Histone modification is highly associated with many biological traits such as developmental states, cell type, and tissue type.
In common with other models of cellular differentiation, the system given by Eqns. (1 2) allows multiple stable steady-states (cell types) to coexist in the same environment.
Briefly, the authors downloaded 476 human GEO datasets from the NCBI Gene Expression Omnibus and categorized each GEO dataset into 24 types of comparisons, such as disease state, cell type, metabolism and so on.
In normal hematopoiesis, the effect of HDAC inhibition is diverse and the outcome depends on the cell state, cell type, and environment 22. MPPs, for example, are maintained in a more immature state and their differentiation is inhibited, when cells are treated with HDAC inhibitors 23, 24.
First, we identified a subset of CpGs in the human genome that appears to be highly stable in their methylated or unmethylated state, across diverse developmental states and cell types.
Specifically, individual attractor states have been suggested to correspond to particular functional cell states or cell types in metazoan [1], [10], [12].
However, these data are either confined to the neural progenitor cell state or in vitro represent a broader range of differentiation states (and cell types) at each time point than may be present at one time and place in the embryonic neural axis.
For example, in Metazoan, individual steady states (attractors) existing in bistable or multistable systems correspond to particular functional cell states or cell types [ 26, 27].
There are also transient or fuzzy states between cell types.
Furthermore, coexpressed genes are different in different states and cell types [ 12].
But this type of data integration often suffers from the system bias caused by the fact that different high-throughput data were performed on different cell states and cell types [ 40, 41].
