Description of the problem:







Number of classes: 2
Number of genes: 16657
Number of genes that passed filtering criteria: 6799
Type of test used: SAM - Significance analysis of Microarray
Column of the Experiment Descriptors sheet that defines class variable : All SSc affected twins  vs population controls and  healthy DZ twin

                 

Genes which discriminate among classes:

Table 1
There are 81 genes significant by SAM
The median false discovery rate among the 81 significant genes is 0.09328 .
The delta value used to identify the significant genes is 0.57426 .
The fudge factor for standard deviation is computed as 0.08062 .

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

  Geom mean of ratios Normal Geom mean of ratios in SSc Fold difference of geom means Qiagen Oligo ID Description GB acc UG cluster Gene symbol
15 2.554 14.186 5.55 H001924_01 Thy-1 cell surface antigen AL161958 125359 THY1
20 1.849 10.168 5.50 H003853_01 Activin A receptor, type IB Z22536 99954 ACVR1B
21 3.098 14.225 4.59 H002800_01 Connective tissue growth factor X78947 75511 CTGF
45 2.813 12.316 4.38 H000899_01 UDP glycosyltransferase 2 family, polypeptide B7 J05428 10319 UGT2B7
50 3.473 15.156 4.36 H005487_01 RHCE S70456 251513  
36 1.753 7.48 4.27 H007489_01 KIAA0943 protein AB023160 272586 KIAA0943
27 2.355 9.975 4.24 H013988_01 Hypothetical protein FLJ21347 NM_022827 103147 FLJ21347
58 3.691 14.522 3.93 H000555_01 MAD2 (mitotic arrest deficient, yeast, homolog)-like 1 U65410 79078 MAD2L1
38 0.321 1.23 3.83 H008524_01 Angiotensin receptor-like 2 NM_005162 279535 AGTRL2
52 1.736 6.615 3.81 H009493_01 Rhesus blood group, CcEe antigens NM_016191 278994 RHCE
61 2.633 9.908 3.76 H004056_01 Murine retrovirus integration site 1 homolog NM_006069 251385 MRVI1
23 3.259 12.005 3.68 H003218_01 Calcium channel, voltage-dependent, L type, alpha 1D subunit M76558 23838 CACNA1D
39 3.646 13.226 3.63 H006619_01 Hypothetical protein FLJ20393 AK000400 326545 FLJ20393
43 3.38 12.07 3.57 H005913_01 Apical protein, Xenopus laevis-like X83543 2391 APXL
48 2.295 8.18 3.56 H012790_01 Phosphatidylinositol 4-kinase type II AF070611 25300 PI4KII
56 3.178 11.31 3.56 H012306_01 Carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 7 AL022165 138155 CHST7
22 1.259 4.463 3.54 H010437_01 NY-REN-24 antigen AF052087 128425 LOC58509
80 1.863 6.474 3.48 H010823_01 Homo sapiens cDNA FLJ11154 fis, clone PLACE1006932 AK002016 114727  
35 2.917 9.772 3.35 H003072_01 Collagen, type I, alpha 2 J03464 179573 COL1A2
33 3.568 11.929 3.34 H004727_01 Putative transmembrane protein; homolog of yeast Golgi membrane protein Yif1p (Yip1p-interacting fac AF004876 5809 54TM
18 2.45 8.168 3.33 H003695_01 Secreted protein, acidic, cysteine-rich (osteonectin) J03040 111779 SPARC
42 1.585 5.146 3.25 H000408_01 Branched chain aminotransferase 2, mitochondrial U68418 101408 BCAT2
59 1.005 3.139 3.12 H005176_01 H3 histone family, member I Z80786 247814 H3FI
67 0.988 2.893 2.93 H003699_01 Chondroitin sulfate proteoglycan 2 (versican) U16306 81800 CSPG2
