open_targets.enhancer_to_gene

Python

In [1]:

import bedrock_bio as bb

rel = bb.load_table('open_targets.enhancer_to_gene')

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()

Out[1]:

	biosampleId	geneId	chromosome	start	end	score	distanceToTss	resourceScore	datasourceId	intervalType	pmid	biosampleName	biosampleFromSourceId	studyId	intervalId	qualityControls	version
0	UBERON_0002113	ENSG00000225880	1	778366	778866	0.645834	48930	[{'name': 'DNase', 'value': 0.3081870079040527...	E2G	intergenic	38014075	right kidney	None	ENCFF229GDZ	c89213ff6f21bcc0326986caac60b8d7	[]	26.09
1	UBERON_0002113	ENSG00000228794	1	778366	778866	0.645622	48436	[{'name': 'DNase', 'value': 0.3081870079040527...	E2G	intergenic	38014075	right kidney	None	ENCFF229GDZ	748ef7c3f98edabfe1e55712a3ba04fe	[]	26.09
2	UBERON_0000948	ENSG00000225880	1	778387	778887	0.616550	48909	[{'name': 'DNase', 'value': 0.3358170092105865...	E2G	intergenic	38014075	heart	None	ENCFF456GKR	dfce4cd3c651c52a07e2e5715690238a	[]	26.09
3	UBERON_0000948	ENSG00000228794	1	778387	778887	0.616328	48415	[{'name': 'DNase', 'value': 0.3358170092105865...	E2G	intergenic	38014075	heart	None	ENCFF456GKR	b9dc57a966e02f67df21c06f831522ff	[]	26.09
4	UBERON_0002167	ENSG00000177757	1	778391	778891	0.756075	38472	[{'name': 'DNase', 'value': 0.3528980016708374...	E2G	intergenic	38014075	right lung	None	ENCFF895IZT	80dc5ccf1cedf3212f42eba911054a44	[]	26.09

R

In [1]:

library(bedrockbio)

lf <- load_table("open_targets.enhancer_to_gene")
df <- head(lf, 5) |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 17 columns)
   biosampleId    | geneId          | chromosome | start  | end    | score              | distanceToTss | datasourceId
   -------------- | --------------- | ---------- | ------ | ------ | ------------------ | ------------- | ------------
0  UBERON_0002113 | ENSG00000225880 | 1          | 778366 | 778866 | 0.645833630694996  | 48930         | E2G
1  UBERON_0002113 | ENSG00000228794 | 1          | 778366 | 778866 | 0.645621568911758  | 48436         | E2G
2  UBERON_0000948 | ENSG00000225880 | 1          | 778387 | 778887 | 0.6165499062332747 | 48909         | E2G
3  UBERON_0000948 | ENSG00000228794 | 1          | 778387 | 778887 | 0.6163281621504378 | 48415         | E2G
4  UBERON_0002167 | ENSG00000177757 | 1          | 778391 | 778891 | 0.7560746769154826 | 38472         | E2G

Description

Genomic regions associated with genes based on epigenetics evidence [Target, Genetics]

Partitions

Not partitioned.

Schema

Column	Type	Description
biosampleId	TEXT	Identifier of the biosample in where the interval was discovered in
geneId	TEXT	Ensembl gene identifier of the target the interval is linked with [bioregistry:ensembl]
chromosome	TEXT	Chromosome the interval is located on
start	BIGINT	Basepair position of the interval start
end	BIGINT	Basepair position of the interval end
score	DOUBLE	Interval evidence score from the datasource, higher values indicate stronger support linking the interval to its target gene
distanceToTss	INT	Distance of the interval from the transcription start site of the gene
resourceScore	STRUCT(name TEXT, value FLOAT)[]	List of contributing score components
datasourceId	TEXT	Identifier of the interval datasource
intervalType	TEXT	Type of the interval
pmid	TEXT	Pubmed identifier of the publication that reported the interval data
biosampleName	TEXT	Name of the cell type/anatomical unit the interval was identified in
biosampleFromSourceId	TEXT	Original identifier of the cell type/anatomical unit the interval was identified in
studyId	TEXT	Identifier of the interval study
intervalId	TEXT	Identifier of the interval
qualityControls	TEXT[]	Quality control flags for this interval
version	TEXT	Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.