12B | IL.12B | P29460 | Interleukin-12 subunit beta (IL-12B) | IL-12B | 5 | 158741791 | 158757895 | ENSG00000113302 | NA | NA | NA | NA | NA |
| IL13 | IL.13 | P35225 | Interleukin-13 (IL-13) | IL-13 | 5 | 131991955 | 131996802 | ENSG00000169194 | NA | NA | NA | NA | NA |
| IL15RA | IL.15RA | Q13261 | Interleukin-15 receptor subunit alpha (IL-15RA) | IL-15RA | 10 | 5990855 | 6020150 | ENSG00000134470 | NA | NA | NA | NA | NA |
| IL17A | IL.17A | Q16552 | Interleukin-17A (IL-17A) | IL-17A | 6 | 52051185 | 52055436 | ENSG00000112115 | NA | NA | NA | NA | NA |
| IL17C | IL.17C | Q9P0M4 | Interleukin-17C (IL-17C) | IL-17C | 16 | 88704999 | 88706881 | ENSG00000124391 | NA | NA | NA | NA | NA |
| IL18 | IL.18 | Q14116 | Interleukin-18 (IL-18) | IL-18 | 11 | 112013974 | 112034840 | ENSG00000150782 | NA | NA | NA | NA | NA |
| IL18R1 | IL.18R1 | Q13478 | Interleukin-18 receptor 1 (IL-18R1) | IL-18R1 | 2 | 102927989 | 103015218 | ENSG00000115604 | NA | NA | NA | NA | NA |
| IL1A | IL.1.alpha | P01583 | Interleukin-1 alpha (IL-1 alpha) | IL-1 alpha | 2 | 113531492 | 113542167 | ENSG00000115008 | NA | NA | NA | NA | NA |
| IL2 | IL.2 | P60568 | Interleukin-2 (IL-2) | IL-2 | 4 | 123372625 | 123377880 | ENSG00000109471 | NA | NA | NA | NA | NA |
| IL20 | IL.20 | Q9NYY1 | Interleukin-20 (IL-20) | IL-20 | 1 | 207038699 | 207042568 | ENSG00000162891 | NA | NA | NA | NA | NA |
| IL20RA | IL.20RA | Q9UHF4 | Interleukin-20 receptor subunit alpha (IL-20RA) | IL-20RA | 6 | 137321108 | 137366298 | ENSG00000016402 | NA | NA | NA | NA | NA |
| IL22RA1 | IL.22.RA1 | Q8N6P7 | Interleukin-22 receptor subunit alpha-1 (IL-22RA1) | IL-22RA1 | 1 | 24446261 | 24469611 | ENSG00000142677 | NA | NA | NA | NA | NA |
| IL24 | IL.24 | Q13007 | Interleukin-24 (IL-24) | IL-24 | 1 | 207070788 | 207077484 | ENSG00000162892 | NA | NA | NA | NA | NA |
| IL2RB | IL.2RB | P14784 | Interleukin-2 receptor subunit beta (IL-2RB) | IL-2RB | 22 | 37521878 | 37571094 | ENSG00000100385 | NA | NA | NA | NA | NA |
| IL33 | IL.33 | O95760 | Interleukin-33 (IL-33) | IL-33 | 9 | 6215805 | 6257983 | ENSG00000137033 | NA | NA | NA | NA | NA |
| IL4 | IL.4 | P05112 | Interleukin-4 (IL-4) | IL-4 | 5 | 132009678 | 132018368 | ENSG00000113520 | NA | NA | NA | NA | NA |
| IL5 | IL.5 | P05113 | Interleukin-5 (IL-5) | IL-5 | 5 | 131877136 | 131892530 | ENSG00000113525 | NA | NA | NA | NA | NA |
| IL6 | IL.6 | P05231 | Interleukin-6 (IL-6) | IL-6 | 7 | 22765503 | 22771621 | ENSG00000136244 | NA | NA | NA | NA | NA |
| IL7 | IL.7 | P13232 | Interleukin-7 (IL-7) | IL-7 | 8 | 79587978 | 79717758 | ENSG00000104432 | NA | NA | NA | NA | NA |
| IL8 | IL.8 | P10145 | Interleukin-8 (IL-8) | IL-8 | 4 | 74606223 | 74609433 | ENSG00000169429 | NA | NA | NA | NA | NA |
| KITLG | SCF | P21583 | Stem cell factor (SCF) | SCF | 12 | 88886570 | 88974628 | ENSG00000049130 | NA | NA | NA | NA | NA |
| LIF | LIF | P15018 | Leukemia inhibitory factor (LIF) | LIF | 22 | 30636436 | 30642840 | ENSG00000128342 | NA | NA | NA | NA | NA |
| LIFR | LIF.R | P42702 | Leukemia inhibitory factor receptor (LIF-R) | LIF-R | 5 | 38475065 | 38608456 | ENSG00000113594 | NA | NA | NA | NA | NA |
