Description of the problem:

Number of classes: 2
Number of genes: 12776
Number of genes that passed filtering criteria: 8324
Type of test used: SAM - Significance analysis of Microarray
Column of the Experiment Descriptors sheet that defines class variable : GROUP


Genes which discriminate among classes:

Table 1
There are 166 genes significant by SAM
The median false discovery rate among the 166 significant genes is 0.08539 .
The delta value used to identify the significant genes is 0.59305 .
The fudge factor for standard deviation is computed as 0.03459 .

Note: For the latest annotations please query the Qiagen website using the Oligo ID number.



Geometric mean of ratios
( Disease / Normal )
Qiagen oligo ID
Description GB acc UG cluster Gene symbol
1 1.553 H002655_01 Collagen, type VII, alpha 1 (epidermolysis bullosa, dystrophic, dominant and recessive) L02870 1640 COL7A1
2 1.453 H007688_01 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 AF109735 195471 PFKFB3
3 1.757 H002994_01 Collagen, type XVIII, alpha 1 AF018081 78409 COL18A1
4 1.689 H016341_01 Platelet derived growth factor C NM_016205 43080 PDGFC
5 1.422 H006183_01 Metallothionein 1X X65607 278462 MT1X
6 1.251 H011854_01 Heterogeneous nuclear ribonucleoprotein C (C1/C2) M16342 182447 HNRPC
7 1.352 H000498_01 Desmoplakin (DPI, DPII) AL031058 74316 DSP
8 1.249 H003776_01 Aldehyde dehydrogenase 2 family (mitochondrial) X05409 195432 ALDH2
9 1.436 H012791_01 Metallothionein 1A (functional) K01383 203967 MT1A
10 1.314 H003383_01 Ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) Z82188 173466 RAC2
11 1.66 H015187_01 Homo sapiens clone N97 immunoglobulin heavy chain variable region mRNA, partial cds AF103295 283882
12 1.483 H008423_01 EH-domain containing 3 NM_014600 87125 EHD3
13 1.333 H007009_01 Fibroblast growth factor receptor-like 1 AK000530 193326 FGFRL1
14 1.23 H000238_01 KRAB-associated protein 1 X97548 228059 TIF1B
15 1.386 H011703_01 Hypothetical protein FLJ20364 AK000371 32471 FLJ20364
16 1.292 H014948_01 Phosphatidylglycerophosphate Synthase NM_024419 278682 PGS1
17 1.375 H006492_01 Homo sapiens CD44 isoform RC (CD44) mRNA, complete cds AF098641 306278
18 1.374 H012664_01 metallothionein 1B (functional) M13485 211924 MT1B
19 1.292 H006579_01 Hypothetical protein FLJ10292 AK001154 104650 FLJ10292
20 1.427 H008064_01 KIAA0008 gene product D13633 77695 KIAA0008
21 1.255 H012398_01 KIAA1118 protein AB029041 209646 KIAA1118
22 1.451 H003725_01 Cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple) AC003107 1584 COMP
23 1.211 H011172_01 Heat shock protein 75 NM_016292 182366 TRAP1
24 1.243 H009594_01 Neuropathy target esterase AJ004832 5038 NTE
25 1.445 H008685_01 Metallothionein 2A V00594 118786 MT2A
26 1.279 H007583_01 Kinesin family member 4A AF071592 279766 KIF4A
27 1.367 H013251_01 KIAA1329 protein AB037750 21061 KIAA1329
28 1.189 H015295_01 Homo sapiens HSPC337 mRNA, partial cds AF161451 284295
29 1.5 H011653_01 Vanilloid receptor-like protein NM_016113 300686 VRL
