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| − | 2/13/18
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| − | mut/WT log2 500/1000 = 0.5 Anything less than 1 is negative
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| − | DESeq2 >>> run htseq-count data with features
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| − | After doing a DESeq2 run, two files will appear in the history
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| − | " First one is tabular. Download that, open in Text Wrangler, then copy and paste that in excel
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| − | " Second one is a pdf. Download and open that to see data visualizations
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| − | 54 & 55 >>> DESeq2 for "Female_MUTvWT"
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| − | 56 & 57 >>> DESeq2 for "Male_MUTvWT"
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| − | 58 & 59 >>> DESeq2 for "MUT_MALEvFEMALE"
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| − | 60 & 61 >>> DESeq2 for "WT_MALEvFEMALE"
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| − | 62 & 63 >>> DESeq2 for "MUT_v_WT"
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| − | Research method for today: look at what genes are significant in each dataset and see where there is overlap between datasets
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| − | In excel sheet:
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| − | " DESeq2 data for all 5 comparisons
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| − | o P-value < 0.05 highlighted in yellow
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| − | o P-adjusted <0.05 highlighted in green
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| − | " List of just the p-adjusted <0.05 genes for all 5 comparisons together
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| − | General observations:
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| − | "
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| − | " # of genes with p-adj < 0.05
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| − | o Female_MUTvWT: 72
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| − | Sphk2 >>> p-adj is less than 0.05 for both MUT_MALEvFEMALE and WT_MALEvFEMALE
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| − | " Sphingosine Kinase 2
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| − | o Paralog with Sphk1, which codes for the other enzyme that has the same function
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| − | " Encodes for an enzyme that catalyzes the phosphorylation of sphingosine into sphingosine 1-phosphate
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| − | o sphingosine 1-phosphate = important in cell migration, proliferation, apoptosis
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| − | o Implicated in some cancers (breast cancer proliferation, chemoresistance)
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| − | " Related pathways
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| − | o Calcium signaling pathway
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| − | " Could be connection to CMT2D
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| − | o Metabolism
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| − | Tsix >>> p-adj is less than 0.05 for both MUT_MALEvFEMALE and WT_MALEvFEMALE
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