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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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.
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.
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:
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.
|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|
Edit this file to update this information.