PO Paper Winter 2011

Link to proposed Plant Physiology paper- 2011

Plans for a publication- TIPS paper

See file on Google Docs 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:

-Provide a 500-600 word summary outlining:

• what will be discussed in the article,
• why the suggested topic would be timely,
• co-author information
• 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).

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)

Look at annotations to 'flower' and compare to the data set from Qifa Zhang (Wang et al, 2010) paper

-problem: this is such a huge category, 2647 pages of annotations on AmiGO. Tried to search .assoc file in Calc, but it crashed. 55MB

-Also: 'flower is not a tissue used in the Wang etal, 2010 expt.

• See: PO flower (PO:0009046)

• Annotations to Arabidopsis Flower ( annotations to Arabidopsis from TAIR)- how many are there? total ~30,000, but includes all the child terms.

What are the genes that are over or under expressed in each set? Annotate those genes based on that,

Then go back to data set from arab and how many genes expressed in flower from arab overlap with gene ontology.

Genevesitgator –Look for common data sets for rice and arab?

How many dots (genes or GO categories) connect these two data sets?

Laurel will work on coming up with an enriched data set (list of genes and expression profile).

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)

Actual use cases

-Virtual Plant

-GCP

-SGN

-Traitnet

-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)

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

Krom and Ramakrishna 2008 Comparative analysis of divergent and convergent gene pairs and their expression patterns in rice, Arabidopsis, and Populus. Plant Phys

Lang et al. 2008 Exploring plant biodiversity: the Physcomitrella genome and beyond. TIPS

Rensing et al. 2008 The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science

Papanov et al. 2009 The evolution of nuclear auxin signalling. BMC Evolutionary Biology

Perez-Rodriguez et al. 2010 PInTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Research

van der Graaf et al. 2009 The WUS homeobox-containing (WOX) protein family. Genome Biology

Wolf et al. 2010 The Molecular and Physiological Responses of Physcomitrella patens to Ultraviolet-B Radiation. Plant Physiology

Bhasi et al. 2010 RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae. Bmc Plant Biology

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

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

Dai et al. 2010 TrichOME: A Comparative Omics Database for Plant Trichomes. Plant Phys

Dharmawardhana et al. 2010 Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa. BMC Genomics

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

He et al. 2010. Mapping genes for plant structure, development and evolution: functional mapping meets ontology. Trends in Genetics

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

Takahashi et al. 2009 KNApSAcK gene classification system for Arabidopsis thaliana: Comparative genomic analysis of unicellular to seed plants. Plant Biotechnology

Horan et al. 2008. Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Phys

Jung et al. 2008 GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Research

Katari et al. 2010. VirtualPlant: A Software Platform to Support Systems Biology Research. Plant Phys

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

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

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

Mukherjee et al. 2009 A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution

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

Rengel et al. 2009 A new genomic resource dedicated to wood formation in Eucalyptus. Bmc Plant Biology

Soldatos et al. 2010 Martini: using literature keywords to compare gene sets. Nucleic Acids Research

Wang et al. 2010 SoyDB: a knowledge database of soybean transcription factors. Bmc Plant Biology

from Lol:

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

Bhasi, A. et al. RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae. BMC Plant Biology 10, 161 (2010)

Castel, R., Kusters, E. & Koes, R. Inflorescence development in petunia: through the maze of botanical terminology. J. Exp. Bot. 61, 2235-2246 (2010)

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).

Eveland, A.L. et al. Digital Gene Expression Signatures for Maize Development. Plant Physiol. 154, 1024-1039 (2010).

Fujita, M. et al. Rice Expression Atlas In Reproductive Development. Plant and Cell Physiology doi:10.1093/pcp/pcq165

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).

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).

Katari, M.S. et al. VirtualPlant: A Software Platform to Support Systems Biology Research. Plant Physiol. 152, 500-515 (2010).

Mukherjee, K., Brocchieri, L. & Burglin, T.R. A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Mol Biol Evol 26, 2775-2794 (2009).

Mungall, C. et al. Integrating phenotype ontologies across multiple species. Genome Biology 11, R2 (2010).

Rensing, S.A. et al. The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants. Science 319, 64-69 (2008).

Wang, L. et al. A dynamic gene expression atlas covering the entire life cycle of rice. The Plant Journal 61, 752-766 (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).