vignettes/simple_ex_gene_info.Rmd
simple_ex_gene_info.Rmd
We demonstrate these associations which correspond to tabs from Monarch Initiative website that result from a search at the website for the human gene NCBIGene:8314.
(DT is the datatables package which we use to display the results. knitr includes kable, another way to generate tables.)
library(monarchr)
library(DT)
library(knitr)
gene <- "NCBIGene:8314"Homologs of gene, displayed using DataTable.
homs <- bioentity_homologs(gene)
datatable(homs$homologs)Diseases associated with gene, displayed using kable.
Note, the publications look clickable, but are not. This is a bug in the formatting. They are meant to be raw text.
dis <- bioentity_diseases_assoc_w_gene(gene)
kable(dis$diseases)| subject.taxon | subject.id | subject | relation | object | object.id | object.taxon | evidence | publications | provided_by |
|---|---|---|---|---|---|---|---|---|---|
| Homo sapiens | HGNC:950 | BAP1 | is marker for | lipoma | MONDO:0005106 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | leukemia (disease) | MONDO:0005059 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | bone cancer | MONDO:0002129 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | epithelioid and spindle cell nevus | MONDO:0006749 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | testicular cancer | MONDO:0005447 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | meningioma (disease) | MONDO:0016642 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | has phenotype | uveal melanoma | MONDO:0006486 | NA | traceable author statement, imported manually asserted information used in automatic assertion | PMID:25231345, PMID:26719535, PMID:21874000 | ctd, orphanet |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | malignant mesothelioma (disease) | MONDO:0006292 | NA | traceable author statement | PMID:25231345, PMID:26463840, PMID:29112861, PMID:26928227, PMID:24928783 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | neuroendocrine carcinoma | MONDO:0002120 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | lung adenocarcinoma | MONDO:0005061 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | mesothelioma | MONDO:0005065 | NA | traceable author statement | PMID:26119930, PMID:26719535, PMID:21874000, PMID:21642991 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | mucoepidermoid carcinoma | MONDO:0003036 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | central nervous system cancer | MONDO:0002714 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | kidney cancer | MONDO:0002367 | NA | traceable author statement | PMID:26719535 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | colonic neoplasm | MONDO:0005401 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | paraganglioma | MONDO:0000448 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | renal cell carcinoma (disease) | MONDO:0005086 | NA | traceable author statement | PMID:25231345, PMID:23797736, PMID:22683710, PMID:22138691 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | pancreatic neoplasm | MONDO:0021040 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | likely_pathogenic_for_condition | BAP1-related tumor predisposition syndrome | MONDO:0013692 | NA | imported manually asserted information used in automatic assertion, sequencing assay evidence | PMID:21941004, PMID:23684012, PMID:21874000, PMID:21874003 | omim, ctd, orphanet, clinvar |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | gastric neoplasm | MONDO:0021085 | NA | traceable author statement | PMID:25231345, PMID:26719535 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | contributes to | familial melanoma | MONDO:0018961 | NA | imported manually asserted information used in automatic assertion | NA | orphanet |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | cholangiocarcinoma | MONDO:0019087 | NA | traceable author statement | PMID:25231345, PMID:24185509 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | ovarian cancer | MONDO:0008170 | NA | traceable author statement | PMID:25231345 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | nasopharyngeal carcinoma | MONDO:0015459 | NA | traceable author statement | PMID:24952746 | ctd |
| Homo sapiens | HGNC:950 | BAP1 | is marker for | uterine cancer | MONDO:0002715 | NA | traceable author statement | PMID:25231345 | ctd |
Phenotypes associated with gene, displayed using kable.
Note, the publications look clickable, but are not. This is a bug in the formatting. They are meant to be raw text.
phe <- bioentity_phenotypes_assoc_w_gene(gene)
kable(head(phe$phenotypes))| subject.taxon | subject.id | subject | relation | object | object.id | object.taxon | evidence | publications | provided_by |
|---|---|---|---|---|---|---|---|---|---|
| Homo sapiens | HGNC:950 | BAP1 | has phenotype | Metamorphopsia | HP:0012508 | NA | traceable author statement used in manual assertion, imported manually asserted information used in automatic assertion | NA | hpoa, orphanet |
| Homo sapiens | HGNC:950 | BAP1 | has phenotype | Zonular cataract | HP:0010920 | NA | traceable author statement used in manual assertion, imported manually asserted information used in automatic assertion | NA | hpoa, orphanet |
| Homo sapiens | HGNC:950 | BAP1 | has phenotype | Intraocular melanoma | HP:0007716 | NA | evidence used in automatic assertion, imported manually asserted information used in automatic assertion, sequencing assay evidence | PMID:21941004, PMID:23684012, PMID:21874000, PMID:21874003 | omim, hpoa, orphanet, clinvar |
| Homo sapiens | HGNC:950 | BAP1 | has phenotype | Mydriasis | HP:0011499 | NA | traceable author statement used in manual assertion, imported manually asserted information used in automatic assertion | NA | hpoa, orphanet |
| Homo sapiens | HGNC:950 | BAP1 | has phenotype | Choroidal melanoma | HP:0012054 | NA | traceable author statement used in manual assertion, imported manually asserted information used in automatic assertion | NA | hpoa, orphanet |
| Homo sapiens | HGNC:950 | BAP1 | has phenotype | Ocular pain | HP:0200026 | NA | traceable author statement used in manual assertion, imported manually asserted information used in automatic assertion | NA | hpoa, orphanet |
Anatomy associated with gene, displayed using kable.
