Component: GOEnrichment

GOEnrichment

Computes enriched GO terms in a set of genes or proteins. Enrichment analysis is done using Fisher's Exact Test. Fisher's test compares the observed frequency of each present GO term to the frequency in a reference gene/protein set. A GO term is present if some input gene/protein is annotated with the GO term or its descendants.

Genome-wide reference sets are provided for six organisms (see the parameter organism). If the study is not a genome-wide study (e.g. a microarray with only 25% of total genes), it is better to use a custom reference table, given as the enrichmentTable input. Custom tables are computed with GOProbabilityTable.

The component also computes adjusted p-values using FDR (Benjamini and Hochberg, 1995). For other multiple comparison correction methods, see MultipleComparisonCorrection. However, note that multiple comparison correction might not work well with GO enrichment analysis since a large number of statistical tests are done and no effort is done to reduce the number of tests.

Visualization of enriched GO terms is created in GraphML format. There is one network for each GO ontology. Nodes can be colorized according to the p-value. Colors have a base 10 logarithmic scale, i.e. p-values 1, 0.1 and 0.01 are equally distant from each other. Nodes contain a URL hyperlink to a description of the GO term in the geneontology.org site by default.

Version	1.0.4
Bundle	microarray
Categories	GO
Authors	Kristian Ovaska (kristian.ovaska@helsinki.fi), Marko Laakso (Marko.Laakso@Helsinki.FI)
Issue tracker	View/Report issues
Requires	csbl.go (R-package) ; igraph (R-package) ; installer (bash)
Source files	component.xml GOEnrichment.r
Usage	Example with default values GOEnrichment( goAnnotations = CSV, //enrichmentTable = CSV, colorEnd = "#ff0000", colorMiddle = "", colorMinP = 0.0001, colorStart = "#ffffff", filterFDR = false, filterParents = true, includeGraphAttributes = true, maxEdgeWidth = 10, maxFrequency = 999999, maxPriori = 1.00, minFrequency = 1, organism = 9606, threshold = 0.05, urlPattern = "http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=%s" )

Version

1.0.4

Bundle

microarray

Categories

Authors

Kristian Ovaska (kristian.ovaska@helsinki.fi), Marko Laakso (Marko.Laakso@Helsinki.FI)

Issue tracker

View/Report issues

Requires

csbl.go (R-package) ; igraph (R-package) ; installer (bash)

Source files

component.xml GOEnrichment.r

Usage

Example with default values

Inputs

Name	Type	Mandatory	Description
goAnnotations	CSV	Mandatory	GO annotations for genes or proteins. GO terms are searched using a regular expression, so the format is very flexible. Each row is considered as a distinct gene or protein.
enrichmentTable	CSV	Optional	Custom GO probability reference table that is used in enrichment computation. If this is not given, a built-in table for a given organism is used (see the parameter organism). Probability tables can be created with GOProbabilityTable component. The table must have columns "goid" (GO accession number with GO: prefix), "prob" (probability of observing the GO term in a random gene product) and "ontology" (one of CC, BP, MF).

Name

Type

Mandatory

Description

goAnnotations

CSV

Mandatory

GO annotations for genes or proteins. GO terms are searched using a regular expression, so the format is very flexible. Each row is considered as a distinct gene or protein.

enrichmentTable

CSV

Optional

Custom GO probability reference table that is used in enrichment computation. If this is not given, a built-in table for a given organism is used (see the parameter organism). Probability tables can be created with GOProbabilityTable component. The table must have columns "goid" (GO accession number with GO: prefix), "prob" (probability of observing the GO term in a random gene product) and "ontology" (one of CC, BP, MF).

Outputs

Name	Type	Description
goTerms	CSV	Enriched GO terms. The list is sorted by corrected p-values if filterFDR is true and by raw p-values otherwise. The following columns are present: GOID; Frequency (number of genes that match the term); Proportion (relative frequency, in the set of IDs that have some annotation in the same ontology); PValue (raw p-value); Priori (relative frequency in the reference set); PValueCorrected (multiple hypotheses corrected p-values); Ontology (one of BP, CC, MF); Description; IDs (list of genes that match the GO term).
graphBP	GraphML	The network of enriched GO terms from the biological process ontology in GraphML format. The network can be rendered using GraphVisualizer.
graphCC	GraphML	The network of enriched GO terms from the cellular component ontology in GraphML format. The network can be rendered using GraphVisualizer.
graphMF	GraphML	The network of enriched GO terms from the molecular function ontology in GraphML format. The network can be rendered using GraphVisualizer.

Name

Type

Description

goTerms

CSV

Enriched GO terms. The list is sorted by corrected p-values if filterFDR is true and by raw p-values otherwise. The following columns are present: GOID; Frequency (number of genes that match the term); Proportion (relative frequency, in the set of IDs that have some annotation in the same ontology); PValue (raw p-value); Priori (relative frequency in the reference set); PValueCorrected (multiple hypotheses corrected p-values); Ontology (one of BP, CC, MF); Description; IDs (list of genes that match the GO term).

graphBP

GraphML

The network of enriched GO terms from the biological process ontology in GraphML format. The network can be rendered using GraphVisualizer.

graphCC

GraphML

The network of enriched GO terms from the cellular component ontology in GraphML format. The network can be rendered using GraphVisualizer.

graphMF

GraphML

The network of enriched GO terms from the molecular function ontology in GraphML format. The network can be rendered using GraphVisualizer.

