Case 4: Target molecule information at KEGG

Starting from a target molecule name, this walkthrough finds the encoding gene and then explores its orthology group, pathways and associated drugs.

1. Find the gene for a target molecule

kegg_find with the genes database searches gene names and descriptions. A popular target such as CD19 matches many organisms, so we show only the first few hits:

genes = KEGGAPI.kegg_find("genes", "CD19")
first(DataFrame(genes.data, genes.colnames), 5)

5×2 DataFrame

Row	ID	Details
	String	String
1	hsa:1233	CCR4, CC-CKR-4, CD194, CKR4, CMKBR4, ChemR13, HGCN:14099, K5-5; C-C chemokine receptor type 4
2	hsa:1230	CCR1, CD191, CKR-1, CKR1, CMKBR1, HM145, MIP1aR, SCYAR1; C-C chemokine receptor type 1
3	hsa:1232	CCR3, C C CKR3, CC-CKR-3, CD193, CKR 3, CKR3, CMKBR3; C-C chemokine receptor type 3 isoform 1
4	hsa:729230	CCR2, CC-CKR-2, CCR-2, CCR2A, CCR2B, CD192, CKR2, CKR2A, CKR2B, CMKBR2, MCP-1-R, PCLUD; C-C chemokine receptor type 2 isoform A
5	hsa:1234	CCR5, CC-CKR-5, CCCKR5, CCR-5, CD195, CKR-5, CKR5, CMKBR5, IDDM22; C-C chemokine receptor type 5

2. Gene entry and orthology group

Retrieve the full entry for the human gene with kegg_get:

gene = KEGGAPI.kegg_get("hsa:930")
println(join(first(split(gene.data, "\n"), 8), "\n"))

ENTRY       930               CDS       T01001
SYMBOL      CD19, B4, CVID3
NAME        (RefSeq) B-lymphocyte antigen CD19 isoform 2 precursor
ORTHOLOGY   K06465  B-lymphocyte antigen CD19
ORGANISM    hsa  Homo sapiens (human)
PATHWAY     hsa04151  PI3K-Akt signaling pathway
            hsa04640  Hematopoietic cell lineage
            hsa04662  B cell receptor signaling pathway

Its orthology (KO) group via kegg_link:

ko = KEGGAPI.kegg_link("ko", "hsa:930")
DataFrame(ko.data, ko.colnames)

1×2 DataFrame

Row	Target ID	Source ID
	String	String
1	hsa:930	ko:K06465

3. Pathways involving the molecule

paths = KEGGAPI.kegg_link("pathway", "hsa:930")
DataFrame(paths.data, paths.colnames)

5×2 DataFrame

Row	Target ID	Source ID
	String	String
1	hsa:930	path:hsa04151
2	hsa:930	path:hsa04640
3	hsa:930	path:hsa04662
4	hsa:930	path:hsa05169
5	hsa:930	path:hsa05340

4. Drugs associated with the molecule

drugs = KEGGAPI.kegg_link("drug", "hsa:930")
DataFrame(drugs.data, drugs.colnames)

15×2 DataFrame

Row	Target ID	Source ID
	String	String
1	hsa:930	dr:D09325
2	hsa:930	dr:D11144
3	hsa:930	dr:D11231
4	hsa:930	dr:D11232
5	hsa:930	dr:D11333
6	hsa:930	dr:D11338
7	hsa:930	dr:D11372
8	hsa:930	dr:D11386
9	hsa:930	dr:D11496
10	hsa:930	dr:D11601
11	hsa:930	dr:D11757
12	hsa:930	dr:D11880
13	hsa:930	dr:D11990
14	hsa:930	dr:D13022
15	hsa:930	dr:D13301

Retrieve information on the associated drugs by passing their identifiers (the second column of drugs.data) to kegg_get:

drug_info = KEGGAPI.kegg_get(drugs.data[2])
println(join(first(split(drug_info.data[1], "\n"), 6), "\n"))

ENTRY       D09325                      Drug
NAME        Blinatumomab (USAN/INN);
            Blinatumomab (genetical recombination) (JAN);
            Blincyto (TN)
PRODUCT     BLINCYTO (Amgen)
FORMULA     C2367H3577N649O772S19

5. Download a pathway map

img = KEGGAPI.kegg_get("hsa04151", :image)
open("hsa04151.png", "w") do io
    write(io, img.data)
end