Supplementary Table 1S-6S
Table 1S. Information of cDNA libraries for cDNA DGED
Library Name / Sequences / Keywords / PoolNIH_MGC_67 / 29771 / non-normalized, retinoblastoma, EST / B (RB)
47028
NIH_MGC_16 / 17257 / non-normalized, retinoblastoma, EST
Stratagene fetal retina 937202 / 6293 / fetus, retina, normal, non-normalized, EST / A
(Normal
Retina)
27400
Soares retina N2b5HR / 2384 / adult,male,retina, normal, non-normalized, EST
Soares retina N2b4HR / 12538 / adult, male,retina, normal, non-normalized, EST
Human retina cDNA Tsp509I-cleaved sublibrary / 1524 / retina, normal, non-normalized, adult, EST, mixed pool by gender
Retina II / 1296 / adult, mixed pool by gender, retina, normal, non-normalized, EST,
Human retina cDNA randomly primed sublibrary / 3365 / adult, mixed pool by gender, retina, normal, EST,
Table 2S.Information of SAGE libraries for SAGE DGED
Library Name / Tags / Keywords / PoolSAGE_Retina_Retinoblastoma_B_1 / 88490 / retinoblastoma / B (RB)
88490
SAGE_Retina_Pigment_epithelium_normal_B_1 / 53666 / retina, non-normalized, normal, epithelium, short SAGE / A
(Normal
Retina )
321056
SAGE_Retina_Peripheral_normal_B_2 / 105312 / retina, non-normalized, normal, short SAGE
SAGE_Retina_Peripheral_normal_B_1 / 59661 / retina, non-normalized, normal, short SAGE
SAGE_Retina_macula_normal_B_HMAC2 / 102417 / retina, non-normalized, normal, macula, short sage
Table 3S. List of Genes down-regulated in RB by cDNA DGED
Symbol /Gene Description
/ Cluster / F / P / Cyt LoCVisual perception or Visual Signal Transduction(15)
ABCA4 / ATP-binding cassette, sub-family A (ABC1), member 4 / Hs.694924 / NaN / 0 / 1p22.1-p21
ARR3 / Arrestin 3, retinal (X-arrestin) / Hs.308 / 23.22 / 0 / Xcen-q21
BBS1 / Bardet-Biedl syndrome 1 / Hs.502915 / NaN / 0 / 11q13.1
GNAT1 / G protein, alpha transducing activity polypeptide 1 / Hs.517978 / NaN / 0 / 3p21
GUCA1A / Guanylate cyclase activator 1A (retina) / Hs.92858 / NaN / 0 / 6p21.1
GUCA1B / Guanylate cyclase activator 1B (retina) / Hs.446529 / NaN / 0 / 6p21.1
MPP4 / Membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4) / Hs.63085 / NaN / 0 / 2q33.2
PDE6A / Phosphodiesterase 6A, cGMP-specific, rod, alpha / Hs.567314 / 95.43 / 0 / 5q31.2-q34
PDE6G / Phosphodiesterase 6G, cGMP-specific, rod, gamma / Hs.654482 / NaN / 0 / 17q25
PLEKHB1 / Pleckstrin homology domain containing, family B (evectins) member 1 / Hs.445489 / 37.53 / 0 / 11q13.5-q14.1
PLEKHG5 / Pleckstrin homology domain containing, family G member 5 / Hs.284232 / NaN / 0.01 / 1p36.31
RCVRN / Recoverin / Hs.80539 / 21.05 / 0 / 17p13.1
RHO / Rhodopsin (opsin 2, rod pigment) / Hs.247565 / NaN / 0 / 3q21-q24
ROM1 / Retinal outer segment membrane protein 1 / Hs.281564 / NaN / 0 / 11q13
SAG / S-antigen; retina and pineal gland (arrestin) / Hs.32721 / NaN / 0 / 2q37.1
Cyctoskeleton / adhesion(15)
ADD3 / Adducin 3 (gamma) / Hs.501012 / 23.22 / 0 / 10q24.2-q24.3
CKAP4 / Cytoskeleton-associated protein 4 / Hs.74368 / 9.77 / 0.01 / 12q23.3
COL1A1 / Collagen, type I, alpha 1 / Hs.172928 / NaN / 0 / 17q21.33
COL1A2 / Collagen, type I, alpha 2 / Hs.489142 / NaN / 0 / 7q22.1
EPB41L2 / Erythrocyte membrane protein band 4.1-like 2 / Hs.486470 / 10.75 / 0 / 6q23
GSN / Gelsolin (amyloidosis, Finnish type) / Hs.522373 / NaN / 0 / 9q33
MAPT / Microtubule-associated protein tau / Hs.101174 / 48.88 / 0 / 17q21.1
MFGE8 / Milk fat globule-EGF factor 8 protein / Hs.3745 / NaN / 0 / 15q25
