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Table 1 Most highly up-modulated transcripts in ERα (+) breast carcinomas identified by SAGE.

From: Gene expression signature of estrogen receptor α status in breast cancer

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%)
  1. * Genes with known or putative high-affinity EREs mapping in the vicinity of the TSS.
  2. # 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.
  3. For the whole list of ERα associated transcripts see additional data file 1.