Difference between revisions of "Talk:Jenna Reed"
| Line 48: | Line 48: | ||
Calca >>> calcium regulator | Calca >>> calcium regulator | ||
| − | About this data | + | About this data: Took the spinal cord of the mice and sent it off for RNASeq |
| − | |||
2-fold change | 2-fold change | ||
-0.7 = 1.62 fold change | -0.7 = 1.62 fold change | ||
| Line 55: | Line 54: | ||
-7.56 = 128fold change, p=10^-14 | -7.56 = 128fold change, p=10^-14 | ||
What's our fold-change cutoff? | 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) | 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 | RNASeq data will always have differential expression from natural variation | ||
Is it enough differential expression that it could be caused by the disease? | Is it enough differential expression that it could be caused by the disease? | ||
Revision as of 02:44, 14 February 2018
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?
