rinnlab BrainMap issues

rinnlab / BrainMap

Mouse lncRNA Brain Map Project Data and Analysis

http://www.pnas.org/content/112/22/6855.abstract

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new names in gtf file?

#16 agroff11 opened 10 years ago
0
hox genes and hox cluster lincRNAs in these datasets? (expression period, and/or de?)

#15 agroff11 closed 10 years ago
0
Hox gene expression and differential regulation in E14.5 or Adult?

#14 Loyale opened 10 years ago
4
Specifically look at expression of HoxB7 in Tug1 KO lines (see paper below)

#13 Loyale opened 10 years ago
1
how KOs made compare to lacZ

#12 agroff11 opened 10 years ago
0
DE gene list aggregate

#11 agroff11 opened 10 years ago
5
Eldr and Tug1 differential association with Lhx6 and 5HT interneurons

#10 Loyale closed 10 years ago
1
linc-Cox2 look for any association with prostaglandin(s) genes or pathways by GSEA or DE (heatmaps of prostaglandin genes in KOvWT)

#9 Loyale opened 10 years ago
2
Make Lhx6- and 5HT-specific gene sets for GSEA testing

#8 Loyale closed 10 years ago
2
occasional track errors (linc-cox2 adult, embryonic, and haunt adult)

#7 agroff11 opened 10 years ago
1
heatmap for every bamfile digital genotyping

#6 agroff11 opened 10 years ago
0
Gender bias!!?!

#5 agroff11 opened 10 years ago
2
Include overlapping / adjacent PC genes in track plots

#4 Loyale opened 10 years ago
0
GSEA on neural subtype gene sets (After Giulio and Loyal curation of sets)

#3 Loyale opened 10 years ago
0
Explicitly state in report whether ratios (for GSEA in particular) are WT vs KO or KO vs WT.

#2 Loyale closed 10 years ago
2
labRow=FALSE for all heatmaps

#1 Loyale closed 10 years ago
0