functional-enrichment-txt

A TXT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Provided by

anvi-compute-functional-enrichment-across-genomes anvi-compute-functional-enrichment-in-pan anvi-compute-metabolic-enrichment anvi-display-functions anvi-script-gen-function-matrix-across-genomes

Required or used by

There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.

Description

This is a TAB-delimited output file that describes enrichment scores and associated groups for functions or metabolic modules in groups of genomes or samples.

General format

Each row in the matrix describes an entity (a function, functional association of a gene cluster, or metabolic module) that is associated with one or more groups of samples or genomes. These are listed with the highest enrichment scores displayed first.

The following columns of information are listed in the file:

• the name of the enriched entity, which can be a functional association, metabolic module, or function. The header of this column is either your functional annotation source, OR ‘KEGG_MODULE’ if you are working with metabolic modules
• enrichment_score: a measure of much this particular entity is enriched in the group it is associated with (i.e., measures how unique this entity [see column 1] is to this group(s) [see column 5])
• unadjusted_p_value: the significance value of the hypothesis test for enrichment, unadjusted for multiple hypothesis testing
• adjusted_q_value: the adjusted p-value after taking into account multiple hypothesis testing
• associated groups: the list of groups that this entity is associated with
• accession: a function accession number or KEGG module number
• a list of gene cluster ids, sample names, or genome names that this entity is found in
• p values for each group: gives the proportion of the group’s member genomes or samples in which this entity was found.
• N values for each group: gives the total number of genomes or samples in each group.

A specific example - enriched functions in pangenomes

When you run anvi-compute-functional-enrichment-in-pan to compute enrichment scores for functions in a pangenome, the resulting matrix describes the gene cluster-level functional associations that are enriched within specific groups of your pangenome. This is described in more detail in the pangenomics tutorial.

Here is a more concrete example (the same example as in the pangenomics tutorial). Note that that tutorial uses COG_FUNCTION as the functional annotation source, and has LL (low light) and HL (high light) as the two pan-groups.

COG_FUNCTION	enrichment_score	unadjusted_p_value	adjusted_q_value	associated_groups	accession	gene_clusters_ids	p_LL	p_HL	N_LL	N_HL
Proteasome lid subunit RPN8/RPN11, contains Jab1/MPN domain metalloenzyme (JAMM) motif	31.00002279	2.58E-08	1.43E-06	LL	COG1310	GC_00002219, GC_00003850, GC_00004483	1	0	11	20
Adenine-specific DNA glycosylase, acts on AG and A-oxoG pairs	31.00002279	2.58E-08	1.43E-06	LL	COG1194	GC_00001711	1	0	11	20
Periplasmic beta-glucosidase and related glycosidases	31.00002279	2.58E-08	1.43E-06	LL	COG1472	GC_00002086, GC_00003909	1	0	11	20
Single-stranded DNA-specific exonuclease, DHH superfamily, may be involved in archaeal DNA replication intiation	31.00002279	2.58E-08	1.43E-06	LL	COG0608	GC_00002752, GC_00003786, GC_00004838, GC_00007241	1	0	11	20
Ser/Thr protein kinase RdoA involved in Cpx stress response, MazF antagonist	31.00002279	2.58E-08	1.43E-06	LL	COG2334	GC_00002783, GC_00003936, GC_00004631, GC_00005468	1	0	11	20
(…)	(…)	(…)	(…)	(…)	(…)	(…)	(…)	(…)	(…)	(…)
Signal transduction histidine kinase	-7.34E-41	1	1	NA	COG5002	GC_00000773, GC_00004293	1	1	11	20
tRNA A37 methylthiotransferase MiaB	-7.34E-41	1	1	NA	COG0621	GC_00000180, GC_00000851	1	1	11	20

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