keggPathwayThis database provides KEGG pathway IDs and a pathway description for genes with CCDS IDs. If you would like to annotate variants to these KEGG pathways, you first need to annotate your variants with CCDS IDs. Variant tools databases such as ccdsGene annotates variants with CCDS IDs (see example below).
vtools show annotation keggPathway -v2
Annotation database keggPathway (version 20110823)
Description: kegg pathway for CCDS genes
Database type: attribute
Number of records: 19,584
Reference genome *: ['ccdsId']
Field: ccdsId
Type: string
Comment: CCDS gene ID
Missing entries: 0
Unique entries: 6,949
Field: KgID
Type: string
Comment: Kegg pathway ID
Missing entries: 0
Unique entries: 209
Field: KgDesc
Type: string
Comment: Description of pathway
Missing entries: 0
Unique entries: 209
First we need to use dbNSFP in our project to annotate our variants with CCDS IDs:
vtools use ccdsGene
We then load the keggPathway database linked by ccdsGene.name
% vtools use keggPathway --linked_by ccdsGene.name
INFO: Opening project RA.proj
WARNING: Cannot locate annotation database /Users/bpeng/vtools/ccdsKeggPathway
WARNING: Cannot open annotation database /Users/bpeng/vtools/ccdsKeggPathway
INFO: Downloading annotation database from https://cge.mdanderson.org/~bpeng1/User/annoDB/keggPathway.DB
keggPathway.DB: 100.0% [=====================================>] 252 0.3/s in 00:00:00
INFO: Failed to download database or downloaded database unusable.
INFO: Downloading keggPathway.txt.gz
keggPathway.txt.gz: 100.0% [=====================================>] 107,677 103.0K/s in 00:00:01
INFO: Importing database keggPathway from sourece files ['/var/folders/7O/7OzyfGRoH+i7iQCDzTkba++++TQ/-Tmp-/tmpKqPYoN/keggPathway.txt.gz']
INFO: Importing annotation data from /var/folders/7O/7OzyfGRoH+i7iQCDzTkba++++TQ/-Tmp-/tmpKqPYoN/keggPathway.txt.gz
keggPathway.txt.gz: 100.0% [=====================================>] 11,719 26.8K/s in 00:00:00
INFO: 19584 records handled, 0 ignored.
INFO: Creating indexes (this can take quite a while)
INFO: Using annotation DB keggPathway in project RA.
At the end of vtools show fields output, we can see
keggPathway.ccdsId CCDS gene ID
keggPathway.KgID Kegg pathway ID
keggPathway.KgDesc Description of pathway
Now, we can see which pathways our variants belong to:
vtools output NS_SNV chr pos ref alt genename kgID kgDesc -l 10
INFO: Opening project RA.proj
INFO: Writing output
1 878522 T C NOC2L NA NA
1 899101 G C PLEKHN1 NA NA
1 939471 G A ISG15 hsa04622 RIG-I-like receptor signaling pathway
1 1190055 C G UBE2J2 hsa04120 Ubiquitin mediated proteolysis
1 1190055 C G UBE2J2 hsa05012 Parkinson's disease
1 1216741 C T SCNN1D NA NA
1 1541790 T C MIB2 NA NA
1 1656111 G A SLC35E2 NA NA
1 1675900 G T NADK hsa00760 Nicotinate and nicotinamide metabolism
1 1675900 G T NADK hsa01100 Metabolic pathways
and we can select variants that belong to a pathway, for example,
vtools select NS_SNV 'kgID="hsa00760"' --output chr pos ref alt genename kgDesc
INFO: Opening project RA.proj
INFO: Writing output
1 1675900 G T NADK Metabolic pathways
1 1675900 G T NADK Nicotinate and nicotinamide metabolism
11 70847195 G C NADSYN1 Metabolic pathways
11 70847195 G C NADSYN1 Nicotinate and nicotinamide metabolism
11 70862326 A C NADSYN1 Metabolic pathways
11 70862326 A C NADSYN1 Nicotinate and nicotinamide metabolism
16 29615851 A G QPRT Metabolic pathways
16 29615851 A G QPRT Nicotinate and nicotinamide metabolism
2 18629604 C T NT5C1B Metabolic pathways
2 18629604 C T NT5C1B Nicotinate and nicotinamide metabolism
2 18629604 C T NT5C1B Purine metabolism
2 18629604 C T NT5C1B Pyrimidine metabolism
2 18629604 C T NT5C1B Metabolic pathways
2 18629604 C T NT5C1B Nicotinate and nicotinamide metabolism
2 18629604 C T NT5C1B Purine metabolism
2 18629604 C T NT5C1B Pyrimidine metabolism
2 201242634 A G AOX1 Drug metabolism - cytochrome P450
2 201242634 A G AOX1 Metabolic pathways
2 201242634 A G AOX1 Nicotinate and nicotinamide metabolism
2 201242634 A G AOX1 Tryptophan metabolism
2 201242634 A G AOX1 Tyrosine metabolism
2 201242634 A G AOX1 Valine, leucine and isoleucine degradation