Molecularly defined by expression data?
anat <- bioentity_exp_anatomy_assoc_w_gene(gene)
kable(head(anat$anatomy))| subject.taxon | subject.id | subject | relation | object | object.id | object.taxon | evidence | publications | provided_by |
|---|---|---|---|---|---|---|---|---|---|
| Homo sapiens | HGNC:950 | BAP1 | expressed in | vastus lateralis | UBERON:0001379 | NA | NA | NA | bgee |
| Homo sapiens | HGNC:950 | BAP1 | expressed in | central nervous system | UBERON:0001017 | NA | NA | NA | bgee |
| Homo sapiens | HGNC:950 | BAP1 | expressed in | nucleus accumbens | UBERON:0001882 | NA | NA | NA | bgee |
| Homo sapiens | HGNC:950 | BAP1 | expressed in | layer of synovial tissue | UBERON:0007616 | NA | NA | NA | bgee |
| Homo sapiens | HGNC:950 | BAP1 | expressed in | paraflocculus | UBERON:0005351 | NA | NA | NA | bgee |
| Homo sapiens | HGNC:950 | BAP1 | expressed in | Brodmann (1909) area 46 | UBERON:0006483 | NA | NA | NA | bgee |
Pathways associated with gene, displayed using kable.
pth <- bioentity_pathways_assoc_w_gene(gene)
kable(pth$pathways)| subject.taxon | subject.id | subject | relation | object | object.id | object.taxon | evidence | publications | provided_by |
|---|---|---|---|---|---|---|---|---|---|
| Homo sapiens | HGNC:950 | BAP1 | involved in | UCH proteinases | REACT:R-HSA-5689603 | NA | traceable author statement used in manual assertion | NA | ctd, reactome |
| Homo sapiens | HGNC:950 | BAP1 | involved in | Post-translational protein modification | REACT:R-HSA-597592 | NA | NA | NA | ctd |
| Homo sapiens | HGNC:950 | BAP1 | involved in | Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks | REACT:R-HSA-5693565 | NA | traceable author statement used in manual assertion | NA | ctd, reactome |
| Homo sapiens | HGNC:950 | BAP1 | involved in | Deubiquitination | REACT:R-HSA-5688426 | NA | NA | NA | ctd |
| Homo sapiens | HGNC:950 | BAP1 | involved in | Metabolism of proteins | REACT:R-HSA-392499 | NA | NA | NA | ctd |
| Homo sapiens | HGNC:950 | BAP1 | involved in | DNA Repair | REACT:R-HSA-73894 | NA | NA | NA | ctd |
| Homo sapiens | HGNC:950 | BAP1 | involved in | DNA Double Strand Break Response | REACT:R-HSA-5693606 | NA | NA | NA | ctd |
| Homo sapiens | HGNC:950 | BAP1 | involved in | DNA Double-Strand Break Repair | REACT:R-HSA-5693532 | NA | NA | NA | ctd |
Interactions associated with gene, displayed using kable.
Note, the publications look clickable, but are not. This is a bug in the formatting. They are meant to be raw text.
intx <- bioentity_interactions_assoc_w_gene(gene)
kable(head(intx$interactions))| subject.taxon | subject.id | subject | relation | object | object.id | object.taxon | evidence | publications | provided_by |
|---|---|---|---|---|---|---|---|---|---|
| Homo sapiens | HGNC:950 | BAP1 | interacts with | IPO4 | HGNC:19426 | Homo sapiens | affinity chromatography evidence | PMID:19615732 | biogrid |
| Homo sapiens | HGNC:950 | BAP1 | interacts with | USP28 | HGNC:12625 | Homo sapiens | enzyme assay evidence | PMID:22626734 | biogrid |
| Homo sapiens | HGNC:950 | BAP1 | interacts with | MAP3K1 | HGNC:6848 | Homo sapiens | enzyme assay evidence | PMID:25260751 | biogrid |
| Homo sapiens | HGNC:950 | BAP1 | interacts with | XRCC3 | HGNC:12830 | Homo sapiens | yeast 2-hybrid evidence | PMID:25640309 | biogrid |
| Homo sapiens | HGNC:950 | BAP1 | interacts with | PSMB2 | HGNC:9539 | Homo sapiens | NA | NA | string |
| Homo sapiens | HGNC:950 | BAP1 | interacts with | AHCYL2 | HGNC:22204 | Homo sapiens | affinity chromatography evidence | PMID:19615732 | biogrid |