Hi Abdullah,

there are several data published on comparative spatio-temporal gene structure and function at epigenetic level in plants. E.g. the ublication by Lafos_M et al., 2011 meets the criteria of your first question.

However, the other questions you raised at the end of your paragraph are more tricky to give ONE conclusove answer. Probably, you might gather a lot of different views from different researches.

In my oppinion:

Whatever you do, you should start from the raw data - -mostly sequence reads - and do it by hand, in a consistent manner forall  your datasets of interest. I don't have a solution for intercomparative analysis on metagenomics NGS data, and I think you can not do as many downstream comparative analyses from NGS data compared with e.g. microarrays - which is why I still like microarrays for expression analyses. In addition, for 'prediction of epigenetic modification' the data coverage is probably still to low and of varying quality - -besides problems of inter-experimental 'noise' and the impossibility to get rid of it.

As intercomparability of NGS data from different labs is possibly consistent with qualitytive information, different experiments will result in very different qualitative  data, which would be required for prediction of spatio-temporal effects at epigenetic level.

At best, make a large epigenmic experiment by yourself with all conditions and points-in-time that might be relevant for you - -this might be the only way to ensure full comparability of the data.