2 201242634 A G AOX1 Vitamin B6 metabolism
4 15318290 G A BST1 Calcium signaling pathway
4 15318290 G A BST1 Metabolic pathways
4 15318290 G A BST1 Nicotinate and nicotinamide metabolism
6 86255952 A G NT5E Metabolic pathways
6 86255952 A G NT5E Nicotinate and nicotinamide metabolism
6 86255952 A G NT5E Purine metabolism
6 86255952 A G NT5E Pyrimidine metabolism
10 104924699 T C NT5C2 Metabolic pathways
10 104924699 T C NT5C2 Nicotinate and nicotinamide metabolism
10 104924699 T C NT5C2 Purine metabolism
10 104924699 T C NT5C2 Pyrimidine metabolism
16 29613945 C T QPRT Metabolic pathways
16 29613945 C T QPRT Nicotinate and nicotinamide metabolism
4 15318350 G A BST1 Calcium signaling pathway
4 15318350 G A BST1 Metabolic pathways
4 15318350 G A BST1 Nicotinate and nicotinamide metabolism
6 132103113 G A ENPP3 Metabolic pathways
6 132103113 G A ENPP3 Nicotinate and nicotinamide metabolism
6 132103113 G A ENPP3 Pantothenate and CoA biosynthesis
6 132103113 G A ENPP3 Purine metabolism
6 132103113 G A ENPP3 Riboflavin metabolism
6 132103113 G A ENPP3 Starch and sucrose metabolism
2 201234575 A G AOX1 Drug metabolism - cytochrome P450
2 201234575 A G AOX1 Metabolic pathways
2 201234575 A G AOX1 Nicotinate and nicotinamide metabolism
2 201234575 A G AOX1 Tryptophan metabolism
2 201234575 A G AOX1 Tyrosine metabolism
2 201234575 A G AOX1 Valine, leucine and isoleucine degradation
2 201234575 A G AOX1 Vitamin B6 metabolism
5 102922572 T C NUDT12 Nicotinate and nicotinamide metabolism
5 102922572 T C NUDT12 Peroxisome
14 20010446 G A PNP Metabolic pathways
14 20010446 G A PNP Nicotinate and nicotinamide metabolism
14 20010446 G A PNP Purine metabolism
14 20010446 G A PNP Pyrimidine metabolism
2 18629637 G T NT5C1B Metabolic pathways
2 18629637 G T NT5C1B Nicotinate and nicotinamide metabolism
2 18629637 G T NT5C1B Purine metabolism
2 18629637 G T NT5C1B Pyrimidine metabolism
2 18629637 G T NT5C1B Metabolic pathways
2 18629637 G T NT5C1B Nicotinate and nicotinamide metabolism
2 18629637 G T NT5C1B Purine metabolism
2 18629637 G T NT5C1B Pyrimidine metabolism
11 70869465 C T NADSYN1 Metabolic pathways
11 70869465 C T NADSYN1 Nicotinate and nicotinamide metabolism
5 43691831 C T NNT Metabolic pathways
5 43691831 C T NNT Nicotinate and nicotinamide metabolism
1 1675941 G A NADK Metabolic pathways
1 1675941 G A NADK Nicotinate and nicotinamide metabolism
6 86255962 T C NT5E Metabolic pathways
6 86255962 T C NT5E Nicotinate and nicotinamide metabolism
6 86255962 T C NT5E Purine metabolism
6 86255962 T C NT5E Pyrimidine metabolism
4 15389158 C T CD38 Calcium signaling pathway
4 15389158 C T CD38 Hematopoietic cell lineage
4 15389158 C T CD38 Metabolic pathways
4 15389158 C T CD38 Nicotinate and nicotinamide metabolism
11 70870707 G A NADSYN1 Metabolic pathways
11 70870707 G A NADSYN1 Nicotinate and nicotinamide metabolism
5 43736078 A G NNT Metabolic pathways
5 43736078 A G NNT Nicotinate and nicotinamide metabolism
11 70886273 G A NADSYN1 Metabolic pathways
11 70886273 G A NADSYN1 Nicotinate and nicotinamide metabolism
17 70638943 G A NT5C Metabolic pathways
17 70638943 G A NT5C Nicotinate and nicotinamide metabolism
17 70638943 G A NT5C Purine metabolism
17 70638943 G A NT5C Pyrimidine metabolism
9 76873744 T G C9orf95 Nicotinate and nicotinamide metabolism
6 132086873 A G ENPP3 Metabolic pathways
6 132086873 A G ENPP3 Nicotinate and nicotinamide metabolism
6 132086873 A G ENPP3 Pantothenate and CoA biosynthesis
6 132086873 A G ENPP3 Purine metabolism
6 132086873 A G ENPP3 Riboflavin metabolism
6 132086873 A G ENPP3 Starch and sucrose metabolism
The result of the above example can be confusing because the output displays multiple pathways, not only the one we specified. The reason is that this query is identifying variants in your specified pathway and then it generates a report of these variants with all the pathways that they might be in. Genes often belong to multiple pathways. You can filter the output again, or output only the variant information (chromosome, position) if you would like to get a list of unique variants.