# An overview of pQTLdata

This package intends to gather information, meta-data 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/`, 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.

Table 2.1: Updated information on Caprion
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.

## 2.2 Olink

This includes 12 qPCR panels, 15 Target 96 panels and Explore panels.

## 2.3 SomaScan

Both `SomaScanV4.1` and the latest `SomaScan11k` are directly from SomaLogic.

## 2.4 SWATH-MS

This panel has been used in an experimental data acquisition and analysis.

## 2.5 Overlap of proteins

It is of interest to compare some of these,

Figure 2.1: Overlap of Olink Explore HT, SomaScan V4.1 and Caprion

Figure 2.2: Overlap of Olink Explore HT, SomaScan 11K and Caprion

# 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.

Table 3.1: Olink/inflammation panel
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.

    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")

Table 4.1: 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

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.