PCDHB4 / Protocadherin beta 4 / Hs.591250 / NaN / 0.01 / 5q31
PPP1R3F / Protein phosphatase 1, regulatory (inhibitor) subunit 3F / Hs.433652 / 39.13 / 0 / Xp11.23
SPP1 / Secreted phosphoprotein 1 (osteopontin, bone sialoprotein I) / Hs.313 / NaN / 0.01 / 4q21-q25
SPTAN1 / Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) / Hs.372331 / 15.88 / 0.01 / 9q33-q34
SPTBN1 / Spectrin, beta, non-erythrocytic 1 / Hs.503178 / 15.88 / 0.01 / 2p21
TMEM178 / Transmembrane protein 178 / Hs.40808 / NaN / 0 / 2p22.1
TMEM56 / Transmembrane protein 56 / Hs.483512 / NaN / 0 / 1p21.3
Cell cycle/apoptosis(8)
APP / Amyloid beta (A4) precursor protein (peptidase nexin-II,) / Hs.434980 / 26.45 / 0 / 21q21.2|21q21.3
CCNI
CCPG1 / Cyclin I
Cell cycle progression 1 / Hs.518827
Hs.612814 / 12.42
46.44 / 0
0 / 4q21.1
15q21.1
CD74 / CD74 molecule, major histocompatibility complex, class II / Hs.694723 / NaN / 0 / 5q32
CLU / Clusterin / Hs.436657 / 53.78 / 0 / 8p21-p12
DUSP1 / Dual specificity phosphatase 1 / Hs.171695 / NaN / 0 / 5q34
FAS / Fas (TNF receptor superfamily, member 6) / Hs.244139 / NaN / 0 / 10q24.1
Table 3S continued
Symbol /
Gene Description
/ Cluster / F / P / Cyt LoCPRKCA / Protein kinase C, alpha / Hs.531704 / NaN / 0.01 / 17q22-q23.2
Protein degradation(1)
TRIM11 / Tripartite motif-containing 11 / Hs.13543 / 34.21 / 0 / 1q42.13
DNA repair(1)
MSH6 / MutS homolog 6 (E. coli) / Hs.445052 / 6.42 / 0.01 / 2p16
Regulation of transcription(10)
BHLHB3 / Basic helix-loop-helix domain containing, class B, 3 / Hs.177841 / NaN / 0 / 12p11.23-p12.1
CSDA / Cold shock domain protein A / Hs.221889 / 14.66 / 0 / 12p13.1
FOXK2 / Forkhead box K2 / Hs.591140 / 18.33 / 0.01 / 17q25
KLF6 / Kruppel-like factor 6 / Hs.4055 / NaN / 0 / 10p15
MBD1 / Methyl-CpG binding domain protein 1 / Hs.405610 / 39.1 / 0 / 18q21
NR1D1 / Nuclear receptor subfamily 1, group D, member 1 / Hs.592130 / NaN / 0 / 17q11.2
PCGF2 / Polycomb group ring finger 2 / Hs.371617 / NaN / 0.01 / 17q12
PRDM8 / PR domain containing 8 / Hs.373642 / NaN / 0 / 4q21
TFAP2B / Transcription factor AP-2 beta / Hs.33102 / NaN / 0 / 6p12
ZBTB17 / Zinc finger and BTB domain containing 17 / Hs.433764 / 26.89 / 0 / 1p36.2-p36.1
Signal transduction(10)
APLP2 / Amyloid beta (A4) precursor-like protein 2 / Hs.370247 / 39.13 / 0 / 11q23-q25|11q24
DDIT3 / DNA-damage-inducible transcript 3 / Hs.505777 / NaN / 0 / 12q13.1-q13.2
DDIT4 / DNA-damage-inducible transcript 4 / Hs.523012 / 24.47 / 0 / 10pter-q26.12
FRZB / Frizzled-related protein / Hs.128453 / NaN / 0 / 2qter
LPHN3 / Latrophilin 3 / Hs.694758 / NaN / 0.01 / 4q13.1
NF1 / Neurofibromin 1 (neurofibromatosis) / Hs.113577 / 31.76 / 0.01 / 17q11.2
SPARC / Secreted protein, acidic, cysteine-rich (osteonectin) / Hs.111779 / NaN / 0 / 5q31.3-q32
TLE1 / Transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila) / Hs.197320 / 31.76 / 0.01 / 9q21.32
WIF1 / WNT inhibitory factor 1 / Hs.284122 / NaN / 0 / 12q14.3
WSB1 / WD repeat and SOCS box-containing 1 / Hs.446017 / NaN / 0 / 17q11.1
Transport(11)
ANKH / Ankylosis, progressive homolog (mouse) / Hs.156727 / 39.1 / 0 / 5p15.1
ATP2B4 / ATPase, Ca++ transporting, plasma membrane 4 / Hs.343522 / NaN / 0 / 1q32.1
PITPNC1 / Phosphatidylinositol transfer protein, cytoplasmic 1 / Hs.591185 / NaN / 0 / 17q24.2
SEC24C / SEC24 related gene family, member C (S. cerevisiae) / Hs.654429 / 13.03 / 0.01 / 10q22.2
SLC12A5 / Solute carrier family 12, (potassium-chloride transporter) member 5 / Hs.21413 / NaN / 0 / 20q13.12
