Compendium of metazoan TF and miRNA target sets

The table below lists the TF and miRNA target sets we collected from the literature.
The "Source" column indicates the experimental procedure or database, from which the target set was derived:
gene expression microarrays (Ex), ChIP-chip (CC), ChIP-DSL (C-DSL), DamID, or Gene Ontology database (GO).

Back to the Amadeus supplementary results page.

Set name Organism TF/miRNA Source Target-set size Ref. Description
CREB_Zhang Human CREB CC 2338 [29] Targets of CREB, identified by ChIP-chip in HEK293T cells in three different time points after forskolin stimulation. The microarray covered the promoter region from -700bp to 200bp of 16K genes.
E2F4_Cam E2F CC 201 [5] Genes that are bound by both E2F4 and p130 in three different growth arrest condtions, identified by ChIP-chip in T98G and U2OS cells under growth arrest. The microarray covered the promoter region from -700bp to 200bp of 13K genes.
E2F_Ren E2F CC 79 [23] Targets of E2F4 that are expressed during cell cycle entry, identified by ChIP-chip in quiescent WI-38 cells. The microarray covered the promoter region from -700bp to 200bp of 1444 genes, ~1200 of which show regulated expression during cell cycle reentry.
ERa_Kwon ESR1 C-DSL 496 [13] Targets of estrogen receptor α, identified by ChIP-DSL in MCF-7 cells. The array covered the promoter region from -800bp to 200bp of 17K genes.
ETS1_Hollenhorst ETS1 CC 1192 [10] Targets of ETS1, identified by ChIP-chip in Jurkat T-cells. The microarray covered the promoter region from -5Kbp to 2Kbp of 17K genes.
HCC-G1S_Whitfield E2F Ex 266 [27] Genes whose expression peaks periodically in the G1/S cell cycle phase.
HCC-G2M_Whitfield NF-Y Ex 344 [27] Genes whose expression peaks periodically in the G2/M cell cycle phase.
HNF1a_Odom HNF1A CC 206 [19] Targets of HNF1α, identified by ChIP-chip in hepatocytes. The microarray covered the promoter region from -750bp to 250bp of 13K genes.
HNF4a_Odom HNF4A CC 1475 [19] Targets of HNF4α, identified by ChIP-chip in hepatocytes. The microarray covered the promoter region from -750bp to 250bp of 13K genes.
HNF6_Odom ONECUT CC 212 [19] Targets of HNF6, identified by ChIP-chip in hepatocytes. The microarray covered the promoter region from -750bp to 250bp of 13K genes.
HSF1_Page HSF1 CC 328 [21] Targets of HSF1, identified by ChIP-chip in HeLa cells under heat shock. The microarray covered the promoter region from -1.3Kbp to 200bp of 24K genes.
ImmuneResponse_GO_Hs IRF/NFKB GO 586 [17] GO Term; Accession - GO:0006955, Name - immune response, Ontology - biological process. In [17], IRF and NF-kB binding sites were found to be enriched in promoters of immune response genes.
Nanog_Boyer NANOG CC 714 [3] Targets of Nanog, identifed by ChIP-chip in embryonic stem cells. The microarray covered the promoter region from -8Kbp to 2Kbp of 18K genes.
NFkB_Schreiber NFKB CC 270 [26] Genes bound by one of the five NF-kB subunits in U937 cells before or 1 hour after lipopolysaccharide stimulation. The microarray covered the promoter region from -700bp to 200bp of 9,496 genes.
Nrf1_Cam NRF1 CC 674 [5] Targets of NRF1, identified by ChIP-chip in quiescent T98G cells. The microarray covered the promoter region from -700bp to 200bp of 13K genes.
