Pathway Signature Genes
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In this presentation, the concept of pathway signature genes is explained. These signatures are used in predicting the abundance of pathways in a metagenomically sequenced community. This presentation was given on the M3 Special Interest Group during the ISMB in Stockholm, 2009.
![Goal How to predict the metabolic capacity in a metagenomic sample, given incomplete data?Current practice: ,[object Object],2 out of 5 sequences map to pathway X:Abundance of X is 40% We propose to identify the (metabolic) pathways present in a community, making fulluse of the metagenomic data available](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)
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Pathway Signature Genes
- 1. Pathway prediction in (meta)genomes usingPathway Signature Genes Lucas Brouwers, MSc student, Nijmegen
- 3. Approach We use presence of OGs to predict presence of pathways Some species have pathway X X X X X OG A OG C X OG B PWY X X PresenceSignature Weak Signature AbsenceSignature
- 4. Approach 630 species and their OGs 1,200 (metabolic) pathways
- 5. Signature genes add information Do the signatures add information on the presence of a pathway? (after all some pathways are rare, others are ubiquitous) Specific information defined as a difference in Shannon entropy: how much extra information does the presence of an OG give about the presence of a pathway?
- 6. What makes a signature? N = 29,661 N = 46,176,543
- 7. Absence signatures in a pathway COG0437 (221 species): Fe-S-cluster-containing hydrogenases Formatedehydrogenase Formylmethanofuran-dehydrogenase Glycolaldehyde-dehydrogenase Nitrate reductase
- 8. Integrate signature scores with pathway prediction in metagenomes For quantitative analysis of pathways in metagenomic samples: Consider Chlorphyll biosynthesis:Sa: Average of all OG scores, of OGs in species without chlorophyll biosynthesis Sp: Average of all OG scores, of OGs in species with … Si: Average of all OG scores found in a metagenomic sample Correcting for genome sizes becomes …
- 11. Hypersaline
- 12. Freshwater
- 13. Fish
- 14. Coral
- 16. Predict percentage of species with pathway & compare with actual occurrenceSampling 1%
- 17. Pathway description of biome diversity Pathway occurrence was predicted in 35 metagenomic datasets Principal component analysis revealed the pathways responsible for differences between the biomes
- 18. Conclusions Pathway signature genes allow us to interpret biomes on a pathway level Genes do not need to be part of a pathway to predict its presence We can quantitatively and accurately describe the pathway content of a metagenome
- 19. Acknowledgements Bas E Dutilh MartijnHuynen