Introduction to an online resource that displays pre-computed phylogenetic trees of gene families alongside experimental gene function data to facilitate inference of unknown gene function in plants. From the same team that brings you TAIR (The Arabidopsis Information Resource)

1. Peifen Zhang
Phoenix Bioinformatics
4/2/2020
PhyloGenes Webinar

2. Outline
• What is phylogenetic function inference
• A case study of phylogenetic function inference using PhyloGenes
• Search and explore info in PhyloGenes

3. A DNA/protein sequence
Function?
Functional annotation

4. A DNA/protein sequence
Predicted function
Relying solely on
sequence similarity
(e.g. BLAST, InterProScan)
Relying on
evolutionary history
Functional annotation

5. Phylogenetic function inference
Evolutionary history of a family of homologs:
human_gene_2
mouse_gene_2
human_gene_3
mouse_gene_3
mouse_gene_3’
human_gene_1
mouse_gene_1
speciation
duplication
ortholog: related by speciation
paralog: related by duplication
paralog: related by duplication
The ortholog conjecture:
Protein function changes rapidly after duplication,
leading to paralogs with different functions, while
orthologs retain the ancestral function.

6. Phylogenetic function inference
Evolutionary history of a family of homologs:
human_gene_2
mouse_gene_2
human_gene_3
mouse_gene_3
human_gene_1
mouse_gene_1
speciation
duplication motion
pigment
???

7. Phylogenetic function inference
Assigning function from a known gene to
an unknown gene using evolutionary
history of the genes
• orthologs
• known function for at least one of
the orthologs

8. phylogenes.org
• Displays phylogenetic trees of gene families across species
• Displays experimentally validated gene function (known function)
and other gene info alongside gene trees
• Facilitates inference of unknown gene function

9. Gene tree
(PANTHER February 2020 release)
Gene info
Family
info
A gene family page

10. • Classification of genes (protein sequence) to gene families
using the PANTHER pipeline (GIGA algorithm)
• 142 genomes across all kingdoms (February 2020 release)
50 genomes (plant-centric)
http://pantherdb.org/

11. Basic features on a PhyloGenes gene tree
Node
types
Gene name and species name
Taxonomic range of a collapsed
internal node
Subfamily:

12. ‘Known function’
‘GO molecular
function’
supported by
Experimental evidence
(EBI GOA)
A distinct function
found in at least one
member of the
family

13. Outline
• What is phylogenetic functional inference
• A case study of phylogenetic functional inference using PhyloGenes

16. Demo

17. •Survey: bit.ly/2JyOFEe
•Slides: bit.ly/39CzZOW