Plant Physiology paper- 2011

Target Journal: Plant Physiology

Target date for submission: Late Winter or Spring (March) 2011

• If we submit a full research article, it will probably go under the section 'bioinformatics'. May want to ask for permission to use a non-standard format.

See: Author instructions

• Could also consider submitting an “update” (7000 word max). Has to be invited, pretty long shot.

Update: "Updates are solicited reviews of recent progress and meant to be teaching tools. Updates are not to exceed 7000 words, including references but excluding supplemental data.

Although these are primarily associated with Focus Issues, scientists wishing to contribute an Update to a regular issue must first correspond with Don Ort (d-ort@uiuc.edu).

All uninvited Updates will be returned to the author(s)."

See: PLANT PHYSIOLOGY® ANNUAL UPDATE COLLECTION

Issues with the ontology arising during writing:

This section is for questions about the PO that came up while were writing the manuscript. These are issues that need to be addressed by the curators, preferably before publication and the next release.

Please visit the POC meeting page POC_Conf._Call_3-29-11 for details of the following topics:

• Rename Plant Structure Ontology (PSO) to Plant Anatomy Ontology (PAO)?
• Use of ontology id's in definitions
• How should we deal with dual parentage for embryonic plant structure?
• How do we deal with the in vitro plant structure- dual parentage again, boundaries
• Issues arising from the use of the has_part relation
• Issues arising from the use of participates_in relation

Parts of the paper: Topics/goals to include:

Intro, results, methods:

Update on the changes to PO in the past 18 months, focus on how it is now applicable to all plants.

Challenges in incorporating such a phylogenetically broad group of species

-Compare to previous publication Ilic et al, Plant Phys.

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

Discussion:

how this will help move research forward in non-angiosperm model species and all non-model species

future directions

Second manuscript will be a full paper to Plant Physiology- Bioinformatics section, target date after the new year, once we complete more revisions.

Ideas from PJ Apple-Pseudo fruit, microarray data,

florets in rice and compositae. Compare large scale sequencing data sets.

-We have been keeping track of the changes on the 'Summary of Changes' page

Look at Qifa Zhang rice datasets see microarry data Gene Expression Atlas

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?

Cytoscape and BinGO