GREAT Input: Genomic Regions Enrichment of Annotations Tool, Bejerano Lab, Stanford University

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Bejerano Lab, Stanford University

Warning: Your set hits a large fraction of the genes in the genome, which often does not work well with the GREAT Significant by Both view due to a saturation of the gene-based hypergeometric test.
See our tips for handling large datasets or try the Significant By Region-based Binomial view.

Job Description

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Job ID:

20240419-public-4.0.4-uXx53c

Display name:

Test set:

SilencerDB: Silencers_Homo_sapiens_HeLa-S3 (16,038 genomic regions)

Show in UCSC genome browser. How do I look at my regions in the genome?

Background:

Whole genome background

Assembly:

Human: GRCh37 (UCSC hg19, Feb. 2009) What gene set does GREAT use?

Associated genomic regions:

Basal+extension (constitutive 5.0 kb upstream and 1.0 kb downstream, up to 1000.0 kb max extension). Curated regulatory domains are included.

696 of all 16,038 genomic regions (4.3%) are not associated with any genes.

View all genomic region-gene associations. Which genes are my regions associated with?

Revise the region-gene association rule. How are my regions associated with genes?

Region-Gene Association Graphs

Region-gene association graphs:

What do these graphs illustrate?

Number of associated genes per region

Download as PDF.

Binned by orientation and distance to TSS

Download as PDF.

Binned by absolute distance to TSS

Download as PDF.

Global Controls Which data is exported by each option?

Ontologies

GO

Phenotype

Genes

GO Molecular Function

Mouse Phenotype

Ensembl Genes

GO Biological Process

Mouse Phenotype Single KO

GO Cellular Component

Human Phenotype

Click a link above to jump to the corresponding table.

What data does each ontology provide?

Can I use other ontologies?

Columns

General

Ontology Term ID

Binomial over Regions

Rank

Raw P-Value

Bonferroni P-Value

FDR Q-Value

Fold Enrichment (Obs/Exp)

Expected (n * p)

Observed Region Hits (k)

Genome Fraction (p)

Region Set Coverage (k/n)

Hypergeometric over Genes

Rank

Raw P-Value

Bonferroni P-Value

FDR Q-Value

Fold Enrichment (Obs/Exp)

Expected (n * K/N)

Observed Gene Hits (k)

Total Genes (K)

Gene Set Coverage (k/n)

Term Gene Coverage (k/K)

Click on a link above to sort all tables by the named column.

What do each of the columns mean?

Top Rows/Table

Minimum Region-based Fold Enrichment

Observed Gene Hits

Term Name Filter

Where is my term?

Term Annotation Count

Min: Max:
What is the term annotation count?

Statistical Significance

Raw P-Value Bonferroni FDR Threshold:
Significant P-Values are bold in the tables below.
Terms are bold when significant by both binomial and hypergeometric tests.
Which statistics does GREAT provide?

View

Significant By Both Significant By Region-based Binomial Ignore statistical significance
Which view should I use?

Results per-ontology

Click the term name to see a term definition and the regions and genes in your set that hit the term.
Use "Export > Shown ontology data as HTML" to view the displayed ontology data in a simple format optimized for reading.
Use "Export > Shown ontology data as .tsv" to download the displayed ontology data for further processing.
Use "Export > All ontology data as .tsv" to download all ontology data for further processing. This includes hidden rows and columns and the genes and regions that hit each term.

Ensembl Genes (no terms) Global controls

Table controls: Shown top rows in this table: Term annotation count: Min: Max: Visualize this table:

The test set of 16,038 genomic regions picked 8,893 (48%) of all 18,549 genes.
Ensembl Genes has 18,549 terms covering 18,549 (100%) of all 18,549 genes, and 18,549 term - gene associations.

18,549 ontology terms (100%) were tested using an annotation count range of [1, Inf].

GO Biological Process (no terms) Global controls

Table controls: Shown top rows in this table: Term annotation count: Min: Max: Visualize this table:

The test set of 16,038 genomic regions picked 8,893 (48%) of all 18,549 genes.
GO Biological Process has 13,145 terms covering 16,621 (90%) of all 18,549 genes, and 1,251,831 term - gene associations.

13,145 ontology terms (100%) were tested using an annotation count range of [1, Inf].

GO Cellular Component (no terms) Global controls

Table controls: Shown top rows in this table: Term annotation count: Min: Max: Visualize this table:

The test set of 16,038 genomic regions picked 8,893 (48%) of all 18,549 genes.
GO Cellular Component has 1,726 terms covering 17,726 (96%) of all 18,549 genes, and 380,581 term - gene associations.

1,726 ontology terms (100%) were tested using an annotation count range of [1, Inf].

GO Molecular Function (no terms) Global controls

Table controls: Shown top rows in this table: Term annotation count: Min: Max: Visualize this table:

The test set of 16,038 genomic regions picked 8,893 (48%) of all 18,549 genes.
GO Molecular Function has 4,219 terms covering 16,545 (89%) of all 18,549 genes, and 229,089 term - gene associations.

4,219 ontology terms (100%) were tested using an annotation count range of [1, Inf].

Human Phenotype (no terms) Global controls

Table controls: Shown top rows in this table: Term annotation count: Min: Max: Visualize this table:

The test set of 16,038 genomic regions picked 8,893 (48%) of all 18,549 genes.
Human Phenotype has 6,672 terms covering 3,411 (18%) of all 18,549 genes, and 256,883 term - gene associations.

6,672 ontology terms (100%) were tested using an annotation count range of [1, Inf].

Mouse Phenotype Single KO (no terms) Global controls

Table controls: Shown top rows in this table: Term annotation count: Min: Max: Visualize this table:

The test set of 16,038 genomic regions picked 8,893 (48%) of all 18,549 genes.
Mouse Phenotype Single KO has 9,149 terms covering 9,408 (51%) of all 18,549 genes, and 554,948 term - gene associations.

9,149 ontology terms (100%) were tested using an annotation count range of [1, Inf].

Mouse Phenotype (no terms) Global controls

Table controls: Shown top rows in this table: Term annotation count: Min: Max: Visualize this table:

The test set of 16,038 genomic regions picked 8,893 (48%) of all 18,549 genes.
Mouse Phenotype has 9,554 terms covering 9,592 (52%) of all 18,549 genes, and 709,451 term - gene associations.

9,554 ontology terms (100%) were tested using an annotation count range of [1, Inf].

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