SLC35A3 / Solute carrier family 35, member A3 / Hs.448979 / NaN / 0 / 1p21
SLCO4A1 / Solute carrier organic anion transporter family, member 4A1 / Hs.235782 / 46.44 / 0 / 20q13.33
SV2B / Synaptic vesicle glycoprotein 2B / Hs.592018 / 17.1 / 0.01 / 15q26.1
TRPM1 / Transient receptor potential cation channel, subfamily M, member 1 / Hs.155942 / NaN / 0 / 15q13-q14
TTR / Transthyretin (prealbumin, amyloidosis type I) / Hs.427202 / NaN / 0 / 18q12.1
TF / Transferrin / Hs.518267 / NaN / 0 / 3q22.1
Metabolism/enzyme(10)
ALDOC / Aldolase C, fructose-bisphosphate / Hs.155247 / 22.82 / 0 / 17cen-q12
Table 3S continued
Symbol /
Gene Description
/ Cluster / F / P / Cyt LoCB3GAT2 / Beta-1,3-glucuronyltransferase 2 (glucuronosyltransferase S) / Hs.653102 / NaN / 0.01 / 6q13
FUT8 / Fucosyltransferase 8 (alpha (1,6) fucosyltransferase) / Hs.654961 / 29.32 / 0.01 / 14q24.3
GPX3 / Glutathione peroxidase 3 (plasma) / Hs.386793 / NaN / 0 / 5q23
GRSF1 / G-rich RNA sequence binding factor 1 / Hs.309763 / 22 / 0 / 4q13
HADHB / Hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA , beta subunit / Hs.534639 / 15.88 / 0.01 / 2p23
IDS / Iduronate 2-sulfatase (Hunter syndrome) / Hs.460960 / NaN / 0 / Xq28
NDUFC1
RPN2 / NADH dehydrogenase (ubiquinone) 1, subcomplex unknown,
Ribophorin II / Hs.84549
Hs.370895 / NaN
6.98 / 0
0.01 / 4q28.2-q31.1
20q12-q13.1
SUCLA2 / Succinate-CoA ligase, ADP-forming, beta subunit / Hs.546323 / 29.32 / 0.01 / 13q12.2-q13.3
Other(23)
C7orf20 / Chromosome 7 open reading frame 20 / Hs.107387 / 48.88 / 0 / 7p22.3
17q25.1
C17orf28 / Chromosome 17 open reading frame 28 / Hs.11067 / NaN / 0
C19orf54 / Chromosome 19 open reading frame 54 / Hs.585105 / 31.76 / 0.01 / 19q13.2
CAMSAP1 / Calmodulin regulated spectrin-associated protein 1 / Hs.522493 / 16.29 / 0 / 9q34.3
DDX51 / DEAD (Asp-Glu-Ala-Asp) box polypeptide 51 / Hs.445168 / NaN / 0 / 12q24.33
DUSP26 / Dual specificity phosphatase 26 (putative) / Hs.8719 / NaN / 0.01 / 8p12
KIAA0143 / KIAA0143 protein / Hs.204564 / 34.21 / 0 / 8q24.22
LOC284106 / Hypothetical protein LOC284106 / Hs.462923 / 28.11 / 0 / 17q12
LOC643280 / Hypothetical LOC643280 / Hs.581867 / NaN / 0 / 4q21.1
MGC42090 / Hypothetical protein MGC42090 / Hs.487670 / NaN / 0 / 7p15.3
MRLC2 / Myosin regulatory light chain MRLC2 / Hs.464472 / 51.33 / 0 / 18p11.31
MSL-1 / Male-specific lethal-1 homolog / Hs.532786 / 46.44 / 0 / 17q21.1
NDRG2 / NDRG family member 2 / Hs.525205 / NaN / 0 / 14q11.2
PHYHIPL / Phytanoyl-CoA 2-hydroxylase interacting protein-like / Hs.499704 / 15.88 / 0.01 / 10q11
SERPING1 / Serpin peptidase inhibitor, clade G (C1 inhibitor), member 1, / Hs.384598 / NaN / 0 / 11q12-q13.1
SERPINA3 / Serpin peptidase inhibitor, clade A, member 3 / Hs.534293 / NaN / 0 / 14q32.1
SPG20 / Spastic paraplegia 20 (Troyer syndrome) / Hs.440414 / NaN / 0 / 13q13.3
WAC / WW domain containing adaptor with coiled-coil / Hs.435610 / 18.33 / 0.01 / Unknown
MALAT1 / Metastasis associated lung adenocarcinoma transcript 1 / Hs.642877 / 17.11 / 0 / 11q13.1
- / CDNA FLJ41661 fis, clone FEBRA2026890 / Hs.145469 / NaN / 0 / Unknown
- / Transcribed locus, moderately similar to NP_004346.1 gamma chain / Hs.436568 / NaN / 0 / Unknown
- / Transcribed locus / Hs.658195 / NaN / 0 / Unknown
- / Full length insert cDNA clone YT05B04 / Hs.658225 / NaN / 0 / Unknown
NaN stands for “Not a number” and occurs when the denominator of the equation is 0, i.e., there are no sequences of a gene in RB.
