An overview of pQTLdata
pQTLdata.RmdThis 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/,pQTLdata.sh,docs.shwhich 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
The Olink qPCR inflammation panel (inf1)1 used in the SCALLOP consortium seeds the collection.
| 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 |
followed by inclusion of Olink_qPCR for all 12 panels, Olink NGS, Caprion and SWATH-MS panels. SomaScanV4.1 is directly from SomaLogic.
It is of interest to compare some of these,
Figure 2.1: Overlap of Olink Explore HT, SomaScan V4.1 and Caprion
and the latest SomaScan 11K
Figure 2.2: Overlap of Olink Explore HT, SomaScan 11K and Caprion
3 Published data
This associates with the analysis of INTERVAL data as reported by1, which includes the panel SomaScan160410, supplementary tables 4, 6, 18.
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, pQTLdata.sh handles package under Cambridge Service for Data Driven Discovery (CSD3) system, and docs.sh operates with GitHub.
6 URLs
- Cell Carta, https://cellcarta.com/
- EndNote, https://endnote.com/
- ENSEMBL BioMart, https://www.ensembl.org/index.html
- GitHub, https://github.com/
- INTERVAL study, https://www.donorhealth-btru.nihr.ac.uk/studies/interval-study/
- NULISA, https://alamarbio.com/technology/nulisa-platform/
- NCI Proteomic Data Commons, https://pdc.cancer.gov/pdc/browse
- Olink, https://olink.com/ (https://olink.com/resources-support/publications-2/)
- 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 and2 formatted in EndNote.
1.
Sun, B. B. et al. Genomic atlas of the human plasma proteome. Nature 558, 73–79 (2018).
2.
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.