| LTA | TNFB | P01374 | TNF-beta (TNFB) | TNFB | 6 | 31539831 | 31542101 | ENSG00000226979 | NA | NA | NA | NA | NA |
| MMP1 | MMP.1 | P03956 | Matrix metalloproteinase-1 (MMP-1) | MMP-1 | 11 | 102660651 | 102668891 | ENSG00000196611 | NA | NA | NA | NA | NA |
| MMP10 | MMP.10 | P09238 | Matrix metalloproteinase-10 (MMP-10) | MMP-10 | 11 | 102641234 | 102651359 | ENSG00000166670 | NA | NA | NA | NA | NA |
| NGF | Beta.NGF | P01138 | Beta-nerve growth factor (Beta-NGF) | Beta-NGF | 1 | 115828539 | 115880857 | ENSG00000134259 | NA | NA | NA | NA | NA |
| NRTN | NRTN | Q99748 | Neurturin (NRTN) | NRTN | 19 | 5823813 | 5828335 | ENSG00000171119 | NA | NA | NA | NA | NA |
| NTF3 | NT.3 | P20783 | Neurotrophin-3 (NT-3) | NT-3 | 12 | 5541278 | 5630702 | ENSG00000185652 | NA | NA | NA | NA | NA |
| OSM | OSM | P13725 | Oncostatin-M (OSM) | OSM | 22 | 30658818 | 30662829 | ENSG00000099985 | NA | NA | NA | NA | NA |
| PLAU | uPA | P00749 | Urokinase-type plasminogen activator (uPA) | uPA | 10 | 75668935 | 75677255 | ENSG00000122861 | NA | NA | NA | NA | NA |
| S100A12 | EN.RAGE | P80511 | Protein S100-A12 (EN-RAGE) | EN-RAGE | 1 | 153346184 | 153348125 | ENSG00000163221 | NA | NA | NA | NA | NA |
| SIRT2 | SIRT2 | Q8IXJ6 | SIR2-like protein 2 (SIRT2) | SIRT2 | 19 | 39369197 | 39390502 | ENSG00000068903 | NA | NA | NA | NA | NA |
| SLAMF1 | SLAMF1 | Q13291 | Signaling lymphocytic activation molecule (SLAMF1) | SLAMF1 | 1 | 160577890 | 160617085 | ENSG00000117090 | NA | NA | NA | NA | NA |
| STAMBP | STAMPB | O95630 | STAM-binding protein (STAMPB) | STAMPB | 2 | 74056086 | 74100786 | ENSG00000124356 | NA | NA | NA | NA | NA |
| SULT1A1 | ST1A1 | P50225 | Sulfotransferase 1A1 (ST1A1) | ST1A1 | 16 | 28616903 | 28634946 | ENSG00000196502 | NA | NA | NA | NA | NA |
| TGFA | TGF.alpha | P01135 | Transforming growth factor alpha (TGF-alpha) | TGF-alpha | 2 | 70674412 | 70781325 | ENSG00000163235 | NA | NA | NA | NA | NA |
| TGFB1 | LAP.TGF.beta.1 | P01137 | Latency-associated peptide transforming growth factor beta 1 (LAP TGF-beta-1) | LAP TGF-beta-1 | 19 | 41807492 | 41859816 | ENSG00000105329 | NA | NA | NA | NA | NA |
| TNF | TNF | P01375 | Tumor necrosis factor (TNF) | TNF | 6 | 31543344 | 31546113 | ENSG00000232810 | NA | NA | NA | NA | NA |
| TNFRSF11B | OPG | O00300 | Osteoprotegerin (OPG) | OPG | 8 | 119935796 | 119964439 | ENSG00000164761 | NA | NA | NA | NA | NA |
| TNFRSF9 | TNFRSF9 | Q07011 | Tumor necrosis factor receptor superfamily member 9 (TNFRSF9) | TNFRSF9 | 1 | 7979907 | 8000926 | ENSG00000049249 | NA | NA | NA | NA | NA |
| TNFSF10 | TRAIL | P50591 | TNF-related apoptosis ligand (TRAIL) | TRAIL | 3 | 172223298 | 172241297 | ENSG00000121858 | NA | NA | NA | NA | NA |
| TNFSF11 | TRANCE | O14788 | TNF-related activation cytokine (TRANCE) | TRANCE | 13 | 43136872 | 43182149 | ENSG00000120659 | NA | NA | NA | NA | NA |
| TNFSF12 | TWEAK | O43508 | Tumor necrosis factor (Ligand) superfamily member 12 (TWEAK) | TWEAK | 17 | 7452208 | 7464925 | ENSG00000239697 | NA | NA | NA | NA | NA |
