March 7, 2012
lncRNA regulation mechanism
lncRNA expression median normalized - DESeq
Conserved lncRNA in mouse and human for further knock down
Paul - H2AZ
active - H3K4mer3
silent - H3K27mer3
poised - both H3K4mer3 and H3K27mer3, bivalent
H2AZ promoter enrichment and 9 human cell types?
February 23, 2012
set up a database and a wiki
lncrna analysis with reduced cutoff at 0.5 from 1
transcription factor & the dip of the histone modification
divide genes into different categories such as lncrnas , mirrnas , and some specific processes/pathways,
February 3, 2012
LncRNAs, their temproal nd spatial function in the regulation of expression.
1. There is a gap between day 3 and day 6, may add day 4 and 5 rna-seq data
2. There possibly a transition during day 1 and day 3 that lunch renascence and mirrnas are associated in early stage of differentiation
3. The network makes sense to the stage specific differentiation. However, add some mirrnasback to the network ?
4. Mesp4 is picked for downstreame study because mesp4 seems to be a master regulator in early stage at the starting point. There is a linear regulation leading to the carjacking differentiation.
5.does mesp1 overexpfession rescue the phenotype?
6. Does mesp1 knock outhave the samephenotype?
7. How lncrna affects expression?