Haynes Lab:Notebook/Synthetic Biology and Bioinformatics for Predictable Control of Therapeutic Genes

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(Phase I/2: Bioinformatics)
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==Project Description/Abstract==
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==Phase 1/2: Bioinformatics==
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* Since a comprehensive ChIP map is not available for osteosarcoma, I will identify genes associated with H3K27me3 in liver (HepG2) and fibroblast (BJ) cell lines. ChIP is available through the Encyclopedia of DNA Elements (ENCODE) (3). I will extract a list of genes with H3K27me3 near the transcription start site (promoter) as well as genes with a broad distribution of H3K27me3 to determine later on if H3K27me3 localization influences Pc-TF function. I will also determine which CBX isoforms are at each locus to determine variations between H3K27me3 sites.
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* ChIP is available through the Encyclopedia of DNA Elements (ENCODE) and GALAXY serves as a tool for biomedical analysis. Using the two tools I extracted a list of genes with H3K27me3 near the transcription start site (promoter) from cancer cells lines (neuroblastoma, liver carcinoma, and erythroleukemia). I then went on to perform GO (Gene Ontology) Term analysis to formulate predictions on how PcTF may affect cell phenotype and growth.
==Notes==
==Notes==
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* Phase 1 is currently in progress
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* Phase 1 is complete

Revision as of 21:06, 16 April 2013

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Phase 1/2: Bioinformatics

  • ChIP is available through the Encyclopedia of DNA Elements (ENCODE) and GALAXY serves as a tool for biomedical analysis. Using the two tools I extracted a list of genes with H3K27me3 near the transcription start site (promoter) from cancer cells lines (neuroblastoma, liver carcinoma, and erythroleukemia). I then went on to perform GO (Gene Ontology) Term analysis to formulate predictions on how PcTF may affect cell phenotype and growth.

Notes

  • Phase 1 is complete


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