Table 4S. List of Genes up-regulated in RB by cDNA DGED
Symbol / Gene Description / Cluster / F / P / Cyt LoCProtein biosyntesis/ folding(24)
EEF1A1 / Eukaryotic translation elongation factor 1 alpha 1 / Hs.644639 / 0.1 / 0 / 6q14.1
EEF1G / Eukaryotic translation elongation factor 1 gamma / Hs.444467 / 0.18 / 0 / 11q12.3
EIF3S6IP / Eukaryotic translation initiation factor 3, subunit 6 interacting protein / Hs.446852 / 0.12 / 0.01 / 22q
EIF3S8 / Eukaryotic translation initiation factor 3, subunit 8, 110kDa / Hs.567374 / 0 / 0 / 16p11.2
RPL3 / Ribosomal protein L3 / Hs.119598 / 0.17 / 0 / 22q13
RPL4 / Ribosomal protein L4 / Hs.644628 / 0.02 / 0 / 15q22
RPL5 / Ribosomal protein L5 / Hs.532359 / 0.16 / 0.01 / 1p22.1
RPL6 / Ribosomal protein L6 / Hs.528668 / 0.12 / 0.01 / 12q24.1
RPL7A / Ribosomal protein L7a / Hs.499839 / 0.13 / 0 / 9q34
RPL8 / Ribosomal protein L8 / Hs.178551 / 0.03 / 0 / 8q24.3
RPL10 / Ribosomal protein L10 / Hs.534404 / 0.13 / 0 / Xq28
RPL10A / Ribosomal protein L10a / Hs.546269 / 0.08 / 0 / 6p21.3-p21.2
RPL21 / Ribosomal protein L21 / Hs.381123 / 0.05 / 0.01 / 13q12.2
RPL13 / Ribosomal protein L13 / Hs.410817 / 0.11 / 0.01 / 16q24.3|17p11.2
RPLP0-like / Similar to ribosomal protein P0 / Hs.655337 / 0.01 / 0 / 2p22.1
RPS2 / Ribosomal protein S2 / Hs.506997 / 0 / 0 / 16p13.3
RPS3 / Ribosomal protein S3 / Hs.546286 / 0.01 / 0 / 11q13.3-q13.5
RPS3A / Ribosomal protein S3A / Hs.356572 / 0.03 / 0 / 4q31.2-q31.3
RPS17 / Ribosomal protein S17 / Hs.433427 / 0 / 0 / 15q
RPSA / Ribosomal protein SA / Hs.449909 / 0.07 / 0 / 3p22.2
DDX1 / DEAD (Asp-Glu-Ala-Asp) box polypeptide 1 / Hs.440599 / 0.05 / 0 / 2p24
TRAP1 / TNF receptor-associated protein 1 / Hs.30345 / 0 / 0.01 / 16p13.3
CCT7 / Chaperonin containing TCP1, subunit 7 (eta) / Hs.368149 / 0 / 0 / 2p13.2
CCT3 / Chaperonin containing TCP1, subunit 3 (gamma) / Hs.491494 / 0.09 / 0 / 1q23
DNA biosynthesis(4)
H3F3B / H3 histone, family 3B (H3.3B) / Hs.180877 / 0.13 / 0.01 / 17q25
HMGA1 / High mobility group AT-hook 1 / Hs.518805 / 0.05 / 0 / 6p21
HMGN2 / High-mobility group nucleosomal binding domain 2 / Hs.181163 / 0.06 / 0 / 1p36.1
MCM7 / Minichromosome maintenance complex component 7 / Hs.438720 / 0 / 0.01 / 7q21.3-q22.1
Cytoskeleton / Adhension/Junction (3)
ACTG1 / Actin, gamma 1 / Hs.514581 / 0.11 / 0 / 17q25
TUBA1B / Tubulin, alpha 1b / Hs.524390 / 0.22 / 0 / 12q13.12
TUBB / Tubulin, beta / Hs.636480 / 0.03 / 0 / 6p21.33
Cell cycle/apoptosis(3)
CCDC5 / Coiled-coil domain containing 5 (spindle associated) / Hs.436617 / 0 / 0 / 18q21.1
KPNA2 / Karyopherin alpha 2 (RAG cohort 1, importin alpha 1) / Hs.594238 / 0 / 0.01 / 17q24.2
NPM1 / Nucleophosmin (nucleolar phosphoprotein B23, numatrin) / Hs.557550 / 0.05 / 0 / 5q35
Table 4S continued
Symbol / Gene Description / Cluster / F / P / Cyt LoC
Regulation of transcription(3)
CRABP2 / Cellular retinoic acid binding protein 2 / Hs.405662 / 0 / 0 / 1q21.3
PTMA / Prothymosin, alpha (gene sequence 28) / Hs.459927 / 0 / 0 / 2q35-q36
