Table 1.
Most highly up-modulated transcripts in ERα (+) breast carcinomas identified by SAGE.
| Gene name | Tag | Locus Link | Fold change (p value) | Frequency# |
| Cell proliferation related | ||||
| TFF1* (trefoil factor 1) | CTGGCCCTCG | 7031 | 51.4 (0.0016) | 15/18 (83%) |
| DUSP4 (dual specificity phosphatase 4) | CGGGCAGAAA | 1846 | 14.7 (0.0016) | 14/18 (78%) |
| NDN* (necdin homolog) | ACCTTGCTGG | 4692 | 13.3 (0.0026) | 11/18 (61%) |
| HDGFRP3 (hepatoma-derived growth factor) | TGTAAAGTTT | 50810 | 9.8 (0.0019) | 12/18 (67%) |
| TSPAN1* (tetraspan 1) | GGAACTGTGA | 10103 | 9.5 (0.0017) | 15/18 (83%) |
| SEP6 (septin 6) | TCAATTTTCA | 23157 | 7.6 (0.0044) | 12/18 (67%) |
| DHX34* (DEAH box polypeptide 34) | GTTGCTCACT | 9704 | 7.1 (0.0129) | 9/18 (50%) |
| Apoptosis related | ||||
| CARD10* (caspase recruitment domain family) | AGAATGTACG | 29775 | 11.1 (0.0030) | 15/18 (83%) |
| Signal transduction related | ||||
| SYTL4* (synaptotagmin-like 4) | TATGTGTGCT | 94121 | 28.0 (0.0003) | 15/18 (83%) |
| ECM1* (extracellular matrix protein 1) | ACTGCCCGCT | 1893 | 10.1 (0.0175) | 13/18 (72%) |
| LEPR* (leptin receptor) | AAAGTTTGAG | 3953 | 9.8 (0.0302) | 10/18 (55%) |
| PTGES (prostaglandin E synthase) | TGAGTCCCTG | 9536 | 8.0 (0.0168) | 8/18 (44%) |
| SCUBE2 (signal peptide, CUB domain EGF-like 2) | TCAGCACAGT | 57758 | 7.5 (0.0024) | 14/18 (78%) |
| ADORA2A* (adenosine A2a receptor) | TGCTGAGTAG | 135 | 7.1 (0.0460) | 11/18 (61%) |
| ITGBL1 (integrin beta-like 1) | CATATTCACA | 9358 | 7.1 (0.0159) | 8/18 (44%) |
| Regulation of transcription related | ||||
| ESR1 (estrogen receptor 1) | AGCAGGTGCC | 2099 | 9.8 (0.0000) | 18/18 (100%) |
| TCEAL1 (transcriptional elongation factor A) | AAAGATGTAC | 9338 | 9.8 (0.0014) | 13/18 (72%) |
| ZNF14 (zinc finger protein 14) | TAAACAGCCC | 7561 | 8.4 (0.0023) | 13/18 (72%) |
| ZNF38* (zinc finger protein 38) | CCAGCATTAC | 7589 | 7.6 (0.0051) | 10/18 (55%) |
| HIF1AN* (hypoxia-inducible factor 1α subunit inhibitor) | CCTGAGTGCG | 55662 | 7.1 (0.0094) | 10/18 (55%) |
| HOXC13 (homeo box C13) | TTTTTAAAAT | 3229 | 7.1 (0.0157) | 9/18 (50%) |
| Cytoskeleton | ||||
| MAPT (microtubule-associated protein tau) | GTAGACTCGC | 4137 | 9.8 (0.0085) | 9/18 (50%) |
| MYLIP (myosin regulatory light chain interacting) | TTTTCCACTC | 29116 | 9.3 (0.0036) | 11/18 (61%) |
| Metabolism and Miscelaneous | ||||
| RIMS4 (regulating synaptic membrane exocytosis) | TTGAAATTAA | 140730 | 24.9 (0.0378) | 8/18 (44%) |