Oct4_Boyer POU5F1 CC 241 [3] Targets of Oct4, identifed by ChIP-chip in embryonic stem cells. The microarray covered the promoter region from -8Kbp to 2Kbp of 18K genes.
p53_Kannan TP53 Ex 38 [12] Primary targets of p53: genes that were up-regulated under the induction of p53 and inhibition of protein synthesis by cycloheximide in H1299Val135 cells (lung cancer cell line that expresses the temperature sensitive murine p53).
Sox2_Boyer SOX2 CC 575 [3] Targets of Sox2, identifed by ChIP-chip in embryonic stem cells. The microarray covered the promoter region from -8Kbp to 2Kbp of 18K genes.
SRF_Cooper SRF CC 172 [8] Targets of SRF, identified by ChIP-chip in different cell lines: Jurkat, T/G HA-VSMC, and Be(2)-C cells. The microarray covered the promoter region from -1Kbp to 300bp of 19K genes.
YY1_XiRen YY1 CC 713 [28] Targets of YY1 identified by ChIP-chip. The microarray covered the promoter region from -1.3Kbp to 200bp of 24K genes.
Foxp3_Marson Mouse Foxp3 CC 1060 [18] Targets of Foxp3, identified by ChIP-chip in Foxp3-CD4+ T-cell hybridomas that were transduced with FLAG-tagged Foxp3 and stimulated by phorbol myristate acetate/ionomycin. The microarray covered the promoter region from -8Kbp to 2Kbp of 16K genes.
ImmuneResponse_GO_Mm Irf/Nfkb GO 329 [17] GO Term; Accession - GO:0006955, Name - immune response, Ontology - biological process. In [17], IRF and NF-kB binding sites were found to be enriched in promoters of immune response genes.
MEF2_Blais Mef2 CC 25 [2] Targets of Myocyte Enhancer Factor 2, identified by ChIP-chip in myotubes. The microarray covered the promoter region from -750bp to 250bp of 4700 genes.
MyoD_Blais Myod CC 102 [2] Targets of MyoD, identified by ChIP-chip in growing cells or myotubes. The microarray covered the promoter region from -750bp to 250bp of 4700 genes.
MyoD_Cao Myod CC 102 [6] Targets of MyoD. The ChIP-chip assay was performed in embryonic fibroblasts derived from mice that were double knockouts for Myod and Myf5, 36 hours after induction of differentiation. The microarray covered the promorer region from -750bp to 250bp of 13K genes.
MyoG_Cao Myog CC 78 [6] Targets of MyoG. The ChIP-chip assay was performed in embryonic fibroblasts derived from mice that were double knockouts for Myod and Myf5, 36 hours after induction of differentiation. The microarray covered the promorer region from -750bp to 250bp of 13K genes.
Myogenin_Blais Myog CC 106 [2] Targets of myogenin, identified by ChIP-chip on myotubes. The microarray covered the promoter region from -750bp to 250bp of 4700 genes.
GATA_Pauli C. elegans GATA Ex 1342 [22] Genes that are expressed in the intestine.
HSF_Machin Fly Hsf CC 183 [1] Targets of heat-shock factor, identified by ChIP-chip in cells of embryos that were heat-shocked. The microarray contained full-length cDNA clones for 5000 genes.
MEF2_Sandmann Mef2 CC+Ex 208 [25] High confidence targets of Mef2. The confidence was measured by a score that took into consideration the distance of the gene from the binding region, its expression in Mef2 mutant embryos and other supporting data. The Mef2 binding regions were identified by ChIP-chip with tiling array.
MSL1_Legube Dref CC 116 [14] Targets of male-specific lethal complex-1, identified by ChIP-chip on 014 h embryos or tightly staged 46 h embryos. The microarray covered 6000 clones.
