Emilie Uffman
Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)
-the limited variation in paternal disomy and trisomy is conserved
-maternal still has variation
-there is no clear divide between gender along PC1--what does this mean?
Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):
Use galaxy sort tool to sort p-value in ascending order
Why is it that for many of the data there is a base mean and all statistics but no p-value?
ENSMUST00000000674.12 Base mean: 8.06384358972545 LogFC: 0.0460016853044759 Std Error: 0.0883691926491015 Wald-Stats: 0.520562471212569 P-value: NA P-adjusted: N
- See Jon's notes for information on question**
Filtered data on galaxy to remove data with 'NA' -skip 0 header line- Only retained 70.41% of data when filtering to remove 'NA'
Copied data to excel and use shortcut to removal decimals without rounding
Copy (100lines of) data into MGI Database
http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0
CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76
(ENSMUST000134372)
-up regulated
"Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system"
"A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis"
CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome -conserved synteny to human 4p16.3
Symptoms:
-'Greek warrior helmut facial appearance'
-mental retardation
Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8
https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=1058
CENP-A expression decreases in senescent cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/
At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule
https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso
-Black Lab discoveries give insight into genetic inheritance -CENP-A could be the 'key' epigenetic marker protein -CENP-A changes shape of the nucleosome
Going forward:Want to investigate the CENP-A gene in maternal strains
ENSMUST000153398 (Brwd1)
-down regulated
-associated with Down Syndrome
-located on Chr16:95992449-96082526 bp within the DS region
-involved in chromatin remodeling
http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651
Excel tools: Truncate numbers in excel: =left (A1, 18)