30 1.405 H012717_01 Metallothionein 1F (functional) M10943 203936 MT1F
31 1.193 H003987_01 PRO0659 protein NM_014138 6451 PRO0659
32 1.415 H009923_01 Vanilloid receptor-like protein 1 NM_015930 279746 VRL-1
33 1.313 H016122_01 TMTSP for transmembrane molecule with thrombospondin module NM_018676 325667 LOC55901
34 1.244 H012710_01 Hepatitis delta antigen-interacting protein A U63825 66713 DIPA
35 0.621 H003528_01 Decay accelerating factor for complement (CD55, Cromer blood group system) M30142 1369 DAF
36 0.548 H003827_01 Serum/glucocorticoid regulated kinase AJ000512 296323 SGK
37 0.548 H016371_01 Hypothetical protein FLJ21212 NM_024642 47099 FLJ21212
38 0.584 H009347_01 Neuronal cell adhesion molecule AB002341 7912 NRCAM
39 0.465 H001509_01 Aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II) D17793 78183 AKR1C3
40 0.517 H003858_01 Aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-a U05598 201967 AKR1C2
41 0.62 H010655_01 Hypothetical protein FLJ20546 AK000953 279896 FLJ20546
42 0.811 H005438_01 Homo sapiens mRNA; cDNA DKFZp434B1620 (from clone DKFZp434B1620) AL137548 43112
43 0.728 H004078_01 Heme-binding protein NM_015987 108675 HEBP
44 0.708 H002860_01 Inositol polyphosphate-1-phosphatase L08488 32309 INPP1
45 0.768 H002574_01 Alcohol dehydrogenase 5 (class III), chi polypeptide M81118 78989 ADH5
46 0.751 H004767_01 Tetraspan 3 AK001326 100090 TSPAN-3
47 0.629 H010640_01 Homo sapiens mRNA; cDNA DKFZp434B1272 (from clone DKFZp434B1272); partial cds AL162032 158258
48 0.689 H000959_01 Glycophorin C (Gerbich blood group) NM_002101 81994 GYPC
49 0.721 H003965_01 Cellular repressor of E1A-stimulated genes AF084523 5710 CREG
50 0.724 H002462_01 Receptor tyrosine kinase-like orphan receptor 1 M97675 274243 ROR1
51 0.664 H007733_01 Retinal short-chain dehydrogenase/reductase retSDR3 NM_016246 18788 LOC51171
52 0.771 H016494_01 Hypothetical protein FLJ12436 NM_024661 69485 FLJ12436
53 0.742 H008089_01 KIAA0469 gene product AB007938 7764 KIAA0469
54 0.631 H007034_01 Histamine N-methyltransferase U44111 81182 HNMT
55 0.706 H000410_01 A kinase (PRKA) anchor protein (gravin) 12 U81607 788 AKAP12
56 0.702 H001356_01 KIAA0537 gene product AB011109 200598 KIAA0537
57 0.538 H001341_01 Platelet-derived growth factor receptor-like D37965 170040 PDGFRL
58 0.815 H002021_01 V-maf musculoaponeurotic fibrosarcoma (avian) oncogene family, protein G AF059195 252229 MAFG
59 0.592 H010453_01 3-alpha hydroxysteroid dehydrogenase type IIb NM_016253 279801 LOC51708
60 0.685 H005634_01 Solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3 NM_014585 5944 SLC11A3
61 0.68 H008745_01 Acid sphingomyelinase-like phosphodiesterase AK000184 42945 ASM3A
62 0.704 H003219_01 Glutathione S-transferase M3 (brain) AF043105 2006 GSTM3
63 0.773 H003951_01 Predicted osteoblast protein D87120 29882 GS3786
64 0.735 H001047_01 Nidogen 2 AB009799 82733 NID2
65 0.792 H002382_01 Limbic system-associated membrane protein U41901 26479 LSAMP
66 0.623 H016583_01 1,2-alpha-mannosidase IC NM_020379 8910 HMIC
67 0.742 H011191_01 Lipin 2 D87436 166318 LPIN2
