PO Paper Winter 2011
Link to proposed Plant Physiology paper- 2011
Plans for a publication- TIPS paper
See file on Dropbox for draft of proposal.
-This is a priority for the fall to promote the application of "Ontologies for Plant Sciences"
-Target journal: 'Trends in Plant Science' for a Review/Opinion article.
-Laurel and Ramona will prepare a summary preproposal to be sent to Trends in Plant Science for their consideration.
Review/Opinion article pre-submission enquiries:
-Title (maximum 8 words)
-Provide a 500-600 word summary outlining:
- what will be discussed in the article,
- why the suggested topic would be timely,
- co-author information (No more than 5 authors for a review)
- up to 20 key references that indicate the intended breadth of the proposed article (most references should be to work published in the past 2-3 years).
We need to decide if we are going to do a 'Review' or an 'Opinion' article TIPS
The full review article will have a maximum of 4 elements (i.e. a combination of Figures, Tables, or Boxes)
Focus will be on the benefits and usefulness of the PO and GO, global perspective, links between PO and GO
Topics/goals to include:
Introduction:
- What the PO is and types of data available on PO (background information), (use info from the grant proposal)
- Overall goals of the PO - take from grant introduction, screen shots of browser
- PO-based annotation can be used to improve analysis
- How to improve the analysis aspect of genomics using ontology-based annotation of expression and phenotypes
- Engage community, encourage folks to provide more annotations
Examples/use cases:
- Compare gene expression data sets from Arabidopsis and rice:
-find common datasets- one each for a tissue and and growth stage***
Sources: from Genevestigator
Also: Wang et al, 2010
To do: Lol- find list of datasets and their descriptions- See: List of useful Datasets
- In the PO we currently have a large # of annotations to Arabidopsis (~532,000, from TAIR and NASC), but not as many to rice (from Gramene, how many?)
- Since the PGDSO will be undergoing major revision between the time this paper is submitted and comes out, it would be better to use two or three examples from the PSO.
-Highlight how we are bridging the range of taxa
Currently we have the comparison between:
- palea/lemma vs petal/ sepal (rice vs Arabidopsis)
- Compare datasets between a leaf vs frond vs needle (example on poster)?
- Include an example from the reproductive shoot system branch: strobilus vs spikelet vs panicle.
Questions to ask/answer:
1. What are the genes that are over or under expressed in each set? Annotate those genes based on that,
2. Then go back to data set from arab and how many genes expressed in flower from arab overlap with gene ontology.
3. How many dots (genes or GO categories) connect these two data sets?
Genevesitgator –Look for common data sets for rice and Arabidopsis?
*Example: Comparison of palea/lemma in rice and petal/sepal expressed genes in Arabidopsis:
-Used the PO to identify homologous organs, eg: in monocots vs dicots (arab vs rice) and then go look at the diffs/similarities in expressed genes
(stretch?)
-Extracted the set of genes expressed in palea/lemma in rice from the Wang et al paper (using the supplemental data files, not the CREP database)
-Found their Arabidopsis homologs using the Gramene tool: GrameneMart
details:
-Compared them to petal/sepal expressed genes in Arabidopsis in Genevestigator
-Next step: Determine how many genes or GO categories connect these two data sets?
Potential uses of PO
-interspecies comparison using Genevestigator
-hot topics in plant genomics and how the PO can help research in those areas
--e.g., rice data sets described above, new genomes being sequenced
-systematics (character descriptions), see Teleost Anatomy Ontology paper.
-evolutionary studies of homology and convergence, evo-devo, GO-type analyses
-crop improvement for non-model species (trait descriptions and gene expression as in SGN or Generation Challenge Program, gene exploration for non-model species based on model organism database in PO)
Sites that use the PO: use cases
- VirtualPlant integrates genomic data and provides visualization and analysis tools for rapid and efficient exploration of genomic data. The goal of VirtualPlant is to provide the tools to aid researchers to generate biological hypotheses.
Note: They are still using the older version of the PSO, not the 10-10 version
-Generation Challenge Program-
-Solanaceae Genomics Network-
Note: no actual mention of the PO on their site
-others?
Recruiting more contributors
-use the article as a way to get encourage contribution of annotations from more groups
Possible citations (up to 20)
(obviously this list will need to be edited somewhat)
x=papers that were tagged by both Lol and Ramona
Other plant genomic databases and data sets (mostly taxon specific)
x Wang, L. et al. A dynamic gene expression atlas covering the entire life cycle of rice. The Plant Journal 61, 752-766 (2010). Gene Expression Atlasin rice
Perez-Rodriguez et al. 2010 PInTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Research
Dai et al. 2010 TrichOME: A Comparative Omics Database for Plant Trichomes. Plant Phys
xBhasi et al. 2010 RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae. Bmc Plant Biology
Jung et al. 2008 GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Research
x Katari, M.S. et al. VirtualPlant: A Software Platform to Support Systems Biology Research. Plant Physiol. 152, 500-515 (2010).