Myc_Oryan Myc/Max/Mad DamID 714 [20] Targets of one or more of the proteins dMax, dMnt, and dMyc, identified by DamID assay on Kc cells.
let7_Brueckner Human hsa-let-7a Ex 177 [4] Genes that were down-regulated in L7-A549 cells following let-7a-3 transfection.
let7_Johnson hsa-let-7b Ex 182 [11] Genes that show altered expression in the presence of exogenously added let-7 in both HepG2 and A549 cells.
miR1_Lim hsa-miR-1 Ex 65 [15] Genes that were down-regulated in HeLa cells that were transfected with miR-1.
miR16_Linsley hsa-miR-16 Ex 90 [16] Genes that were down-regulated in HCT116 Dicerex5 and DLD-1 Dicerex5 cells that were transfected with miR-16.
miR34_Chang hsa-miR-34a Ex 89 [7] Genes that were down-regulated in HCT116 cells that were transfected with miR-34a.
miR34_He hsa-miR-34a Ex 367 [9] Genes that were down-regulated in HCT116 Dicerex5 cells that were transfected with miR-34a.
miR106b_Linsley hsa-miR-106b Ex 88 [16] Genes that were down-regulated in HCT116 Dicerex5 and DLD-1 Dicerex5 cells that were transfected with miR-106b.
miR124_Lim hsa-miR-124 Ex 116 [15] Genes that were down-regulated in HeLa cells that were transfected with miR-124.
miR373_Lim hsa-miR-373 Ex 43 [15] Genes that were down-regulated in HeLa cells that were transfected with miR-373.
miR155_Rodriguez Mouse mmu-miR-155 Ex 95 [24] Genes that were up-regulated in CD4+ T cells of mice deficient for bic/miR-155.
References
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3. Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG et al: Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 2005, 122(6):947-956.
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7. Chang TC, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ et al: Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Mol Cell 2007, 26(5):745-752.
8. Cooper SJ, Trinklein ND, Nguyen L, Myers RM: Serum response factor binding sites differ in three human cell types. Genome Res 2007, 17(2):136-144.
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13. Kwon YS, Garcia-Bassets I, Hutt KR, Cheng CS, Jin M, Liu D, Benner C, Wang D, Ye Z, Bibikova M et al: Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proc Natl Acad Sci U S A 2007, 104(12):4852-4857.
14. Legube G, McWeeney SK, Lercher MJ, Akhtar A: X-chromosome-wide profiling of MSL-1 distribution and dosage compensation in Drosophila. Genes Dev 2006, 20(7):871-883.
15. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM: Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 2005, 433(7027):769-773.
16. Linsley PS, Schelter J, Burchard J, Kibukawa M, Martin MM, Bartz SR, Johnson JM, Cummins JM, Raymond CK, Dai H et al: Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression. Mol Cell Biol 2007, 27(6):2240-2252.
17. Long F, Liu H, Hahn C, Sumazin P, Zhang MQ, Zilberstein A: Genome-wide prediction and analysis of function-specific transcription factor binding sites. In Silico Biol 2004, 4(4):395-410.
18. Marson A, Kretschmer K, Frampton GM, Jacobsen ES, Polansky JK, MacIsaac KD, Levine SS, Fraenkel E, von Boehmer H, Young RA: Foxp3 occupancy and regulation of key target genes during T-cell stimulation. Nature 2007, 445(7130):931-935.
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22. Pauli F, Liu Y, Kim YA, Chen PJ, Kim SK: Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegans. Development 2006, 133(2):287-295.
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24. Rodriguez A, Vigorito E, Clare S, Warren MV, Couttet P, Soond DR, van Dongen S, Grocock RJ, Das PP, Miska EA et al: Requirement of bic/microRNA-155 for normal immune function. Science 2007, 316(5824):608-611.
25. Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE: A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development. Dev Cell 2006, 10(6):797-807.
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28. Xi H, Yu Y, Fu Y, Foley J, Halees A, Weng Z: Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1. Genome Res 2007, 17(6):798-806.
29. Zhang X, Odom DT, Koo SH, Conkright MD, Canettieri G, Best J, Chen H, Jenner R, Herbolsheimer E, Jacobsen E et al: Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proc Natl Acad Sci U S A 2005, 102(12):4459-4464.