YBX1 / Y box binding protein 1 / Hs.473583 / 0.02 / 0 / 1p34
Signal transduction(4)
CFL1 / Cofilin 1 (non-muscle) / Hs.170622 / 0.05 / 0.01 / 11q13
BSG / Basigin (Ok blood group) / Hs.591382 / 0.08 / 0.01 / 19p13.3
GNB2L1 / Guanine nucleotide binding protein (G protein), βpolypeptide 2-like 1 / Hs.5662 / 0.15 / 0 / 5q35.3
STMN1 / Stathmin 1/oncoprotein 18 / Hs.209983 / 0.07 / 0 / 1p36.1-p35
Spliceosomal Assembly(1)
SNRPB / Small nuclear ribonucleoprotein polypeptides B and B1 / Hs.83753 / 0.05 / 0.01 / 20p13
Transport(2
SLC25A3 / Solute carrier family 25, member 3 / Hs.290404 / 0.04 / 0 / 12q23
ATP5A1 / ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1 / Hs.298280 / 0.02 / 0 / 18q12-q21
Metabolism/enzyme(7)
CA12 / Carbonic anhydrase XII / Hs.210995 / 0 / 0 / 15q22
ENO1 / Enolase 1, (alpha) / Hs.517145 / 0.27 / 0.01 / 1p36.3-p36.2
FASN / Fatty acid synthase / Hs.83190 / 0 / 0.01 / 17q25
FDPS / Farnesyl diphosphate synthase / Hs.335918 / 0 / 0.01 / 1q22
LDHA / Lactate dehydrogenase A / Hs.2795 / 0.07 / 0 / 11p15.4
LDHB / Lactate dehydrogenase B / Hs.446149 / 0.2 / 0 / 12p12.2-p12.1
IMPDH2 / IMP (inosine monophosphate) dehydrogenase 2 / Hs.654400 / 0 / 0 / 3p21.2
Other(4)
GSG1 / Germ cell associated 1 / Hs.240053 / 0 / 0 / 12p13.1
- / CDNA: FLJ21700 fis, clone COL09849, highly similar to HSU14972 / Hs.406620 / 0 / 0 / Unknown
- / Transcribed locus, strongly similar to XP_001099771.1 similar toRPS3a / Hs.567702 / 0.04 / 0 / Unknown
- / Transcribed locus, moderately similar to XP_001104698.1 / Hs.694863 / 0 / 0 / Unknown
Table 5S. List of Genes up-regulated in RB by SAGE DGED
Symbol Sym / Gene Description / Tag / UniGene / F / P / chr.posProtein biosyntesis (11)
EEF1B2 / Eukaryotic translation elongation factor 1 beta 2 / GCATTTAAAT / Hs.421608 / 0.08 / 0 / 2q33-q34
RPS11 / Ribosomal protein S11 / TCTGTACACC / Hs.433529 / 0.03 / 0 / 19q13.3
RPL36A / Ribosomal protein L36a / GTTAACGTCC / Hs.432485 / 0.05 / 0.01 / Xq22.1
RPLP0 / Ribosomal protein, large, P0 / CTCAACATCT / Hs.546285 / 0.05 / 0 / 12q24.2
RPS18 / Ribosomal protein S18 / TGGTGTTGAG / Hs.627414 / 0.07 / 0 / 6p21.3
RPL37 / Ribosomal protein L37 / CAATAAATGT / Hs.558601 / 0.1 / 0 / 5p13
RPS8 / Ribosomal protein S8 / TAATAAAGGT / Hs.512675 / 0.11 / 0 / 1p34.1-p32
RPSA / Ribosomal protein SA / GAAAAATGGT / Hs.449909 / 0.11 / 0 / 3p22.2
RPS27 / Ribosomal protein S27 (metallopanstimulin 1) / CACAAACGGT / Hs.654475 / 0.14 / 0 / 1q21
DDX39 / DEAD (Asp-Glu-Ala-Asp) box polypeptide 39 / CAGCTTCACC / Hs.311609 / 0.04 / 0.01 / 19p13.12
UBE2S / Ubiquitin-conjugating enzyme E2S / CTGGCGAGCG / Hs.396393 / 0.02 / 0 / 19q13.43
DNA biosyntesis/mitosis (9)
GINS1 / GINS complex subunit 1 (Psf1 homolog) / TGTTCTATGA / Hs.658464 / 0 / 0 / 20p11.21
H2AFV / H2A histone family, member V / TGGTGACAGT / Hs.488189 / 0.04 / 0 / 7p13
HMGA1 / High mobility group AT-hook 1 / ATTTGTCCCA / Hs.518805 / 0.06 / 0 / 6p21
MCM7 / Minichromosome maintenance complex component 7 / CTGCACTTAC / Hs.438720 / 0.05 / 0 / 7q21.3-q22.1
