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# System prepended metadata

title: Project 2 Proposal

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# Project 2 Proposal
Group 4: Tida Feepakproh, Cristina Gonzalez, Emily Montes-Martinez

**Research Proposal**:

Symbiodinium dinoflagellates are a type of algae that are able to form symbiotic relationships with coral. We want to analyze the change in gene expression of *Fugacium kawagutii* when in heat stress compared to phosphorous stress and/or controlled conditions (if we can find them). We will analyze gene alignments and length to elucidate if size correlates with higher expression in the SAGER genome browser. As climate change continues to raise global temperatures, the relationship between symbiotic algae and coral are crucial for oceanic environments. 

**Databases**:
1. Supplementary data from the following research papers: [1](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6517890/), [2](https://www.nature.com/articles/s41598-018-35620-z#MOESM2)


Lin, S., Yu, L., Zhang, H., 2019. Transcriptomic Responses to Thermal Stress and Varied Phosphorus Conditions in Fugacium kawagutii. Microorganisms 7, 96. https://doi.org/10.3390/microorganisms7040096

Stephens, T.G., Ragan, M.A., Bhattacharya, D., Chan, C.X., 2018. Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions. Sci Rep 8, 17175. https://doi.org/10.1038/s41598-018-35620-z

2. [Symbiodiniaceae and Algal Genomic Resource (SAGER)](http://sampgr.org.cn/index.php/genomebrowser/fugacium-kawagutii-v1)


**Analysis Plan:**
* Analyze gene alignments and length to elucidate if size correlates with higher expression in the SAGER genome browser.
* Due to unkown functions and lack of annotated data, we will filter out "dark genes" from both tabular data sets in R studio. 
* We will select and filter p-values to above a threshold  or  use only top p-vaues in R. 
* Create a gene visual interaction model through Cytoscape. 
* SAGER provides an in-browser BLAST tool that can help with nucleotide and protein analysis. 
