Difference between revisions of "Talk:Jenna Reed"
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| + | == 2/8/18 == | ||
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2/8/18 | 2/8/18 | ||
Bio343 HTSeq Results | Bio343 HTSeq Results | ||
| − | Male Mutant | + | Male Mutant 25 and 24 = paired reads, Male mouse 2078, C201R 15 and 14 = paired reads, Male mouse 2073, C201R 3 and 2 = paired reads, Male mouse 2079, C201R |
| − | 25 and 24 = paired reads, Male mouse 2078, C201R | ||
| − | 15 and 14 = paired reads, Male mouse 2073, C201R | ||
| − | 3 and 2 = paired reads, Male mouse 2079, C201R | ||
| − | Male WT | + | Male WT 21 and 20 = paired reads, Male mouse 2076, WT 19 and 18 = paired reads, Male mouse 2075, WT 17 and 16 = paired reads, Male mouse 2074, WT |
| − | 21 and 20 = paired reads, Male mouse 2076, WT | ||
| − | 19 and 18 = paired reads, Male mouse 2075, WT | ||
| − | 17 and 16 = paired reads, Male mouse 2074, WT | ||
| − | Female Mutant | + | Female Mutant 13 and 12 = paired reads, Female mouse 2072, C201R 11 and 10 = paired reads, Female mouse 2071, C201R 9 and 8 = paired reads, Female mouse 2070, C201R |
| − | 13 and 12 = paired reads, Female mouse 2072, C201R | ||
| − | 11 and 10 = paired reads, Female mouse 2071, C201R | ||
| − | 9 and 8 = paired reads, Female mouse 2070, C201R | ||
| − | Female WT | + | Female WT 23 and 22 = paired reads, Female mouse 2077, WT 7 and 6 = paired reads, Female mouse 2081, WT 5 and 4 = paired reads, Female mouse 2080, WT |
| − | 23 and 22 = paired reads, Female mouse 2077, WT | ||
| − | 7 and 6 = paired reads, Female mouse 2081, WT | ||
| − | 5 and 4 = paired reads, Female mouse 2080, WT | ||
| + | Gene Cards Gene Weaver GO rilla FNTM String NCBI | ||
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| + | 2/8/18 Loaded data from "Histories Shared with Me" | ||
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| + | NefL >>> deltaCMT 1F 2E NefH >>> deltaALS Sphk2 >>> kinase | ||
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| + | Male v Female | ||
| + | MaleWT v MaleCMT | ||
| + | FemaleWT v FemaleCMT | ||
| + | Gm4210 NefM (neurofilament medium) Close with NefL, and Gm2410 Calca >>> calcium regulator | ||
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| + | About this data: Took the spinal cord of the mice and sent it off for RNASeq 2-fold change | ||
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| + | -0.7 = 1.62 fold change | ||
| + | -0.8 = 1.74 fold change | ||
| + | -7.56 = 128fold change, p=10^-14 | ||
| + | What's our fold-change cutoff? JAX had a strict cutoff and got only 20 genes Lack of signal because of CMT could cause repression of transcription (because usually ligand binding induces transcription) RNASeq data will always have differential expression from natural variation Is it enough differential expression that it could be caused by the disease? | ||
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== 2/13/18 == | == 2/13/18 == | ||
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Tsix >>> p-adj is less than 0.05 for both MUT_MALEvFEMALE and WT_MALEvFEMALE | Tsix >>> p-adj is less than 0.05 for both MUT_MALEvFEMALE and WT_MALEvFEMALE | ||
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Revision as of 02:47, 14 February 2018
2/8/18
2/8/18
Bio343 HTSeq Results
Male Mutant 25 and 24 = paired reads, Male mouse 2078, C201R 15 and 14 = paired reads, Male mouse 2073, C201R 3 and 2 = paired reads, Male mouse 2079, C201R
Male WT 21 and 20 = paired reads, Male mouse 2076, WT 19 and 18 = paired reads, Male mouse 2075, WT 17 and 16 = paired reads, Male mouse 2074, WT
Female Mutant 13 and 12 = paired reads, Female mouse 2072, C201R 11 and 10 = paired reads, Female mouse 2071, C201R 9 and 8 = paired reads, Female mouse 2070, C201R
Female WT 23 and 22 = paired reads, Female mouse 2077, WT 7 and 6 = paired reads, Female mouse 2081, WT 5 and 4 = paired reads, Female mouse 2080, WT
Gene Cards Gene Weaver GO rilla FNTM String NCBI
2/8/18 Loaded data from "Histories Shared with Me"
NefL >>> deltaCMT 1F 2E NefH >>> deltaALS Sphk2 >>> kinase
Male v Female MaleWT v MaleCMT FemaleWT v FemaleCMT
Gm4210 NefM (neurofilament medium) Close with NefL, and Gm2410 Calca >>> calcium regulator
About this data: Took the spinal cord of the mice and sent it off for RNASeq 2-fold change
-0.7 = 1.62 fold change -0.8 = 1.74 fold change -7.56 = 128fold change, p=10^-14
What's our fold-change cutoff? JAX had a strict cutoff and got only 20 genes Lack of signal because of CMT could cause repression of transcription (because usually ligand binding induces transcription) RNASeq data will always have differential expression from natural variation Is it enough differential expression that it could be caused by the disease?
2/13/18
2/13/18
mut/WT log2 500/1000 = 0.5 Anything less than 1 is negative
DESeq2 >>> run htseq-count data with features After doing a DESeq2 run, two files will appear in the history First one is tabular. Download that, open in Text Wrangler, then copy and paste that in excel Second one is a pdf. Download and open that to see data visualizations
54 & 55 >>> DESeq2 for "Female_MUTvWT" 56 & 57 >>> DESeq2 for "Male_MUTvWT" 58 & 59 >>> DESeq2 for "MUT_MALEvFEMALE" 60 & 61 >>> DESeq2 for "WT_MALEvFEMALE" 62 & 63 >>> DESeq2 for "MUT_v_WT"
Research method for today: look at what genes are significant in each dataset and see where there is overlap between datasets
In excel sheet: DESeq2 data for all 5 comparisons P-value < 0.05 highlighted in yellow P-adjusted <0.05 highlighted in green List of just the p-adjusted <0.05 genes for all 5 comparisons together
General observations:
of genes with p-adj < 0.05 Female_MUTvWT: 72
Sphk2 >>> p-adj is less than 0.05 for both MUT_MALEvFEMALE and WT_MALEvFEMALE Sphingosine Kinase 2 Paralog with Sphk1, which codes for the other enzyme that has the same function Encodes for an enzyme that catalyzes the phosphorylation of sphingosine into sphingosine 1-phosphate sphingosine 1-phosphate = important in cell migration, proliferation, apoptosis Implicated in some cancers (breast cancer proliferation, chemoresistance) Related pathways: Calcium signaling pathway (could be connection to CMT2D), Metabolism
Tsix >>> p-adj is less than 0.05 for both MUT_MALEvFEMALE and WT_MALEvFEMALE
