We describe the definition of S-MAP's non-redundant set of modules, collection of the stem cell expression compendium, and the various scores for classifying modules and datasets.
Search results and images may be downloaded and direct visualization of each individual cell in the compendium is available through the companion Image Viewer and Cell Viewer.
We then consulted the ES cell ChIP-seq compendium (http://bioinformatics.cscr.cam.ac.uk/ES_Cell_ChIP-seq_compendium.html) to interrogate available ChIP-seq data sets (Martello et al, 2012).
For every segmented cell in the compendium, ensLOC generated a 16-element vector, where each element is an independent assessment of the cell's membership in a localization class.
Interestingly, genome location data indicate that Tbx3, Esrrb, and Nanog are bound by Tfcp2l1 (data from Chen et al, 2008 and ES cell ChIP-seq Compendium) and upon Tfcp2l1 knockdown we noted downregulation of the three genes.
Furthermore, the Tfcp2l1 promoter is bound by Oct4, Sox2, Nanog, Esrrb, and Klf4 (ES cell ChIP-seq compendium), and is targeted by the pluripotency repressor Tcf3 (Martello et al, 2012), indicating that Tfcp2l1 is hard-wired into the pluripotency gene regulatory network.
S-MAP identified 350 non-redundant up-regulated modules with reproducibly higher expression in stem cells compared to their matched differentiated cells across the compendium (<5% recurrence FDR).
For example, "Root Cells," which is a compendium of expression profiles from cell types [ 28, 29], ranked 2nd for all attributes.
At any given moment, the compendium of cell surface proteins present on normal or abnormal cells is determined by the net effects of all of these trafficking processes.