68 0.803 H002185_01 Niemann-Pick disease, type C1 AF002020 76918 NPC1
69 0.775 H000509_01 Neural precursor cell expressed, developmentally down-regulated 4 D42055 1565 NEDD4
70 0.786 H007419_01 Progesterone membrane binding protein AJ002030 9071 PMBP
71 0.774 H002121_01 Paraoxonase 2 AF001601 169857 PON2
72 0.805 H008087_01 HSPC019 protein NM_014028 163724 HSPC019
73 0.696 H002393_01 Sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C AB000220 171921 SEMA3C
74 0.785 H014975_01 Homo sapiens mRNA; cDNA DKFZp564N1272 (from clone DKFZp564N1272); complete cds AF087847 282654
75 0.614 H001215_01 Pentaxin-related gene, rapidly induced by IL-1 beta M31166 2050 PTX3
76 0.756 H002423_01 Vascular endothelial growth factor B U43368 78781 VEGFB
77 0.768 H010087_01 Destrin (actin depolymerizing factor) S65738 82306 ADF
78 0.742 H000025_01 Neutral sphingomyelinase (N-SMase) activation associated factor X96586 78687 NSMAF
79 0.744 H005560_01 WAS protein family, member 1 D87459 75850 WASF1
80 0.786 H014051_01 Very long-chain acyl-CoA synthetase homolog 2 NM_012254 111401 VLCS-H2
81 0.644 H004741_01 Fibroblast growth factor 13 AF100143 6540 FGF13
82 0.764 H001605_01 Annexin A4 NM_001153 77840 ANXA4
83 0.71 H016019_01 Duodenal cytochrome b AL136693 31297 FLJ23462
84 0.804 H001346_01 Inositol(myo)-1(or 4)-monophosphatase 2 NM_014214 5753 IMPA2
85 0.635 H010918_01 WNT1 inducible signaling pathway protein 2 AF100780 194679 WISP2
86 0.791 H001101_01 CD164 antigen, sialomucin D14043 43910 CD164
87 0.787 H004431_01 Rag C protein AF131773 110950 GTR2
88 0.792 H012626_01 Beta-2-microglobulin AB021288 75415 B2M
89 0.805 H002819_01 Protective protein for beta-galactosidase (galactosialidosis) AL008726 118126 PPGB
90 0.684 H002497_01 Complement component 1, r subcomponent M14058 1279 C1R
91 0.691 H006676_01 Lung type-I cell membrane-associated glycoprotein AF030428 135150 T1A-2
92 0.653 H012777_01 KIAA1199 protein AB033025 50081 KIAA1199
93 0.721 H003789_01 Colony stimulating factor 1 (macrophage) M37435 173894 CSF1
94 0.849 H008439_01 SCO (cytochrome oxidase deficient, yeast) homolog 1 AF026852 14511 SCO1
95 0.774 H008994_01 Solute carrier family 31 (copper transporters), member 2 U83461 24030 SLC31A2
96 0.774 H010497_01 Interferon induced transmembrane protein 3 (1-8U) X57352 182241 IFITM3
97 0.762 H011175_01 Opsin 3 (encephalopsin) NM_014322 279926 OPN3
98 0.701 H011671_01 Short-chain dehydrogenase/reductase 1 AF061741 17144 SDR1
99 0.767 H002804_01 Prion protein (p27-30) (Creutzfeld-Jakob disease, Gerstmann-Strausler-Scheinker syndrome, fatal fami U29185 74621 PRNP
100 0.792 H002258_01 UDP-glucose pyrophosphorylase 2 U27460 77837 UGP2
101 0.659 H001491_01 Cyclin T2 AF048731 155478 CCNT2
102 0.762 H002746_01 TNF receptor-associated factor 5 AB000509 29736 TRAF5
103 0.766 H013070_01 Sarcoglycan, epsilon AJ000534 110708 SGCE
104 0.761 H001062_01 N-acylsphingosine amidohydrolase (acid ceramidase) U70063 75811 ASAH
105 0.814 H002694_01 Glutathione peroxidase 4 (phospholipid hydroperoxidase) X71973 2706 GPX4
