Noerholm et al. BMC Cancer 2012, 12:22 http://www.biomedcentral.com/1471-2407/12/22 Page 5 of 11 Table 1 Down-and up-regulated genes passing the criteria described in “Results” Down-regulated genes No Gene Symbol Fold Description 1 TMSL3 -4.21 Homo sapiens thymosin-like 3 (TMSL3), mRNA [NM_183049] 2 A_24_P530977 -4.00 Unknown 3 GNG11 -3.86 Homo sapiens guanine nucleotide binding protein (G protein), gamma 11 (GNG11), mRNA [NM_004126] 4 RPS4Y2 -3.80 Homo sapiens ribosomal protein S4, Y-linked 2 (RPS4Y2), mRNA [NM_001039567] 5 RGS10 -3.63 Homo sapiens regulator of G-protein signalling 10 (RGS10), transcript variant 1, mRNA [NM_001005339] 6 RPS4Y1 -3.62 Homo sapiens ribosomal protein S4, Y-linked 1 (RPS4Y1), mRNA [NM_001008] 7 B2M -3.60 Homo sapiens beta-2-microglobulin (B2M), mRNA [NM_004048] 8 CCL5 -3.35 Homo sapiens chemokine (C-C motif) ligand 5 (CCL5), mRNA [NM_002985] 9 AL049447 -3.35 Homo sapiens mRNA; cDNA DKFZp586A0722 (from clone DKFZp586A0722). [AL049447] 10 GPX1 -3.27 Homo sapiens glutathione peroxidase 1 (GPX1), transcript variant 2, mRNA [NM_201397] 11 RPS29 -3.12 Homo sapiens ribosomal protein S29 (RPS29), transcript variant 1, mRNA [NM_001032] 12 IER2 -3.12 Homo sapiens immediate early response 2 (IER2), mRNA [NM_004907] 13 RAP1B -2.94 Homo sapiens RAP1B, member of RAS oncogene family (RAP1B), transcript variant 1, mRNA [NM_015646] 14 MMD -2.93 Homo sapiens monocyte to macrophage differentiation-associated (MMD), mRNA [NM_012329] 15 MAX -2.89 Homo sapiens MYC associated factor × (MAX), transcript variant 3, mRNA [NM_145113] 16 TMEM111 -2.87 Homo sapiens transmembrane protein 111 (TMEM111), mRNA [NM_018447] 17 RPS29 -2.82 Homo sapiens ribosomal protein S29 (RPS29), transcript variant 1, mRNA [NM_001032] 18 RPL19 -2.81 Homo sapiens ribosomal protein L19 (RPL19), mRNA [NM_000981] 19 RPL13 -2.80 Homo sapiens ribosomal protein L13 (RPL13), transcript variant 2, mRNA [NM_033251] 20 LOC392497 -2.78 PREDICTED: Homo sapiens similar to 40S ribosomal protein S6 (LOC392497), mRNA [XR_018138] 21 MRCL3 -2.74 Homo sapiens myosin regulatory light chain MRCL3 (MRCL3), mRNA [NM_006471] 22 RPL30 -2.72 Homo sapiens ribosomal protein L30 (RPL30), mRNA [NM_000989] 23 RPS27 -2.70 Homo sapiens ribosomal protein S27 (metallopanstimulin 1) (RPS27), mRNA [NM_001030] 24 ENST00000337102 -2.70 40S ribosomal protein S21. [Source:Uniprot/SWISSPROT;Acc:P63220] [ENST00000337102] 25 RPA1 -2.68 Homo sapiens replication protein A1, 70 kDa (RPA1), mRNA [NM_002945] Up-regulated genes No Gene Symbol Fold Description 1 CV575560 3.80 oe37f10.y1 Human keratoconus cornea, unamplified, od [CV575560] 2 RKHD1 2.32 Homo sapiens ring finger and KH domain containing 1 (RKHD1), mRNA [NM_203304] 3 ZNF784 2.65 Homo sapiens zinc finger protein 784 (ZNF784), mRNA [NM_203374] 4 SERPINB1 2.62 Leukocyte elastase inhibitor (LEI) (Serpin B1) (Monocyte/neutrophil elastase inhibitor) (M/NEI) (EI). 5 LOC390427 2.00 PREDICTED: Homo sapiens similar to TBP-associated factor 15 isoform 1 (LOC390427), mRNA [XM_372498] 6 FOXD3 2.32 Homo sapiens forkhead box D3 (FOXD3), mRNA [NM_012183] 7 C17orf74 1.97 Homo sapiens chromosome 17 open reading frame 74 (C17orf74), mRNA [NM_175734] 8 ENST00000357697 1.67 Unknown 9 SLITRK4 2.30 Homo sapiens SLIT and NTRK-like family, member 4 (SLITRK4), mRNA [NM_173078] 10 AGRP 2.03 Homo sapiens agouti related protein homolog (mouse) (AGRP), transcript variant 1, mRNA [NM_001138] 11 ENST00000359466 1.77 chromosome × open reading frame 18 (CXorf18), misc RNA [RefSeq_dna;Acc:XR_018001] [ENST00000359466] 12 THC2760960 1.41 Unknown 13 TNXB 2.06 Homo sapiens tenascin XB (TNXB), transcript variant XB, mRNA [NM_019105] 14 THC2755576 1.90 ALU1_HUMAN (P39188) Alu subfamily J sequence contamination warning entry, partial (13%) [THC2755576] 15 SIN3B 1.60 Homo sapiens SIN3 homolog B, transcription regulator (yeast), complete cds. [BC063531] 16 CRLF1 1.66 Homo sapiens cytokine receptor-like factor 1 (CRLF1), mRNA [NM_004750] 17 ZNF219 1.97 Homo sapiens zinc finger protein 219 (ZNF219), mRNA [NM_016423] 18 THC2654039 1.78 ALU2_HUMAN (P39189) Alu subfamily SB sequence contamination warning entry, partial (4%) [THC2654039] 19 AA418814 1.59 AA418814 Soares_NhHMPu_S1 Homo sapiens cDNA clone IMAGE:767978 3’, mRNA sequence [AA418814]