46 0.637 1.85 2.90 H002468_01 Homo sapiens inducible nitric oxide synthase (iNOS) mRNA, complete cds AF049656 248084  
40 1.45 4.056 2.80 H009480_01 Tropomyosin 1 (alpha) AL050179 77899 TPM1
76 5.997 16.427 2.74 H010386_01 Human DNA sequence from clone RP5-1103G7 on chromosome 20p12.2-13. Contains up to three novel genes, AL034548 96151  
71 1.699 4.652 2.74 H002915_01 Collagen, type VIII, alpha 1 X57527 114599 COL8A1
28 1.714 4.608 2.69 H002144_01 Serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1 X61598 241579 SERPINH1
41 0.828 2.145 2.59 H008112_01 TATA box binding protein (TBP)-associated factor, RNA polymerase II, J, 20kD U57693 82037 TAF2J
17 0.658 1.685 2.56 H015129_01 Gap junction protein, alpha 3, 46kD (connexin 46) NM_021954 283746 GJA3
30 0.77 1.942 2.52 H015287_01 Homo sapiens HSPC080 mRNA, partial cds AF161343 284278  
29 0.785 1.947 2.48 H004244_01 75 kda infertility-related sperm protein [human, testis, mRNA Partial, 2427 nt] S58544 62608  
77 2.326 5.749 2.47 H010247_01 ADP-ribosylation factor related protein 1 X91504 64904 ARFRP1
31 1.248 3.002 2.41 H008600_01 Paralemmin Y16270 78482 PALM
44 0.58 1.377 2.37 H014899_01 Hypothetical protein FLJ13346 NM_024918 266273 FLJ13346
70 0.97 2.281 2.35 H005180_01 Tubby like protein 3 AF045583 169084 TULP3
25 0.637 1.488 2.34 H002448_01 Fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism) M64347 1420 FGFR3
81 1.321 3.084 2.33 H001268_01 ELL-RELATED RNA POLYMERASE II, ELONGATION FACTOR U88629 173334 ELL2
16 1.042 2.336 2.24 H014431_01 Hypothetical protein FLJ12876 NM_022754 16131 FLJ12876
53 1.529 3.303 2.16 H008340_01 Hypothetical protein 24636 AF070643 4187 LOC55977
47 0.746 1.608 2.16 H006032_01 Homo sapiens clone 24418 mRNA sequence AF052185 13434  
62 0.626 1.338 2.14 H001113_01 Calcium channel, voltage-dependent, alpha 2/delta subunit 1 M76559 1295 CACNA2D1
64 0.827 1.746 2.11 H000456_01 Adenylate kinase 3 X60673 274691 AK3
73 1.229 2.577 2.10 H000277_01 Four and a half LIM domains 2 L42176 8302 FHL2
26 0.18 0.375 2.08 H007495_01 H1 histone family, member 2 X57129 7644 H1F2
60 0.949 1.912 2.01 H000168_01 NGFI-A binding protein 1 (ERG1 binding protein 1) AF045451 107474 NAB1
19 0.609 1.222 2.01 H013132_01 Human DNA sequence from clone RP3-329A5 on chromosome 6p21.1-21.33 Contains a pseudogene similar to Z97832 272289  
65 0.911 1.784 1.96 H004028_01 clg01 protein AL021578 251374 CLG01
51 1.98 3.86 1.95 H009379_01 Annexin A2 pseudogene 2 M62895 166072 ANXA2P2
32 0.89 1.725 1.94 H014653_01 Ras homolog gene family, member B NM_004040 204354 ARHB
63 0.606 1.174 1.94 H001752_01 Ran GTPase activating protein 1 X82260 183800 RANGAP1
54 0.521 1.003 1.93 H002024_01 Cadherin 3, type 1, P-cadherin (placental) X63629 2877 CDH3
37 0.694 1.31 1.89 H001445_01 A disintegrin and metalloproteinase domain 19 (meltrin beta) AL049415 278679 ADAM19
66 0.687 1.295 1.89 H010888_01 High-mobility group 20B AF072836 32317 HMG20B
24 0.504 0.937 1.86 H000365_01 Zinc finger protein 43 (HTF6) X59244 74107 ZNF43
