The PRIMO analysis demonstrated that up-regulated genes have an over-representation of HNF4α binding sequences or HNF4α-like sequences (COUP-TF, PPAR) and GC-rich sequences (Sp1, E2F, ETF) (Table 1).
Enter the two-month-old Van Eck Market Vectors Coal ETF (44, KOL), which tracks the price and yield performance of the Stowe Coal Index.
These are AP-2, C/EBP, E2F, ETF, LEF1, MAZ, MAZR, MZF1, Pax-4, Sp1, Spz1, TATA, TFII-I, VDR, ZF5.
They identified Etf, E2f1 and Sp1 as having a potentially pronounced role in mediation of the proliferative effect within the first 24 hours after isolation.
The specific sites for primates are Sp1, LRF, LFA1, MZF1, ZF5, ETF, HNF4, Churchill, MZF114 and Kid3; and the specific sites for rodents are FOXO1, CDPCR3, CIZ, FOXO3, FOXD1, Sox5, FOXL1, Kid3/ZNF354 and Prrx2.
The large overlap of commonly enriched TFBS between all test systems and compounds provides evidence for the existence of a set of 'common transcription factors' (including, e.g., E2F, ETF, SP1 and AP-2 (Fig. S8).
For example, a group of genes upregulated by HTV mechanical ventilation alone (ETF, E2F, Nrf1, CREB, and HIF1) is not found in the list of genes upregulated by LPS [ 49].
Thus, the IPA predicted HNF4A, Myc, p53 and NFkB to be the dominant transcription factors; in contrast, the Core_TF program predicted the preponderance of E2F1, AP2, EGR2, ETF, Sp1 and KROX.
Expression levels of 64 genes were significantly upregulated in the lungs, including early transcriptional factors ETF, E2F, NRF-1, CRE, and HIF1; inflammatory mediators IL-1β, IL-6, MIP1, MIP2, and GRO1; cell cycle control genes Btg2, Jun, IRF-1, and Atf-3; and others involved in cell signaling and metabolism, consistent with other microarray studies [ 5].
Several other possible pathways, e.g. p38, p42/44 MAPK and transcription factors, e.g. SP1 and possibly AP2, Adh1 (ETF), PEA3 sites [ 32] which could also contribute to NF-kB dependent gene activation and might participate in NO mediated MAdCAM-1 regulation by cytokines.
Previously, Elkon et al. [ 36] reported in silico identified transcriptional regulators associated with c-Myc activity in human Burkitt's lymphoma cells and this included overrepresentation of binding sites of the transcription factors ETF, SP1, Nrf-1, NF-Y, CREB, Egr-1, Elk-1, E2F and AhR/Arnt in c-Myc target genes.
