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Supplementary table 5. Functions of genes connected to lncRNA-HEIH in subnetwork Gene Description References symbol CDC27 Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that 1 controls progression through mitosis and the G1 phase of the cell cycle. EDG3 Receptor for the lysosphingolipid sphingosine 1-phosphate. When expressed in rat HTC4 hepatoma cells, is capable of 2 mediating S1P-induced cell proliferation and suppression of apoptosis. HAX1 Promotes cell survival MVP MVP tyrosyl phosphorylation by SHP-2 may play an 3 4 important role in cell survival signaling. PSMC5 PSMC5 positively regulates p53-mediated transcription at 5 p21waf1 promoter. RBM10 X-chromosome RBM genes play a formerly unknown role in the regulation of programmed cell death (apoptosis) in 6 breast cancer TBPL1 TBP (TATA-binding protein)-like protein (TLP) contributes 7 to the regulation of stress-mediated cell cycle checkpoint and apoptotic pathways UBE2E3 UBE2E3 is a major enzyme in modulating the balance 8 between cell proliferation and differentiation DENR Plays a role in the modulation of the translational profile of a subset of cancer-related mRNAs when recruited to the 9 translational initiation complex by the oncogene MCTS1. 1. Topper, L.M., et al. The dephosphorylated form of the anaphase-promoting complex protein Cdc27/Apc3 concentrates on kinetochores and chromosome arms in mitosis. Cell Cycle 1, 282-292 (2002). 2. An, S., Zheng, Y. & Bleu, T. Sphingosine 1-phosphate-induced cell proliferation, survival, and related signaling events mediated by G protein-coupled receptors Edg3 and Edg5. J Biol Chem 275, 288-296 (2000). 3. Kang, Y.J., et al. Molecular interaction between HAX-1 and XIAP inhibits apoptosis. Biochem Biophys Res Commun 393, 794-799 (2010). 4. Kolli, S., Zito, C.I., Mossink, M.H., Wiemer, E.A. & Bennett, A.M. The major vault protein is a novel substrate for the tyrosine phosphatase SHP-2 and scaffold protein in epidermal growth factor signaling. J Biol Chem 279, 29374-29385 (2004). 5. Zhu, Q., et al. The ubiquitin-proteasome system regulates p53-mediated transcription at p21waf1 promoter. Oncogene 26, 4199-4208 (2007). 6. Martinez-Arribas, F., et al. Positive correlation between the expression of X-chromosome RBM genes (RBMX, RBM3, RBM10) and the proapoptotic Bax gene in human breast cancer. J Cell Biochem 97, 1275-1282 (2006). 7. Suenaga, Y., et al. TATA-binding Protein (TBP)-like Protein Is Engaged in Etoposide-induced Apoptosis through Transcriptional Activation of Human TAp63 Gene. J Biol Chem 284, 35433-35440 (2009). 8. Plafker, K.S., Farjo, K.M., Wiechmann, A.F. & Plafker, S.M. The human ubiquitin conjugating enzyme, UBE2E3, is required for proliferation of retinal pigment epithelial cells. Invest Ophthalmol Vis Sci 49, 5611-5618 (2008). 9. Reinert, L.S., et al. MCT-1 protein interacts with the cap complex and modulates messenger RNA translational profiles. Cancer Res 66, 8994-9001 (2006).