SAM (Significance Analysis of Microarray) Results
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 (external link) | 125359 | THY1 (external link) |
| 20 | 1.849 | 10.168 | 5.50 | H003853_01 | Activin A receptor, type IB |
Z22536 (external link) | 99954 | ACVR1B (external link) |
| 21 | 3.098 | 14.225 | 4.59 | H002800_01 | Connective tissue growth factor |
X78947 (external link) | 75511 | CTGF (external link) |
| 45 | 2.813 | 12.316 | 4.38 | H000899_01 | UDP glycosyltransferase 2 family, polypeptide B7 |
J05428 (external link) | 10319 | UGT2B7 (external link) |
| 50 | 3.473 | 15.156 | 4.36 | H005487_01 | RHCE | S70456 (external link) | 251513 | |
| 36 | 1.753 | 7.48 | 4.27 | H007489_01 | KIAA0943 protein |
AB023160 (external link) | 272586 | KIAA0943 (external link) |
| 27 | 2.355 | 9.975 | 4.24 | H013988_01 | Hypothetical protein FLJ21347 |
NM_022827 (external link) | 103147 | FLJ21347 (external link) |
| 58 | 3.691 | 14.522 | 3.93 | H000555_01 | MAD2 (mitotic arrest deficient, yeast, homolog)-like 1 |
U65410 (external link) | 79078 | MAD2L1 (external link) |
| 38 | 0.321 | 1.23 | 3.83 | H008524_01 | Angiotensin receptor-like 2 |
NM_005162 (external link) | 279535 | AGTRL2 (external link) |
| 52 | 1.736 | 6.615 | 3.81 | H009493_01 | Rhesus blood group, CcEe antigens |
NM_016191 | 278994 | RHCE (external link) |
| 61 | 2.633 | 9.908 | 3.76 | H004056_01 | Murine retrovirus integration site 1 homolog |
NM_006069 (external link) | 251385 | MRVI1 (external link) |
| 23 | 3.259 | 12.005 | 3.68 | H003218_01 | Calcium channel, voltage-dependent, L type, alpha 1D subunit |
M76558 (external link) | 23838 | CACNA1D (external link) |
| 39 | 3.646 | 13.226 | 3.63 | H006619_01 | Hypothetical protein FLJ20393 |
AK000400 (external link) | 326545 | FLJ20393 (external link) |
| 43 | 3.38 | 12.07 | 3.57 | H005913_01 | Apical protein, Xenopus laevis like |
X83543 (external link) | 2391 | APXL (external link) |
| 48 | 2.295 | 8.18 | 3.56 | H012790_01 | Phosphatidylinositol 4-kinase type II |
AF070611 (external link) | 25300 | PI4KII (external link) |
| 56 | 3.178 | 11.31 | 3.56 | H012306_01 | Carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 7 |
AL022165 (external link) | 138155 | CHST7 (external link) |
| 22 | 1.259 | 4.463 | 3.54 | H010437_01 | NY-REN-24 antigen |
AF052087 (external link) | 128425 | LOC58509 (external link) |
| 80 | 1.863 | 6.474 | 3.48 | H010823_01 | Homo sapiens cDNA FLJ11154 fis, clone PLACE1006932 |
AK002016 (external link) | 114727 | |
| 35 | 2.917 | 9.772 | 3.35 | H003072_01 | Collagen, type I, alpha 2 |
J03464 (external link) | 179573 | COL1A2 (external link) |
| 33 | 3.568 | 11.929 | 3.34 | H004727_01 | Putative transmembrane protein; homolog of yeast Golgi membrane protein Yif1p (Yip1p-interacting fac |
AF004876 (external link) | 5809 | 54TM (external link) |
| 18 | 2.45 | 8.168 | 3.33 | H003695_01 | Secreted protein, acidic, cysteine-rich (osteonectin) |
J03040 (external link) | 111779 | SPARC (external link) |
| 42 | 1.585 | 5.146 | 3.25 | H000408_01 | Branched chain aminotransferase 2, mitochondrial |
U68418 (external link) | 101408 | BCAT2 (external link) |
| 59 | 1.005 | 3.139 | 3.12 | H005176_01 | H3 histone family, member I |
Z80786 (external link) | 247814 | H3FI (external link) |
| 67 | 0.988 | 2.893 | 2.93 | H003699_01 | Chondroitin sulfate proteoglycan 2 (versican) |
U16306 (external link) | 81800 | CSPG2 (external link) |
| 46 | 0.637 | 1.85 | 2.90 | H002468_01 | Homo sapiens inducible nitric oxide synthase (iNOS) mRNA, complete cds |
AF049656 (external link) | 248084 | |
| 40 | 1.45 | 4.056 | 2.80 | H009480_01 | Tropomyosin 1 (alpha) |
