yc_pseudo_ectomycorrhizal — NovInvenio reports

Lineage-specific gene analysis · one folder, three interactive reports

Notes

yeast_convergence contrast (pseudo): none (control). Design and caveats: studies/fungi/yeast_convergence/README.md

Reports

Each page is self-contained — open it directly, no network needed.

Novelty candidatesLineage-specific genes: present across the ingroup, absent from every outgroup proteome. Core genesNear-universally conserved genes shared by essentially every proteome, ingroup and outgroup. Candidate gene lossesGene families conserved across the outgroups but (nearly) absent from the ingroup. Functional enrichment (novelty)Pfam, InterPro and GO term enrichment of the novelty candidates against the proteome background. Functional enrichment (loss)Pfam, InterPro and GO term enrichment of the loss candidates against the proteome background.

Run summary

Parameters and proteomes from config.csv.

Ingroup proteomes
4
Outgroup proteomes
4
Search tool
diamond
Ingroup min fraction
0.75
Outgroup min fraction
0.75
Loss ingroup max fraction
0
Core min fraction
0.95
Pipeline version
v0.7.0+gd03f5a2 (dev)

Ingroup (4)

Genes are called lineage-specific relative to this clade.

ShortSpeciesTaxon group
LaccbicoLaccaria bicolorAgaricales
LaccametLaccaria amethystinaAgaricales
HebecyliHebeloma cylindrosporumAgaricales
AmanmuscAmanita muscariaAgaricales

Outgroup (4)

Background proteomes used to exclude broadly conserved genes.

ShortSpeciesTaxon group
AmanthieAmanita thiersiiAgaricales
CcinCoprinopsis cinerea Okayama-7/130Agaricales
AgbisAgaricus bisporus var. burnettii JB137-S8Agaricales
PleuostrPleurotus ostreatusAgaricales