LncRNA ToDoList

March 7, 2012

lncRNA regulation mechanism

CIS model

Trans model

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

Joe

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

February 8,2012

h2az

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?