AL050179 (external link) | 77899 | TPM1 (external link) |
| 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 (external link) | 96151 | |
| 71 | 1.699 | 4.652 | 2.74 | H002915_01 | Collagen, type VIII, alpha 1 |
X57527 (external link) | 114599 | COL8A1 (external link) |
| 28 | 1.714 | 4.608 | 2.69 | H002144_01 | Serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1 |
X61598 (external link) | 241579 | SERPINH1 (external link) |
| 41 | 0.828 | 2.145 | 2.59 | H008112_01 | TATA box binding protein (TBP)-associated factor, RNA polymerase II, J, 20kD |
U57693 (external link) | 82037 | TAF2J (external link) |
| 17 | 0.658 | 1.685 | 2.56 | H015129_01 | Gap junction protein, alpha 3, 46kD (connexin 46) |
NM_021954 (external link) | 283746 | GJA3 (external link) |
| 30 | 0.77 | 1.942 | 2.52 | H015287_01 | Homo sapiens HSPC080 mRNA, partial cds |
AF161343 (external link) | 284278 | |
| 29 | 0.785 | 1.947 | 2.48 | H004244_01 | 75 kda infertility-related sperm protein [human, testis, mRNA Partial, 2427 nt] |
S58544 (external link) | 62608 | |
| 77 | 2.326 | 5.749 | 2.47 | H010247_01 | ADP-ribosylation factor related protein 1 |
X91504 (external link) | 64904 | ARFRP1 (external link) |
| 31 | 1.248 | 3.002 | 2.41 | H008600_01 | Paralemmin | Y16270 (external link) | 78482 | PALM (external link) |
| 44 | 0.58 | 1.377 | 2.37 | H014899_01 | Hypothetical protein FLJ13346 |
NM_024918 (external link) | 266273 | FLJ13346 (external link) |
| 70 | 0.97 | 2.281 | 2.35 | H005180_01 | Tubby like protein 3 |
AF045583 (external link) | 169084 | TULP3 (external link) |
| 25 | 0.637 | 1.488 | 2.34 | H002448_01 | Fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism) |
M64347 (external link) | 1420 | FGFR3 (external link) |
| 81 | 1.321 | 3.084 | 2.33 | H001268_01 | ELL-RELATED RNA POLYMERASE II, ELONGATION FACTOR |
U88629 (external link) | 173334 | ELL2 (external link) |
| 16 | 1.042 | 2.336 | 2.24 | H014431_01 | Hypothetical protein FLJ12876 |
NM_022754 (external link) | 16131 | FLJ12876 (external link) |
| 53 | 1.529 | 3.303 | 2.16 | H008340_01 | Hypothetical protein 24636 |
AF070643 (external link) | 4187 | LOC55977 (external link) |
| 47 | 0.746 | 1.608 | 2.16 | H006032_01 | Homo sapiens clone 24418 mRNA sequence |
AF052185 (external link) | 13434 | |
| 62 | 0.626 | 1.338 | 2.14 | H001113_01 | Calcium channel, voltage-dependent, alpha 2/delta subunit 1 |
M76559 (external link) | 1295 | CACNA2D1 (external link) |
| 64 | 0.827 | 1.746 | 2.11 | H000456_01 | Adenylate kinase 3 |
X60673 (external link) | 274691 | AK3 (external link) |
| 73 | 1.229 | 2.577 | 2.10 | H000277_01 | Four and a half LIM domains 2 |
L42176 (external link) | 8302 | FHL2 (external link) |
| 26 | 0.18 | 0.375 | 2.08 | H007495_01 | H1 histone family, member 2 |
X57129 (external link) | 7644 | H1F2 (external link) |
| 60 | 0.949 | 1.912 | 2.01 | H000168_01 | NGFI-A binding protein 1 (ERG1 binding protein 1) |
AF045451 (external link) | 107474 | NAB1 (external link) |
| 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 (external link) | 272289 | |
| 65 | 0.911 | 1.784 | 1.96 | H004028_01 | clg01 protein | AL021578 (external link) | 251374 | CLG01 (external link) |
| 51 | 1.98 | 3.86 | 1.95 | H009379_01 | Annexin A2 pseudogene 2 |
M62895 (external link) | 166072 | ANXA2P2 (external link) |
| 32 | 0.89 | 1.725 | 1.94 | H014653_01 | Ras homolog gene family, member B |
NM_004040 (external link) | 204354 | ARHB (external link) |
| 63 | 0.606 | 1.174 | 1.94 | H001752_01 | Ran GTPase activating protein 1 |
X82260 (external link) | 183800 | RANGAP1 (external link) |
| 54 | 0.521 | 1.003 | 1.93 | H002024_01 | Cadherin 3, type 1, P-cadherin (placental) |