49 1.382 2.496 1.81 H016173_01 Homo sapiens HSPC134 protein (HSPC134), mRNA XM_007306 326630  
34 0.706 1.257 1.78 H008649_01 Parathymosin M24398 171814 PTMS
57 1.101 1.942 1.76 H011917_01 Sorting nexin 3 AF034546 12102 SNX3
69 0.864 1.509 1.75 H014475_01 Mitochondrial uncoupling protein 1 NM_021734 16786 MUP1
72 0.994 1.735 1.75 H003496_01 Small inducible cytokine subfamily B (Cys-X-Cys), member 10 X02530 2248 SCYB10
55 3.978 6.902 1.74 H001149_01 Microfibrillar-associated protein 2 U19718 83551 MFAP2
74 0.6 1.039 1.73 H000192_01 Putative mitochondrial outer membrane protein import receptor AF026031 31334 TOM
79 0.792 1.36 1.72 H007580_01 Homo sapiens mRNA; cDNA DKFZp761G151 (from clone DKFZp761G151); partial cds AL157475 35453  
78 0.661 1.133 1.71 H004407_01 SH3 protein AF178432 102929 AF3P21
75 0.341 0.537 1.57 H004497_01 KIAA0116 protein D29958 182877 KIAA0116
68 0.536 0.779 1.45 H006665_01 KIAA1081 protein AB029004 293705 KIAA1081
8 1.387 0.734 0.53 H006223_01 Hypothetical protein AJ012409 8170 YR-29
5 2.149 1.093 0.51 H001615_01 Calmodulin 3 (phosphorylase kinase, delta) X52606 141011 CALM3
9 0.738 0.374 0.51 H012558_01 H2A histone family, member G Z80776 239458 H2AFG
12 1.873 0.946 0.51 H007570_01 KIAA0171 gene product D79993 155623 KIAA0171
10 1.692 0.843 0.50 H002764_01 Lipase, hepatic X07228 9994 LIPC
11 1.079 0.526 0.49 H009598_01 Sulfotransferase family, cytosolic, 1A, phenol-preferring, member 3 L19956 274614 SULT1A3
4 1.236 0.572 0.46 H009251_01 Splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated) X70944 180610 SFPQ
13 0.858 0.391 0.46 H013222_01 DKFZP564I122 protein AL080062 13024 DKFZP564I122
14 1.96 0.863 0.44 H011937_01 Dimethylarginine dimethylaminohydrolase 2 AJ012008 247362 DDAH2
1 1.757 0.763 0.43 H015502_01 Hypothetical protein FLJ22242 NM_025070 288057 FLJ22242
6 1.197 0.445 0.37 H007811_01 Serologically defined colon cancer antigen 3 AK001296 94300 SDCCAG3
7 10.506 3.254 0.31 H002995_01 Apolipoprotein D J02611 75736 APOD
2 0.68 0.159 0.23 H007802_01 CGI-134 protein AK002008 3385 LOC51023
3 0.245 0.05 0.20 H006006_01 Human Ig rearranged lambda-chain mRNA, subgroup VL3, V-J region, partial cds L21961 247947  

                 






                 

Observed v. Expected' table of GO classes and parent classes, in list of 81 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 Expected in Observed/
selected subset selected subset Expected
31012 extracellular matrix 6 1.12 5.38
5578 extracellular matrix (sensu Metazoa) 6 1.12 5.38
5576 extracellular region 8 3.19 2.5
267 cell fraction 6 2.99 2

Molecular Function

GO id GO classification Observed in Expected in Observed/
selected subset selected subset Expected
5198 structural molecule activity 5 2.35 2.13

Biological Process

GO id GO classification Observed in Expected in Observed/
selected subset selected subset Expected
6811 ion transport 5 1.81 2.76
48513 organ development 6 2.78 2.16
9887 organogenesis 6 2.78 2.16

                 





                 

View expression of significant genes.