NASP / Nuclear autoantigenic sperm protein (histone-binding) / TTAAGAGGGG / Hs.319334 / 0.07 / 0.01 / 1p34.1
NUSAP1 / Nucleolar and spindle associated protein 1 / TAATTGCCAT / Hs.615092 / 0 / 0 / 15q15.1
TOP2A / Topoisomerase (DNA) II alpha 170kDa / CTCAGCAATG / Hs.156346 / 0 / 0 / 17q21-q22
TPX2 / TPX2, microtubule-associated, homolog (Xenopus laevis) / GGGAGCCTCA / Hs.244580 / 0 / 0 / 20q11.2
TYMS / Thymidylate synthetase / ATGTAGAGTG / Hs.592338 / 0.02 / 0 / 18p11.32
Cyctoskeleton (3)
ACTG1 / Actin, gamma 1 / CTAGCCTCAC / Hs.514581 / 0.09 / 0 / 17q25
FSCN1 / Fascin homolog 1, actin-bundling protein / ATAGTAGCTT / Hs.118400 / 0.07 / 0.01 / 7p22
TMSL8 / Thymosin-like 8 / CTTTTGCAGC / Hs.56145 / 0 / 0 / Xq21.33-q22.3
Cell cycle/apoptosis(13)
CKAP2 / Cytoskeleton associated protein 2 / TTCTAGAGAG / Hs.444028 / 0 / 0 / 13q14
CKS1B / CDC28 protein kinase regulatory subunit 1B / TTAAAAGCCT / Hs.374378 / 0.06 / 0.01 / 1q21.2
CKS2 / CDC28 protein kinase regulatory subunit 2 / AGCTGTATTC / Hs.83758 / 0.01 / 0 / 9q22
KIF11 / Kinesin family member 11 / GTTAATAAAT / Hs.8878 / 0.02 / 0 / 10q24.1
MAD2L1 / MAD2 mitotic arrest deficient-like 1 (yeast) / TGTTTTATAA / Hs.591697 / 0.01 / 0 / 4q27
MIF / Macrophage migration inhibitory factor / AACGCGGCCA / Hs.407995 / 0.11 / 0 / 22q11.23
MKI67 / Antigen identified by monoclonal antibody Ki-67 / AGGGCCGACT / Hs.80976 / 0 / 0.01 / 10q25-qter
NDC80 / NDC80 homolog, kinetochore complex component / TATATATATC / Hs.414407 / 0 / 0 / 18p11.32
NPM1 / Nucleophosmin (nucleolar phosphoprotein B23, numatrin) / TGAAATAAAA / Hs.557550 / 0.14 / 0.01 / 5q35
NUF2 / NUF2, NDC80 kinetochore complex component, homolog. / TCTCTACTCT / Hs.651950 / 0.01 / 0 / 1q23.3
PTMA / Prothymosin, alpha (gene sequence 28) / TTCATTATAA / Hs.459927 / 0.08 / 0 / 2q35-q36
PTTG1 / Pituitary tumor-transforming 1 / GGAATCCAAT / Hs.350966 / 0 / 0 / 5q35.1
SMC3 / Structural maintenance of chromosomes 3 / CTAAATATTC / Hs.24485 / 0.03 / 0 / 10q25
Regulation of transcription(6)
BACH1 / BTB and CNC homology 1 / TAATAAACTA / Hs.154276 / 0 / 0 / 21q22.11
DEK / DEK oncogene (DNA binding) / CTGTTTATGA / Hs.484813 / 0.03 / 0 / 6p22.3
PAX8 / Paired box gene 8 / ACTCAATAAA / Hs.469728 / 0.02 / 0 / 2q12-q14
PBX1 / Pre-B-cell leukemia homeobox 1 / CAGGAAGAAG / Hs.654412 / 0.01 / 0 / 1q23
SOX4 / SRY (sex determining region Y)-box 4 / TCAAGTTCAC / Hs.643910 / 0.02 / 0 / 6p22.3
ZEB1 / Zinc finger E-box binding homeobox 1 / GTCATTTTCT / Hs.124503 / 0.06 / 0 / 10p11.2
Signal transduction(7)
CHRNA3 / Cholinergic receptor, nicotinic, alpha 3 / TACTACACTT / Hs.89605 / 0.07 / 0.01 / 15q24
GNG4 / Guanine nucleotide binding protein (G protein), gamma 4 / GTGACAGCAG / Hs.591531 / 0 / 0 / 1q42.3
Table 5S continued
Symbol Sym / Gene Description / Tag / UniGene / F / P / chr.pos
GRIN2C / Glutamate receptor, ionotropic, N-methyl D-aspartate 2C / GTGACCACGG / Hs.436980 / 0.08 / 0 / 17q25
SNRPB / Small nuclear ribonucleoprotein polypeptides B and B1 / GGATTGTCTG / Hs.83753 / 0.06 / 0.01 / 20p13