| TNFSF14 | TNFSF14 | O43557 | Tumor necrosis factor ligand superfamily member 14 (TNFSF14) | TNFSF14 | 19 | 6663148 | 6670599 | ENSG00000125735 | NA | ENSG00000125735 | 19 | 6661253 | 6670588 |
| TSLP | TSLP | Q969D9 | Thymic stromal lymphopoietin (TSLP) | TSLP | 5 | 110405760 | 110413722 | ENSG00000145777 | NA | NA | NA | NA | NA |
| VEGFA | VEGF.A | P15692 | Vascular endothelial growth factor A (VEGF_A) | VEGF_A | 6 | 43737921 | 43754224 | ENSG00000112715 | NA | NA | NA | NA | NA |
4 Reference data
We showcase EnsDb.Hsapiens.v75 from Bioconductor.
options(new_options)
ensembldb::metadata(EnsDb.Hsapiens.v75)
#> name value
#> 1 Db type EnsDb
#> 2 Type of Gene ID Ensembl Gene ID
#> 3 Supporting package ensembldb
#> 4 Db created by ensembldb package from Bioconductor
#> 5 script_version 0.3.0
#> 6 Creation time Thu May 18 09:15:45 2017
#> 7 ensembl_version 75
#> 8 ensembl_host localhost
#> 9 Organism homo_sapiens
#> 10 taxonomy_id 9606
#> 11 genome_build GRCh37
#> 12 DBSCHEMAVERSION 2.0
ensembldb::keytypes(EnsDb.Hsapiens.v75)
#> [1] "ENTREZID" "EXONID" "GENEBIOTYPE"
#> [4] "GENEID" "GENENAME" "PROTDOMID"
#> [7] "PROTEINDOMAINID" "PROTEINDOMAINSOURCE" "PROTEINID"
#> [10] "SEQNAME" "SEQSTRAND" "SYMBOL"
#> [13] "TXBIOTYPE" "TXID" "TXNAME"
#> [16] "UNIPROTID"
exon_info <- ensembldb::exons(EnsDb.Hsapiens.v75)
gene_info <- ensembldb::genes(EnsDb.Hsapiens.v75)
transcript_info <- ensembldb::transcripts(EnsDb.Hsapiens.v75)
colnames(S4Vectors::mcols(gene_info))
#> [1] "gene_id" "gene_name" "gene_biotype" "seq_coord_system"
#> [5] "symbol" "entrezid"
colnames(S4Vectors::mcols(transcript_info))
#> [1] "tx_id" "tx_biotype" "tx_cds_seq_start" "tx_cds_seq_end"
#> [5] "gene_id" "tx_name"
overlaps <- IRanges::findOverlaps(transcript_info, gene_info)
overlapping_transcripts <- transcript_info[queryHits(overlaps)]
overlapping_genes <- gene_info[subjectHits(overlaps)]
overlap_data <- data.frame(
transcript_id = mcols(overlapping_transcripts)$tx_id,
gene_id = S4Vectors::mcols(overlapping_genes)$gene_id,
gene_name = S4Vectors::mcols(overlapping_genes)$gene_name,
start = pmax(start(overlapping_transcripts), start(overlapping_genes)),
end = pmin(end(overlapping_transcripts), end(overlapping_genes))
)
gene_symbols <- c("BRCA1", "TP53")
gene_data <- subset(overlap_data,gene_name%in%gene_symbols,select=-c(gene_id,gene_name))
cols <- c("UNIPROTID","PROTEINID","GENEID","GENENAME","SEQNAME","TXID")
info <- ensembldb::select(EnsDb.Hsapiens.v75, keys = gene_symbols,
columns = cols, keytype = "SYMBOL") |>
dplyr::left_join(head(gene_data,15),by=c('TXID'='transcript_id')) |>
subset(!is.na(UNIPROTID)&!is.na(start)&!is.na(end))
knitr::kable(head(info,15),caption="Annotation for BRCA1 and TP53")| SYMBOL | UNIPROTID | PROTEINID | GENEID | GENENAME | SEQNAME | TXID | start | end | |
|---|---|---|---|---|---|---|---|---|---|
