The implementation of functions to define the portal design and select preferred datasets in the mashup page are possible as well as the addition of social functions like comments, ratings and quoting.
In this example, the respective unique code for grapevine CEB1 (VIT_01s0244g00010) was input into the 'CoexQuery' field and selected 'all' and 'HRR' for the preferred predefined datasets and co-expression measure options, respectively or by using the keyword query 'CEB1' and choosing 'all' under the 'CoexQuery' column in the 'keyword query' results page.
It seems that GLOBALTEST and PLAGE have generally comparable performances with other methods according to their performances on many preferred datasets of other methods.
Our preferred dataset (12n3rRTn: RY-coding) reproduces the most basal Caulophrynidae, followed by divergence of the Ceratiidae, Gigantactinidae, Thaumatichthyidae plus Linophrynidae, Neoceratiidae plus Centrophrynidae, Oneirodidae (including Lasiognathus; see below), Himantolophidae, and Melanocetidae plus Diceratiidae at the top of the tree in sequential step-wise manner.
To search for interesting modules involved in phenylpropanoid metabolism, a query using broad keyword terms such as "GO 0009698" or "phenylpropanoid metabolic process" and selecting the preferred condition (all datasets and HCCA clustering), returned a list of modules in which the query term was enriched (Additional file 3: Figure S1).
When the anatomical image is matching the PET dataset and it clearly differentiates between healthy and scarred tissue, then it is definitely the preferred choice (Bowsher MR -perf).
Of course, on the preference-specific datasets (i.e., approach-specific datasets), the preferred method should have the best performance; meanwhile, some other methods would have comparable performances.
Preferred = The preferred and natural pace.
Indeed, the results from the model selection experiments clearly indicate that the model without array effect is the preferred model for both datasets.
Bayes factor results showed that the most highly partitioned dataset is the preferred strategy among different partitioning schemes.