SNRPG / Small nuclear ribonucleoprotein polypeptide G / TACATTTTCA / Hs.631639 / 0.11 / 0 / 2p14
TGM2
WSB2 / Transglutaminase 2
WD repeat and SOCS box-containing 2 / TATATTTTCT
TCTTTTCAAA / Hs.517033
Hs.506985 / 0.04
0.04 / 0
0 / 20q12
12q24.23
Transport(2)
SLC38A5 / Solute carrier family 38, member 5 / GGAGGAGGAG / Hs.195155 / 0.02 / 0 / Xp11.23
STX3 / Syntaxin 3 / TGAAGGTTTT / Hs.180711 / 0.05 / 0.01 / 11q12.1
Metabolism/enzyme(11)
ARPP-19 / Cyclic AMP phosphoprotein, 19 kD / TCTATAGAGT / Hs.512908 / 0.03 / 0.01 / 15q21.2
ATAD2 / ATPase family, AAA domain containing 2 / CATACTTGCT / Hs.370834 / 0 / 0 / 8q24.13
DCT / Dopachrome tautomerase / TATGATTTTA / Hs.301865 / 0 / 0 / 13q32
ELOVL2 / Elongation of very long chain fatty acids -like 2 / AATGGAGTAG / Hs.656436 / 0.06 / 0.01 / 6p24.2
HMGCS1 / 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 / GTGTAACACA / Hs.397729 / 0.08 / 0 / 5p14-p13
LOC644941 / Similar to fatty acid amide hydrolase / AGACACCCAG / Hs.170205 / 0 / 0 / 1p33
MTHFD2 / Methylenetetrahydrofolate dehydrogenase 2, / TGTGTTGTCA / Hs.469030 / 0.03 / 0.01 / 2p13.1
PLA2G3 / Phospholipase A2, group III / TGTAATGTAA / Hs.149623 / 0.03 / 0 / 22q11.2-q13.2
SATL1 / Spermidine/spermine N1-acetyl transferase-like 1 / CACTTTCTTG / Hs.512181 / 0.01 / 0 / Xq21.1
SGPL1 / Sphingosine-1-phosphate lyase 1 / TTTTATTATT / Hs.499984 / 0.06 / 0.01 / 10q21
SUOX / Sulfite oxidase / TGTAAGAAAA / Hs.558403 / 0.01 / 0 / 12q13.2
Other(22)
C1orf67 / Chromosome 1 open reading frame 67 / TTATTTAATA / Hs.133977 / 0.02 / 0 / 1q42.12
C19orf30 / Chromosome 19 open reading frame 30 / TGTTGAATCA / Hs.326728 / 0.03 / 0 / 19p13.3
CCDC23 / Coiled-coil domain containing 23 / AAACTCTATA / Hs.113919 / 0.04 / 0 / 1p34.2
LBR / Lamin B receptor / TTTATTTGGC / Hs.435166 / 0 / 0 / 1q42.1
METTL9 / Methyltransferase like 9 / CTAATAAACT / Hs.279583 / 0.08 / 0 / 16p13-p12
NCL / Nucleolin / GTTTTTGCTT / Hs.79110 / 0.12 / 0.01 / 2q12-qter
NT5DC2 / 5'-nucleotidase domain containing 2 / GCCCACATCC / Hs.84753 / 0.01 / 0 / 3p21.1
PSG2 / Pregnancy specific beta-1-glycoprotein 2 / GAAACTGTGA / Hs.654453 / 0.03 / 0 / 19q13.1-q13.2
RBM10 / RNA binding motif protein 10 / TTGGGTGTCC / Hs.401509 / 0.03 / 0 / Xp11.23
SCG3 / Secretogranin III / GGAGGGGACA / Hs.232618 / 0.02 / 0 / 15q21
SPATA18 / Spermatogenesis associated 18 homolog (rat) / CTCTTCACCT / Hs.527090 / 0 / 0 / 4q12
Hs.566597 / Transcribed locus, / CAGATGGTAG / Hs.566597 / 0.01 / 0.01 / Unknown
Hs.680769 / CDNA clone IMAGE:4616798 / CCTTGTAAAT / Hs.680769 / 0.01 / 0 / Unknown
Hs.593575 / Chromosome 6 isolate HA_003120 / TTTTTATGAT / Hs.593575 / 0.03 / 0.01 / Unknown
Hs.614740 / Transcribed locus / TTTAAAATAC / Hs.614740 / 0.03 / 0.01 / Unknown
Hs.553178 / Transcribed locus, / AGAGGTGTAG / Hs.553178 / 0.04 / 0 / Unknown
Hs.271003 / Transcribed locus / GTAATCCTGC / Hs.271003 / 0.06 / 0 / Unknown
Hs.434957 / Homo sapiens, clone IMAGE:3618365, mRNA / AAGTAAGTCT / Hs.434957 / 0 / 0 / Unknown
Hs.680613 / CDNA FLJ30447 fis, clone BRACE2009270 / AATGGATGAA / Hs.680613 / 0 / 0 / Unknown