| NAT1 (N-acetyltransferase 1) | TATCTTCTGT | 9 | 11.7 (0.0385) | 15/18 (83%) |
| ATP6V1B1* (ATPase, H+ transporting) | CCTCCCCCTC | 525 | 10.7 (0.0111) | 10/18 (55%) |
| JDP1 (J domain containing protein 1) | TCTGTGAATT | 56521 | 10.0 (0.0035) | 12/18 (67%) |
| CHST11 (carbohydrate sulfotransferase 11) | AACCTTCCTC | 50515 | 9.8 (0.0009) | 13/18 (72%) |
| CILP (nucleotide pyrophosphohydrolase) | GTTTTGCCCA | 8483 | 9.3 (0.0054) | 14/18 (78%) |
| ABCA3 (ATP-binding cassette sub-family A) | GTAGTCACCG | 21 | 8.9 (0.0149) | 10/18 (55%) |
| SEC14L2 | GGAAGGCGGC | 23541 | 8.7 (0.0487) | 9/18 (50%) |
| ANXA9* (annexin A9) | ACATCCGAGG | 8416 | 8.4 (0.0145) | 10/18 (55%) |
| KCTD3 (K channel tetramerisation domain 3) | ATAATTAAAT | 51133 | 8.4 (0.0001) | 17/18 (94%) |
| SFRS7 (splicing factor) | TAGCTAATAT | 6432 | 8.0 (0.0031) | 12/18 (67%) |
| SNRPA* (small nuclear ribonucleoprot. polypep. A) | AAGATCTCCT | 6626 | 7.6 (0.0009) | 15/18 (83%) |
| NNMT (nicotinamide N-methyltransferase) | CCTGCAATTC | 4837 | 7.6 (0.0120) | 10/18 (55%) |
| SLC1A4 (solute carrier family 1 member 4) | GACTCACAGG | 6509 | 7.6 (0.0254) | 9/18 (50%) |
| TIPARP (TCDD-inducible polymerase) | AAATGGCCAA | 25976 | 7.6 (0.0051) | 10/18 (55%) |
| SLC7A2 (solute carrier family 7 member 2) | CACTGACAGC | 6542 | 7.3 (0.0190) | 11/18 (61%) |
| GA* (liver mitochondrial glutaminase) | CTGCTGCTAC | 27165 | 7.1 (0.0126) | 9/18 (50%) |
| Function unknown | ||||
| C1orf34 | AGGATGTACA | 22996 | 13.3 (0.0025) | 14/18 (78%) |
| SMILE (hypothetical protein FLJ90492) | TAGAGAGTTT | 160418 | 11.1 (0.0004) | 15/18 (83%) |
| RHBDL4 (rhomboid, veinlet-like 4) | TTGTTTCTAA | 162494 | 10.7 (0.0099) | 9/18 (50%) |
| KIAA0882 | GTCTCATTTC | 23158 | 10.1 (0.0007) | 18/18 (100%) |
| C20orf103* | TTTAGTGATT | 24141 | 9.3 (0.0277) | 10/18 (55%) |
| FLJ33387 | GCAGGGAGAG | 161145 | 9.3 (0.0118) | 10/18 (55%) |
| TRALPUSH | GTTTCCAGAG | 116931 | 8.9 (0.0458) | 9/18 (50%) |
| KIAA0980* | TGGTGCTTCC | 22981 | 7.6 (0.0096) | 11/18 (61%) |
| C10orf32 | AGTCTGTTGT | 119032 | 7.3 (0.0002) | 15/18 (83%) |
| FLJ13611 | TAATCACACT | 80006 | 7.1 (0.0069) | 10/18 (55%) |
* Genes with known or putative high-affinity EREs mapping in the vicinity of the TSS.
# Transcripts tags changing > 2-fold when compared with the average expression of ER (-) tumors in at least 8 of 18 (44%) ERα (+) invasive carcinomas SAGE libraries.
For the whole list of ERα associated transcripts see additional data file 1.