Table 1. A selection of the deregulated genes and corresponding pathways affected in Ring1b-deficient ES cells. Symbol EntrezID Regulation bound Symbol EntrezID Regulation bound Focal Adhesion Actg2 Actn3 Capn2 Capn5 Ccnd1 Ccnd2 Col4a2 Grb2 Ilk Nras Pdgfc Pten Rras2 Shc2 Thbs1 Vegfa Zyx 11464 11474 12334 12337 12443 12444 12827 14784 16202 18176 54635 19211 20130 216148 21825 22339 22793 Gap junction Itpr1 16438 Adcy2 210044 Csnk1d 104318 Edg2 14745 Gja1 14609 Grb2 14784 Nras 18176 Pdgfc 54635 Rras2 20130 Adherens junctions Actn3 11474 Baiap2 108100 Iqgap1 29875 Lmo7 380928 Mapk3 26417 Pvrl4 71740 Vcl 22330 Wasl 73178 up down up down up up up down up down up up down down up down up down up up down up down down up down down up up down down down down up 0 0 0 0 0 1 1 0 0 0 ND 0 0 ND 0 0 0 0 1 0 0 1 0 0 ND 0 0 0 0 ND ND 0 0 0 TGFbeta signaling Amhr2 Bmp7 Bmpr1a Cul1 Id1 Id2 Id3 Lefty1 Mapk3 Nodal Pitx2 Thbs1 Cell cycle Anapc10 Ccnd2 Cdc20 Cdc27 Cdc7 Cdkn1c Chek1 Cul1 Gadd45a Gadd45g Mcm6 Sfn Smc1l2 110542 12162 12166 26965 15901 15902 15903 13590 26417 18119 18741 21825 68999 12444 107995 217232 12545 12577 12649 26965 13197 23882 17219 55948 140557 down up up up up up up up down up up up up up up up down up down up down up down up down Ring1b Regulates ES Cell Fate ND 1 0 0 0 0 1 0 ND 0 0 0 0 1 0 0 0 1 0 0 0 1 0 ND 0 DAVID Pathway analysis revealed the pathways deregulated in Ring1b-deficient ES cells. Shown are the deregulated genes per pathway, their EntrezIDs, the deregulated expression state, and binding of Ring1b to the promoter (1 = bound, 0 = not bound, ND = no data). For a complete overview of all identified pathways see Table S3. doi:10.1371/journal.pone.0002235.t001 derepressed following differentiation [21,25]. These data support a role for Ring1b/PcG in direct repression of TGFbeta signaling in ES cells. In agreement with the GO classification analysis, we found altered expression of several components of the cell cycle pathway. Changes in cell cycle regulation have been observed following differentiation of ES cells, characterized by amongst others activation of the pRb-E2f controlled G1 checkpoint, which is inoperative in ES cells [37,38]. In line with this, key cell cycle regulators involved in activation of the G1/S checkpoint (derepressed Cdkn1c; downregulated E2f1, Cdc7 and Mcm6) were transcriptionally deregulated. However, deregulation of other key cell cycle genes suggest promotion of S phase (derepressed Ccnd2/ Cyclin D2 and Cul1), G2/M arrest (derepressed Gadd45g and Sfn/ 14-3-3-sigma) or bypass of G2/M arrest (downregulated Gadd45a) and mitotic exit (derepressed Cdc20 and Cdc27). This could imply PLoS ONE | www.plosone.org 6 May 2008 | Volume 3 | Issue 5 | e2235