Parameters

Name	Type	Default	Description
colorEnd	string	"#ff0000"	When colorizing GO graphs, this is the color of a node with a minimally low p-value. The threshold depends on the colorMinP parameter. All nodes with p-value less than the threshold also get this color.
colorMiddle	string	""	When colorizing GO graphs, this is a color between the two extreme colors. This allows to create color slides between three colors. If the value is empty, a color slide with two colors is used.
colorMinP	float	0.0001	When colorizing GO graphs, all nodes with p-value below this get the color given with color colorEnd. If the value is 0, the node with the smallest p-value gets the color colorEnd, i.e. the color range is scaled using the p-values present in the data.
colorStart	string	"#ffffff"	When colorizing GO graphs, this is the color of a node with p-value 1. Setting this to empty disables node coloring.
filterFDR	boolean	false	If true, use FDR-corrected p-values for filtering (column: pvalueCorrected). Otherwise, use raw p-values (colum: pvalue).
filterParents	boolean	true	if true, then a GO term is excluded from the result if a child of the term has occurred higher in the list (with a lower p-value).
includeGraphAttributes	boolean	true	If true, frequency and p-value of each GO term is included in the graph.
maxEdgeWidth	float	10	Maximum edge line width in the graphs, in points. Edge widths are computed based on the frequency of the target node so that nodes with a large number of annotations have wide in-coming edges. Setting this to 1 gives the same width for all edges.
maxFrequency	int	999999	For output GO terms, maximum number of gene products that are annotated with the given term. GO terms are filtered from the output if their associated frequency is above this threshold. Filtering is done before FDR correction.
maxPriori	float	1.00	Maximum value of the priori probability that can be accepted for a GO term. Filtering is done before FDR correction.
minFrequency	int	1	For output GO terms, minimum number of gene products that are annotated with the given term. GO terms are filtered from the output if their associated frequency is below this threshold. Filtering is done before FDR correction.
organism	int	9606	NCBI taxonomy ID for the organism whose gene set is used for GO probabilities. This is used if the input enrichmentTable is not given. Supported organisms: Homo sapiens: 9606, Saccharomyces cerevisiae: 4932, Caenorhabditis elegans: 6239, Drosophila melanogaster: 7227, Mus musculus: 10090, Rattus norvegicus: 10116.
threshold	float	0.05	P-value threshold for filtering GO terms.
urlPattern	string	"http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=%s"	A printf-like pattern for creating a URL for a GO term. The pattern must contain one %s string that is expanded with the GO term in question, e.g. GO:0005575. If the value is empty, no hyperlinks are created in graphs.

Name

Type

Default

Description

colorEnd

string

"#ff0000"

When colorizing GO graphs, this is the color of a node with a minimally low p-value. The threshold depends on the colorMinP parameter. All nodes with p-value less than the threshold also get this color.

colorMiddle

string

When colorizing GO graphs, this is a color between the two extreme colors. This allows to create color slides between three colors. If the value is empty, a color slide with two colors is used.

colorMinP

float

0.0001

When colorizing GO graphs, all nodes with p-value below this get the color given with color colorEnd. If the value is 0, the node with the smallest p-value gets the color colorEnd, i.e. the color range is scaled using the p-values present in the data.

colorStart

string

"#ffffff"

When colorizing GO graphs, this is the color of a node with p-value 1. Setting this to empty disables node coloring.

filterFDR

boolean

false

If true, use FDR-corrected p-values for filtering (column: pvalueCorrected). Otherwise, use raw p-values (colum: pvalue).

filterParents

boolean

true

if true, then a GO term is excluded from the result if a child of the term has occurred higher in the list (with a lower p-value).

includeGraphAttributes

boolean

true

If true, frequency and p-value of each GO term is included in the graph.

maxEdgeWidth

float

Maximum edge line width in the graphs, in points. Edge widths are computed based on the frequency of the target node so that nodes with a large number of annotations have wide in-coming edges. Setting this to 1 gives the same width for all edges.

maxFrequency

int

999999

For output GO terms, maximum number of gene products that are annotated with the given term. GO terms are filtered from the output if their associated frequency is above this threshold. Filtering is done before FDR correction.

maxPriori

float

1.00

Maximum value of the priori probability that can be accepted for a GO term. Filtering is done before FDR correction.

minFrequency

int

For output GO terms, minimum number of gene products that are annotated with the given term. GO terms are filtered from the output if their associated frequency is below this threshold. Filtering is done before FDR correction.

organism

int

9606

NCBI taxonomy ID for the organism whose gene set is used for GO probabilities. This is used if the input enrichmentTable is not given. Supported organisms: Homo sapiens: 9606, Saccharomyces cerevisiae: 4932, Caenorhabditis elegans: 6239, Drosophila melanogaster: 7227, Mus musculus: 10090, Rattus norvegicus: 10116.

threshold

float

0.05

P-value threshold for filtering GO terms.

urlPattern

string

"http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=%s"

A printf-like pattern for creating a URL for a GO term. The pattern must contain one %s string that is expanded with the GO term in question, e.g. GO:0005575. If the value is empty, no hyperlinks are created in graphs.

Test cases

Test case	Parameters▼	IN goAnnotations	IN enrichmentTable	OUT goTerms	OUT graphBP	OUT graphCC	OUT graphMF
case1	properties	goAnnotations	(missing)	goTerms	graphBP	graphCC	graphMF
	threshold=0.1, filterFDR=false, minFrequency=2
case2_empty	(missing)	goAnnotations	(missing)	goTerms	graphBP	graphCC	graphMF
case3	(missing)	goAnnotations	(missing)	(missing)	(missing)	(missing)	(missing)
case4_p0	properties	goAnnotations	enrichmentTable	goTerms	graphBP	graphCC	graphMF
	minFrequency=2, colorMinP=0

Test case

Parameters▼

IN
goAnnotations

IN
enrichmentTable

OUT
goTerms

OUT
graphBP

OUT
graphCC

OUT
graphMF

case1

properties

goAnnotations

(missing)