| 242 | TP53 | Q761V2_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 243 | TP53 | Q6IT77_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 244 | TP53 | Q1HGV1_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 245 | TP53 | Q0PKT5_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 246 | TP53 | L0ES54_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 247 | TP53 | G4Y083_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 248 | TP53 | E9PCY9_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 249 | TP53 | E7EQX7_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 250 | TP53 | E7EMR6_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 251 | TP53 | B5AKF6_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 252 | TP53 | A4GWD0_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 253 | TP53 | A4GWB8_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 254 | TP53 | A4GWB5_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 255 | TP53 | A2I9Z0_HUMAN | ENSP00000410739 | ENSG00000141510 | TP53 | 17 | ENST00000413465 | 7565097 | 7579912 |
| 256 | TP53 | S5LQU8_HUMAN | ENSP00000352610 | ENSG00000141510 | TP53 | 17 | ENST00000359597 | 7569404 | 7579912 |
keytypes(org.Hs.eg.db)
#> [1] "ACCNUM" "ALIAS" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS"
#> [6] "ENTREZID" "ENZYME" "EVIDENCE" "EVIDENCEALL" "GENENAME"
#> [11] "GENETYPE" "GO" "GOALL" "IPI" "MAP"
#> [16] "OMIM" "ONTOLOGY" "ONTOLOGYALL" "PATH" "PFAM"
#> [21] "PMID" "PROSITE" "REFSEQ" "SYMBOL" "UCSCKG"
#> [26] "UNIPROT"
uniprot_ids <- ensembldb::select(org.Hs.eg.db, keys = gene_symbols, columns = "UNIPROT", keytype = "SYMBOL")
#> 'select()' returned 1:many mapping between keys and columns
options(sys_options)where org.Hs.eg.db is more focused on genes.
5 Scripts
An analysis involving COVID-19 data is in Olink/ directory, while the scripts/ directory records data generation which potentially can be extended.
Specifically, docs.sh operates with GitHub while cran.sh builds, installs, and checks for compliance with the Comprehensive R Archive Network (CRAN).
6 URLs
- CellCarta, https://cellcarta.com/
- EndNote, https://endnote.com/
- ENSEMBL BioMart, https://www.ensembl.org/index.html
- GitHub, https://github.com/
- NULISA, https://alamarbio.com/technology/nulisa-platform/
- NCI Proteomic Data Commons, https://pdc.cancer.gov/pdc/browse
- Olink, https://olink.com/ (https://olink.com/publications)
- SCALLOP consortium, http://www.scallop-consortium.com/
- Seer, https://seer.bio/
- SomaLogic, https://somalogic.com/
- SWATH-MS, https://www.creative-proteomics.com/ngpro/swath-ms.html
- Thermo Fisher Scientific - LSMS, https://github.com/thermofisherlsms
- UCSC, https://genome.ucsc.edu/
References
The EndNote/ directory includes references in1 and4 formatted in EndNote.
1.
Sun, B. B. et al. Genomic atlas of the human plasma proteome. Nature 558, 73–79 (2018).
2.
Zhao, J. H. et al. Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets. Nature Immunology 24, 1540–1551 (2023).
3.
Suhre, K. et al. A genome-wide association study of mass spectrometry proteomics using the seer proteograph platform. BioRxiv (2024) doi:10.1101/2024.05.27.596028.
4.
Suhre, K., McCarthy, M. I. & Schwenk, J. M. Genetics meets proteomics: Perspectives for large population-based studies. Nat Rev Genet (2020) doi:10.1038/s41576-020-0268-2.