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

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Bejerano Lab, Stanford University

Job Description

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Job ID:

20240416-public-4.0.4-j5sOOO

Display name:

Test set:

SilencerDB: Silencers_Mus_musculus_Pancreas (2 genomic regions)

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

Background:

Whole genome background

Assembly:

Mouse: NCBI build 37 (UCSC mm9, Jul. 2007) 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.

0 of all 2 genomic regions (0%) 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 2 genomic regions picked 2 (0%) of all 19,996 genes.
Ensembl Genes has 19,996 terms covering 19,996 (100%) of all 19,996 genes, and 19,996 term - gene associations.

19,996 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 2 genomic regions picked 2 (0%) of all 19,996 genes.
GO Biological Process has 13,065 terms covering 16,916 (85%) of all 19,996 genes, and 1,132,266 term - gene associations.

13,065 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 2 genomic regions picked 2 (0%) of all 19,996 genes.
GO Cellular Component has 1,690 terms covering 18,017 (90%) of all 19,996 genes, and 358,956 term - gene associations.

1,690 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 2 genomic regions picked 2 (0%) of all 19,996 genes.
GO Molecular Function has 4,127 terms covering 16,278 (81%) of all 19,996 genes, and 219,672 term - gene associations.

4,127 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 2 genomic regions picked 2 (0%) of all 19,996 genes.
Human Phenotype has 6,586 terms covering 3,198 (16%) of all 19,996 genes, and 243,974 term - gene associations.

6,586 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 2 genomic regions picked 2 (0%) of all 19,996 genes.
Mouse Phenotype Single KO has 9,160 terms covering 9,393 (47%) of all 19,996 genes, and 548,017 term - gene associations.

9,160 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 2 genomic regions picked 2 (0%) of all 19,996 genes.
Mouse Phenotype has 9,567 terms covering 9,580 (48%) of all 19,996 genes, and 700,827 term - gene associations.

9,567 ontology terms (100%) were tested using an annotation count range of [1, Inf].

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