About keggPathway

This 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).

Fields

  • ccdsId CCDS gene ID
  • KgID Kegg pathway ID
  • KgDesc Description of pathway

keggPathway

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

Examples

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.