Hox gene expression and differential regulation in E14.5 or Adult?

[Loyale]

No description provided.

[agroff11]

At the end of the file where I generate all the DE lists:

for GENES:
for(i in 1:length(DE_lists)){
genelist<-DE_lists[[i]]
name<-names(DE_lists[i])
hoxlist<-grep("Hox",genelist)
if(length(hoxlist)>0){
print(paste(name,length(hoxlist),sep=":"))
print(genelist[hoxlist])
}
}

[1] "eldr_embryo_DE:2"
[1] "Hoxb9" "Hoxb4"
[1] "kantr_embryo_DE:3"
[1] "Hoxa2" "Hoxc4" "Hoxa3"
[1] "lincbrn1b_embryo_DE:1"
[1] "Hoxb4"
[1] "lincCox2_embryo_DE:1"
[1] "Hoxb4"

for ISOFORMS:

for(i in 1:length(iso_DE_lists)){
genelist<-iso_DE_lists[[i]]
name<-names(iso_DE_lists[i])
hoxlist<-grep("Hox",genelist)
if(length(hoxlist)>0){
print(paste(name,length(hoxlist),sep=":"))
print(genelist[hoxlist])
}
}

[1] "eldr_embryo_iso:2"
[1] "Hoxb9" "Hoxb4"
[1] "kantr_embryo_iso:2"
[1] "Hoxa2" "Hoxc4"
[1] "lincbrn1b_embryo_iso:1"
[1] "Hoxb4"

for CDS:

for(i in 1:length(cds_DE_lists)){
genelist<-cds_DE_lists[[i]]
name<-names(cds_DE_lists[i])
hoxlist<-grep("Hox",genelist)
if(length(hoxlist)>0){
print(paste(name,length(hoxlist),sep=":"))
print(genelist[hoxlist])
}
}

[1] "brn1a_adult_CDS:1"
[1] "Hoxb8"
[1] "eldr_embryo_CDS:2"
[1] "Hoxb9" "Hoxb4"
[1] "kantr_embryo_CDS:2"
[1] "Hoxa2" "Hoxc4"
[1] "lincbrn1b_embryo_CDS:1"
[1] "Hoxb4"

let me go check out expression levels for a few of these...

[agroff11]

Hoxb4, lincBrn1b embryo

hoxb4<-getGene(cuff,"Hoxb4")
expressionPlot(hoxb4,replicates=T)

Hoxb8, lincBrn1a ADULT
dir<-"/n/rinn_data1/seq/lgoff/Projects/BrainMap/data/diffs/linc-Brn1a_vs_WT_Adult/"
cuff<-readCufflinks(dir=dir,gtfFile="/n/rinn_data1/seq/lgoff/Projects/BrainMap/data/annotation/mm10_gencode_vM2_with_lncRNAs_and_LacZ.gtf",genome="mm10")
hoxb8<-getGene(cuff,"Hoxb8")
expressionPlot(hoxb8,replicates=T)

huh: http://capecchi.genetics.utah.edu/PDFs/GreerNeuron2002.pdf
Do Brn1a mice groom less? o.O

HoxA2, HoxC4, KANTR embryo

dir<-"/n/rinn_data1/seq/lgoff/Projects/BrainMap/data/diffs/Kantr_vs_WT_Embryonic"
cuff<-readCufflinks(dir=dir, gtfFile="/n/rinn_data1/seq/lgoff/Projects/BrainMap/data/annotation/mm10_gencode_vM2_with_lncRNAs_and_LacZ.gtf",genome="mm10")
genes<-c("Hoxa2","Hoxc4")
hoxgenes<-getGenes(cuff,genes)
expressionPlot(hoxgenes,replicates=T)

[agroff11]

more hoxb8 papers

lof: http://www.sciencedirect.com/science/article/pii/S0925477399002129
gof: http://www.sciencedirect.com/science/article/pii/009286749490524X

[agroff11]

from the first paper: "additionally, we have also found that numerous hox genes are expressed in the audlt CNS (unpublished results and 2 other papers). Herein we demonstrate that hoxb8 is extensively expressed in the adult CNS in regions previously implicated in the control of rodent grooming behavior"

http://capecchi.genetics.utah.edu/PDFs/GreerNeuron2002.pdf

on page 29 they have a solid description of where hoxb8 is expressed in adult brain