106 0.774 H011917_01 Sorting nexin 3 AF034546 12102 SNX3
107 0.754 H006813_01 Homo sapiens cDNA FLJ11309 fis, clone PLACE1010076 AK002171 28005
108 0.821 H002793_01 Antigen identified by monoclonal antibodies 12E7, F21 and O13 M16279 177543 MIC2
109 0.844 H000474_01 Testis-specific kinase 1 D50863 79358 TESK1
110 0.731 H000930_01 Low density lipoprotein receptor (familial hypercholesterolemia) L00352 213289 LDLR
111 0.802 H009135_01 Electron-transferring-flavoprotein dehydrogenase S69232 323468 ETFDH
112 0.767 H008544_01 Atrophin-1 interacting protein 1; activin receptor interacting protein 1 AB014605 22599 KIAA0705
113 0.789 H000400_01 Growth arrest-specific 6 L13720 78501 GAS6
114 0.762 H016469_01 MEK partner 1 NM_021970 6361 MP1
115 0.731 H002820_01 Ectodermal-neural cortex (with BTB-like domain) AF059611 104925 ENC1
116 0.75 H016592_01 Hypothetical protein FLJ12816 NM_022060 9175 FLJ12816
117 0.792 H006873_01 CGI-149 protein NM_016079 189658 LOC51652
118 0.592 H002066_01 Aldehyde dehydrogenase 1 family, member A1 M31994 76392 ALDH1A1
119 0.689 H013490_01 H.sapiens polyA site DNA Z24724 4934
120 0.76 H015305_01 Hypothetical protein FLJ22029 NM_024949 285243 FLJ22029
121 0.704 H002566_01 Membrane metallo-endopeptidase (neutral endopeptidase, enkephalinase, CALLA, CD10) NM_007289 1298 MME
122 0.81 H002169_01 Sortilin-related receptor, L(DLR class) A repeats-containing NM_003105 278571 SORL1
123 0.88 H003649_01 Protein tyrosine phosphatase, non-receptor type 6 X62055 63489 PTPN6
124 0.744 H011942_01 Activating transcription factor 5 AB021663 9754 ATF5
125 0.806 H007715_01 KIAA1091 protein AL117448 26797 KIAA1091
126 0.823 H012019_01 Epithelial protein lost in neoplasm beta NM_016357 10706 EPLIN
127 0.838 H010079_01 Hypothetical protein FLJ10337 AB037858 173484 KIAA1437
128 0.772 H003031_01 Glycoprotein A repetitions predominant Z24680 151641 GARP
129 0.762 H002785_01 Serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1 X54486 151242 SERPING1
130 0.631 H000082_01 Deiodinase, iodothyronine, type II NM_013989 154424 DIO2
131 0.755 H007381_01 Hypothetical protein FLJ10044 AK000906 127273 FLJ10044
132 0.699 H014982_01 Tuftelin 1 NM_020127 283009 TUFT1
133 0.813 H003637_01 Protein tyrosine phosphatase, non-receptor type 12 M93425 62 PTPN12
134 0.821 H002684_01 Bone morphogenetic protein 6 NM_001718 285671 BMP6
135 0.847 H001078_01 ATPase, Na+/K+ transporting, beta 3 polypeptide NM_001679 76941 ATP1B3
136 0.785 H009413_01 KIAA0321 protein AB002319 8663 KIAA0321
137 0.806 H003439_01 Protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform M60484 80350 PPP2CB
138 0.811 H011488_01 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5 AL035683 107526 B4GALT5
139 0.631 H002334_01 Cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile) U03688 154654 CYP1B1
140 0.797 H006973_01 Homo sapiens cDNA FLJ10598 fis, clone NT2RP2004841 AK001460 170873
141 0.737 H008497_01 Amyloid beta (A4) precursor-like protein 2 NM_016160 279518 APLP2
