dCIN5 and Wildtype Transcription Factor Mapping in Cold Shock

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Presentation transcript:

dCIN5 and Wildtype Transcription Factor Mapping in Cold Shock William Gendron and Jeffrey Crosson

Outline Background: Yeast, Transcription Factors and Cold Shock Results GO Terms GRN Weighting+Production GRN Mapping Comparison between our respective networks Discussion and future plans

Background Saccharomyces cerevisae is the eukaryotic model organism Chemostat models have been used to limit the stress to one variable Cold shock has not been as analyzed as other stressors (Tai et al, 2007)

Novel Cold Shock Analysis with mutant dCIN5 and wildtype Received microarray data Purpose: to create a novel model of yeast under cold shock focusing on interactions in combination with dCIN5

GO Terms GO:0031505 - fungal-type cell wall organization: This showed an increase in expression of the cell wall construction genes. This is a known response, probably to rebuild damage. GO:0005654 - nucleoplasm: This is involved with regulating the genome and RNA, which is to be expected when the cell is reacting to new conditions. GO:0006402 - mRNA catabolic process: Similar to the one above, this is involved in the breakdown of RNA molecules. GO:1901361 organic cyclic compound catabolic process: This would break down organic cyclic compounds and therefore could be related to the RNA.

Wil’s Weight Comparison

Jeff’s Weight Comparison

Wil’s Production Rate Comparison

Jeff’s Production Rate Comparison

Fixed B Weight Comparison

Estimated B Comparison

Fixed B Production Rate Comparison

Compared Production: Estimated

Wil’s Fixed B GRNsight Map

Wil’s Estimated B GRNsight Map

Jeff’s Fixed B GRNsight Map

Jeff’s Estimated B GRNsight Map

CIN5 Graph Comparison Fixed B Estimated B Wil

HMO1 Graph Comparison Fixed B Estimated B

STB5 Graph Comparison Fixed B Estimated B Wil

Wil’s Estimated-b GRNmap

MIG2 Graph Comparison Fixed B Estimated B

Wil’s Estimated-b GRNmap

CYC8 Fixed B Estimated B Wil

Concluding thoughts Discrepancies between our weights Even slight changes to the network composition will alter the genes expected effect Can visualize alterations that result from deletion. Can be seen in maps and plots. Wil

Overview Background: Yeast, Transcription Factors and Cold Shock Results GO Terms GRN Weighting+Production GRN Mapping Comparison between our respective networks Discussion and future plans

Ideas for the future Larger maps Is this possible? Will this create the most representative/accurate values? Find which gene is temperature sensitive? Can we use these networks to find genes that are the first to react to the temperature change? Wil

Acknowledgements and References Dr. Kam Dahlquist Dr. Ben Fitzpatrick The class: MATH 388-01: Survey of Biomathematics 2014, Gene Ontology Consortation, http://geneontology.org/, 7 April 2015 Tai, Siwe L. "Acclimation of Saccharomyces Cerevisiae to Low Temperature: A Chemostat-based Transcriptome Analysis."Http://www.molbiolcell.org/. The American Society for Cell Biology, 1 Dec. 2007. Web. 1 May 2015. <http%3A%2F%2Fwww.molbiolcell.org%2Fcontent%2F18%2F12%2F5100.full> Coller, John. Sample Microarray. Digital image. Microarray.org. The Board of Trustees of Leland Stanford Junior University, 2008. Web. 1 May 2015. <https://microarray.org/sfgf/>.

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