BM743199 / TGGCGTACGG / 0.03 / 0.01
AV736741 / CTAACTAGTT / 0.06 / 0.01
BE067833 / GCTACTATTA / 0 / 0.01
Table 6S. List of Genes down-regulated in RB by SAGE DGED
Gene Sym / Description / Tag / UniGene / F / P / Chr.posVisual perception or Visual Signal Transduction (6)
CRYAA / Crystallin, alpha A / AGAGCGCAGC / Hs.184085 / NaN / 0 / 21q22.3
PDE6G / Phosphodiesterase 6G, cGMP-specific, rod, gamma / CTGGGTAGCA / Hs.654482 / 67.63 / 0 / 17q25
RDH12 / Retinol dehydrogenase 12 (all-trans/9-cis/11-cis) / CAGATGGTTT / Hs.415322 / 59.85 / 0 / 14q24.1
ROM1 / Retinal outer segment membrane protein 1 / AGAAGGCCTG / Hs.281564 / NaN / 0 / 11q13
RP11-143M1.1 / F379 retina-specific protein / GATTTGGATG / Hs.640260 / 25.93 / 0 / 9p24.3
SAG / S-antigen; retina and pineal gland (arrestin) / CACCCTCAGC / Hs.32721 / NaN / 0 / 2q37.1
Cyctoskeleton/cell adhesion(2)
PCDHB16 / Protocadherin beta 16 / CTCACCACCA / Hs.147674 / NaN / 0 / 5q31
SPINK5 / Serine peptidase inhibitor, Kazal type 5 / AGGGAAAAAA / Hs.331555 / NaN / 0 / 5q32
Cell cycle/apoptosis(3)
CLU / Clusterin / CAACTAATTC / Hs.436657 / NaN / 0 / 8p21-p12
CLUL1 / Clusterin-like 1 (retinal) / GTACATTAGT / Hs.632357 / NaN / 0.01 / 18p11.32
Signal transduction(2)
ARHGAP29 / Rho GTPase activating protein 29 / GGTTGAAAAA / Hs.483238 / NaN / 0 / 1p22.1
GNGT1 / G protein,γtransducing activity polypeptide 1 / TACGTGAATT / Hs.655402 / 124.1 / 0 / 7q21.3
Transport(2)
TF / Transferrin / TGTGCTGAAC / Hs.518267 / NaN / 0 / 3q22.1
TTR / Transthyretin (prealbumin, amyloidosis type I) / TAACCAAGAG / Hs.427202 / 66.75 / 0 / 18q12.1
Metabolism/enzyme(3)
ALDOC / Aldolase C, fructose-bisphosphate / CCTTGAGTAC / Hs.155247 / NaN / 0 / 17cen-q12
GPX3 / Glutathione peroxidase 3 (plasma) / AGGGAGGGGC / Hs.386793 / NaN / 0 / 5q23
NDUFA4 / NADH dehydrogenase 1 alpha subcomplex, 4 / TTGGAGATCT / Hs.50098 / 13.74 / 0 / 7p21.3
Other(15)
C16orf57 / Chromosome 16 open reading frame 57 / TTGCTTTTAT / Hs.588873 / NaN / 0.01 / 16q13
GPRASP2 / G proteincoupled recep. associated sort pro. 2 / GGGTTGGCTT / Hs.656888 / 18.82 / 0 / Xq22.1
SLFN13 / Schlafen family member 13 / GTGGCTCACA / Hs.462833 / 98.35 / 0 / 17q12
SNCB / Synuclein, beta / AATAAAGCTA / Hs.90297 / 18.83 / 0.01 / 5q35
Hs.536923 / Transcribed locus / TCCCCGTACA / Hs.536923 / NaN / 0 / Unknown
Hs.615061 / Transcribed locus / TCCCTATTAA / Hs.615061 / NaN / 0 / Unknown
Hs.631491 / Transcribed locus, / CACTACTCAC / Hs.631491 / NaN / 0.01 / Unknown
Hs.658225 / Full length insert cDNA clone YT05B04 / TGGTTGCTGG / Hs.658225 / NaN / 0 / Unknown
Hs.644254 / CDNA clone IMAGE:5271818 / AAAACATTCT / Hs.644254 / 11 / 0 / Unknown
Hs.349570 / CDNA clone IMAGE:4328048 / ACTTTTTCAA / Hs.349570 / 55.4 / 0 / Unknown
AL524966 / TCTCCATACC / NaN / 0
NC_001807 / GTAAGTGTAC / 18.55 / 0.01
GACTGACCCT / NaN / 0
TAACACATTC / NaN / 0
CGGGGTAGCA / NaN / 0
NaN stands for “Not a number” and occurs when the denominator of the equation is 0, i.e., there are no sequences of a gene in RB.
1