Rengel et al. 2009 A new genomic resource dedicated to wood formation in Eucalyptus. Bmc Plant Biology
Wang et al. 2010 SoyDB: a knowledge database of soybean transcription factors. Bmc Plant Biology
Keller et al. 2009 Development and functional annotation of an 11,303-EST collection from Eucalyptus for studies of cold tolerance. Tree Genetics and Genomes
Miozzi et al. 2010 ORTom: a multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato. Plant Molecular Biology
Ogata et al. 2010 CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics
Proost et al. 2009 PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants. Plant Cell
Soldatos et al. 2010 Martini: using literature keywords to compare gene sets. Nucleic Acids Research
Takahashi et al. 2009 KNApSAcK gene classification system for Arabidopsis thaliana: Comparative genomic analysis of unicellular to seed plants. Plant Biotechnology
Fujita, M. et al. Rice Expression Atlas In Reproductive Development. Plant and Cell Physiology doi:10.1093/pcp/pcq165
Eveland, A.L. et al. Digital Gene Expression Signatures for Maize Development. Plant Physiol. 154, 1024-1039 (2010).
Examples of analyses (mostly using GO)
Hayes et al. 2010 Maize global transcriptomics reveals pervasive leaf diurnal rhythms but rhythms in developing ears are largely limited to the core oscillator. PLoS One
x Dharmawardhana, P., Brunner, A. & Strauss, S. Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa. BMC Genomics 11, 150 (2010).
Horan et al. 2008. Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Phys
Allen, A.M., Lexer, C. & Hiscock, S.J. Comparative Analysis of Pistil Transcriptomes Reveals Conserved and Novel Genes Expressed in Dry, Wet, and Semidry Stigmas. Plant Physiol. 154, 1347-1360 (2010). Allen etal, 2010
Jain, M. et al. F-Box Proteins in Rice. Genome-Wide Analysis, Classification, Temporal and Spatial Gene Expression during Panicle and Seed Development, and Regulation by Light and Abiotic Stress. Plant Physiol. 143, 1467-1483 (2007).
Ontologies in systematics
Mabee et al. 2007 Connecting evolutionary morphology to genomics using ontologies: A case study from cypriniformes including zebrafish. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution
Cui 2010. Semantic annotation of morphological descriptions: an overall strategy. BMC Bioinformatics
Dahdul et al. 2010 Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoS one
Comparative evo-devo (potential use of PO)
x Rensing, S.A. et al. The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants. Science 319, 64-69 (2008).
Papanov et al. 2009 The evolution of nuclear auxin signalling. BMC Evolutionary Biology
van der Graaf et al. 2009 The WUS homeobox-containing (WOX) protein family. Genome Biology
Lang et al. 2010 Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity. Genome Biology and Evolution
Duarte et al. 2010 Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evolutionary Biology
Krom and Ramakrishna 2008 Comparative analysis of divergent and convergent gene pairs and their expression patterns in rice, Arabidopsis, and Populus. Plant Phys
Kawai et al. 2010 Class 1 KNOX Gene Expression Supports the Selaginella Rhizophore Concept. Journal of Plant Biology
Langdale 2008 Evolution of developmental mechanisms in plants. Current Opinion in Genetics & Development
x Mukherjee, K., Brocchieri, L. & Burglin, T.R. A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Mol Biol Evol 26, 2775-2794 (2009).
Miscellaneous
x He, Q., Berg, A., Li, Y., Vallejos, C.E. & Wu, R. Mapping genes for plant structure, development and evolution: functional mapping meets ontology. Trends in Genetics 26, 39-46 (2010).
Lang et al. 2008 Exploring plant biodiversity: the Physcomitrella genome and beyond. TIPS
Wolf et al. 2010 The Molecular and Physiological Responses of Physcomitrella patens to Ultraviolet-B Radiation. Plant Physiology
Mungall, C. et al. Integrating phenotype ontologies across multiple species. Genome Biology 11, R2 (2010).
Castel, R., Kusters, E. & Koes, R. Inflorescence development in petunia: through the maze of botanical terminology. J. Exp. Bot. 61, 2235-2246 (2010)
Yadav, R.K., Girke, T., Pasala, S., Xie, M. & Reddy, G.V. Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. Proceedings of the National Academy of Sciences 106, 4941-4946 (2009).
Madin et al. 2007. Advancing ecological research with ontologies. Trends in Ecology and Evolution 23:159-168
Mari L. Salmi, Thomas J. Bushart, Stephen C. Stout and Stanley J. Roux. Profile and Analysis of Gene Expression Changes during Early Development in Germinating Spores of Ceratopteris richardii. Plant Physiology 138:1734-1745 (2005) http://www.plantphysiol.org/cgi/content/full/138/3/1734
