Micromonas Pathways
The Stuart lab is working with Alex Worden's lab at MBARI to study the biological pathways of the eukaryote, Micromonas pusilla (38833).
Data is scarce for Micromonas with regard to biological pathways, so the initial steps of the project will involve two other organisms: Chlamydomonas reinhardtii (3055) and Arabidopsis thaliana (3702). Micromonas genes will be mapped to Chlamydomonas and Arabidopsis via best reciprocal BLAST. Once this has been done, it will be possible to see how many mapped Micromonas genes participate in known Chlamydomonas or Arabidopsis biological pathways.
| source | A. thaliana | C. reinhardtii |
|---|---|---|
| pathway commons | biopax | biopax |
| plantcyc | 423 pathways as of 29MAR11 | 159 + 6 pathways as of 29MAR11 |
| Gramene | text dumps | none found |
| WikiPathways | 7 pathways as of 29MAR11 | none found |
We'll include Ostreococcus tauri in our analysis on the advise of Jeltje van Baren. She mentioned that its pathways may be found in KEGG.
| source | A. thaliana | C. reinhardtii | O. tauri | P patens patens |
|---|---|---|---|---|
| KEGG | 3680 genes in 125 pathways | 1515 genes in 106 pathways | 1185 genes in 102 pathways | 3023 genes in 118 pathways |
| pathway commons | 4144 genes in 39945 links | 28 genes in 99 links | ||
| plantcyc | 2096 genes in 588 pathways | 3065 genes in 165 pathways |
(note: pathway commons data was downloaded in link-based form rather than pathway-based. It may be helpful to match up each link with at least one pathway for use in subsequent analysis.)
(28APR11)
Alex Worden has just related the following:
"Another super important genome to use is Physcomitrella patens subsp. patens (moss). Micro has a bunch of stuff in moss, that is not in ostreo, leafy plants (e.g. arabidopsis) or chlamy...."
We'll look for the moss (TAX:145481) pathways in KEGG.