142 0.802 H000517_01 Phorbol-12-myristate-13-acetate-induced protein 1 D90070 96 PMAIP1
143 0.799 H007506_01 Clock (mouse) homolog AB002332 50722 CLOCK
144 0.831 H002305_01 Accessory proteins BAP31/BAP29 S74039 291904 DXS1357E
145 0.813 H002571_01 Meiotic recombination (S. cerevisiae) 11 homolog B AF022778 202379 MRE11B
146 0.795 H002782_01 Wee1+ (S. pombe) homolog X62048 75188 WEE1
147 0.814 H002076_01 Interleukin-1 receptor-associated kinase 1 L76191 182018 IRAK1
148 0.82 H000048_01 PRKC, apoptosis, WT1, regulator U63809 176090 PAWR
149 0.578 H005801_01 Purkinje cell protein 4 U52969 80296 PCP4
150 0.834 H002311_01 Transcription factor 7-like 2 (T-cell specific, HMG-box) Y11306 173638 TCF7L2
151 0.774 H008367_01 KIAA0623 gene product AB014523 151406 KIAA0623
152 0.809 H005443_01 Interferon-related developmental regulator 1 AC005192 7879 IFRD1
153 0.796 H005941_01 Hypothetical protein FLJ20043 AK000050 103853 FLJ20043
154 0.731 H009185_01 KIAA1144 protein AB032970 22675 KIAA1144
155 0.737 H011708_01 Homo sapiens clone 24405 mRNA sequence AF070632 23729
156 0.848 H016365_01 Core1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3-galactosyltransferase NM_020156 46744 C1GALT1
157 0.763 H010122_01 Homo sapiens mRNA; cDNA DKFZp586F1223 (from clone DKFZp586F1223) AL050204 28540
158 0.71 H002475_01 Pim-1 oncogene M54915 81170 PIM1
159 0.794 H007334_01 SH3 domain binding glutamic acid-rich protein like AF042081 14368 SH3BGRL
160 0.817 H000893_01 Major histocompatibility complex, class I, E X56841 181392 HLA-E
161 0.737 H010951_01 LIM domain only 4 NM_006769 3844 LMO4
162 0.846 H001759_01 Chloride channel 7 AL031600 80768 CLCN7
163 0.845 H001612_01 RAP1, GTP-GDP dissociation stimulator 1 AF237413 7940 RAP1GDS1
164 0.753 H007858_01 Glutaminyl-peptide cyclotransferase (glutaminyl cyclase) X71125 79033 QPCT
165 0.808 H002897_01 Cathepsin L X12451 78056 CTSL
166 0.84 H004099_01 Phosphatidic acid phosphatase type 2A AF014403 41569 PPAP2A



'Observed v. Expected' table of GO classes and parent classes, in list of 166 genes shown above:

Only GO classes and parent classes with at least 5 observations in the selected subset and with an 'Observed vs. Expected' ratio of at least 2 are shown.


Cellular Component

GO id GO classification Observed in
selected subset
Expected in
selected subset
Observed/
Expected
0005887 integral to plasma membrane 19 9.37 2.03


Molecular Function

GO id GO classification Observed in
selected subset
Expected in
selected subset
Observed/
Expected
0016791 phosphoric monoester hydrolase activity 6 2.04 2.94
0005489 electron transporter activity 7 2.54 2.76
0042578 phosphoric ester hydrolase activity 6 2.4 2.5
0004713 protein-tyrosine kinase activity 5 2.16 2.31


Biological Process

GO id GO classification Observed in
selected subset
Expected in
selected subset
Observed/
Expected
0007600 sensory perception 6 1.92 3.13
0009581 detection of external stimulus 6 2.13 2.82
0006812 cation transport 6 2.93 2.05



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    View expression of significant genes.