X63629 (external link) | 2877 | CDH3 (external link) |
| 37 | 0.694 | 1.31 | 1.89 | H001445_01 | A disintegrin and metalloproteinase domain 19 (meltrin beta) |
AL049415 (external link) | 278679 | ADAM19 (external link) |
| 66 | 0.687 | 1.295 | 1.89 | H010888_01 | High-mobility group 20B |
AF072836 (external link) | 32317 | HMG20B (external link) |
| 24 | 0.504 | 0.937 | 1.86 | H000365_01 | Zinc finger protein 43 (HTF6) |
X59244 (external link) | 74107 | ZNF43 (external link) |
| 49 | 1.382 | 2.496 | 1.81 | H016173_01 | Homo sapiens HSPC134 protein (HSPC134), mRNA |
XM_007306 (external link) | 326630 | |
| 34 | 0.706 | 1.257 | 1.78 | H008649_01 | Parathymosin | M24398 (external link) | 171814 | PTMS (external link) |
| 57 | 1.101 | 1.942 | 1.76 | H011917_01 | Sorting nexin 3 | AF034546 (external link) | 12102 | SNX3 (external link) |
| 69 | 0.864 | 1.509 | 1.75 | H014475_01 | Mitochondrial uncoupling protein 1 |
NM_021734 (external link) | 16786 | MUP1 (external link) |
| 72 | 0.994 | 1.735 | 1.75 | H003496_01 | Small inducible cytokine subfamily B (Cys-X-Cys), member 10 |
X02530 (external link) | 2248 | SCYB10 (external link) |
| 55 | 3.978 | 6.902 | 1.74 | H001149_01 | Microfibrillar-associated protein 2 |
U19718 (external link) | 83551 | MFAP2 (external link) |
| 74 | 0.6 | 1.039 | 1.73 | H000192_01 | Putative mitochondrial outer membrane protein import receptor |
AF026031 (external link) | 31334 | TOM (external link) |
| 79 | 0.792 | 1.36 | 1.72 | H007580_01 | Homo sapiens mRNA; cDNA DKFZp761G151 (from clone DKFZp761G151); partial cds |
AL157475 (external link) | 35453 | |
| 78 | 0.661 | 1.133 | 1.71 | H004407_01 | SH3 protein | AF178432 (external link) | 102929 | AF3P21 (external link) |
| 75 | 0.341 | 0.537 | 1.57 | H004497_01 | KIAA0116 protein |
D29958 (external link) | 182877 | KIAA0116 (external link) |
| 68 | 0.536 | 0.779 | 1.45 | H006665_01 | KIAA1081 protein |
AB029004 (external link) | 293705 | KIAA1081 (external link) |
| 8 | 1.387 | 0.734 | 0.53 | H006223_01 | Hypothetical protein |
AJ012409 (external link) | 8170 | YR-29 (external link) |
| 5 | 2.149 | 1.093 | 0.51 | H001615_01 | Calmodulin 3 (phosphorylase kinase, delta) |
X52606 (external link) | 141011 | CALM3 (external link) |
| 9 | 0.738 | 0.374 | 0.51 | H012558_01 | H2A histone family, member G |
Z80776 (external link) | 239458 | H2AFG (external link) |
| 12 | 1.873 | 0.946 | 0.51 | H007570_01 | KIAA0171 gene product |
D79993 (external link) | 155623 | KIAA0171 (external link) |
| 10 | 1.692 | 0.843 | 0.50 | H002764_01 | Lipase, hepatic | X07228 (external link) | 9994 | LIPC (external link) |
| 11 | 1.079 | 0.526 | 0.49 | H009598_01 | Sulfotransferase family, cytosolic, 1A, phenol-preferring, member 3 |
L19956 (external link) | 274614 | SULT1A3 (external link) |
| 4 | 1.236 | 0.572 | 0.46 | H009251_01 | Splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated) |
X70944 (external link) | 180610 | SFPQ (external link) |
| 13 | 0.858 | 0.391 | 0.46 | H013222_01 | DKFZP564I122 protein |
AL080062 (external link) | 13024 | DKFZP564I122 (external link) |
| 14 | 1.96 | 0.863 | 0.44 | H011937_01 | Dimethylarginine dimethylaminohydrolase 2 |
AJ012008 (external link) | 247362 | DDAH2 (external link) |
| 1 | 1.757 | 0.763 | 0.43 | H015502_01 | Hypothetical protein FLJ22242 |
NM_025070 (external link) | 288057 | FLJ22242 (external link) |
| 6 | 1.197 | 0.445 | 0.37 | H007811_01 | Serologically defined colon cancer antigen 3 |
AK001296 (external link) | 94300 | SDCCAG3 (external link) |
| 7 | 10.506 | 3.254 | 0.31 | H002995_01 | Apolipoprotein D |
J02611 (external link) | 75736 | APOD (external link) |
| 2 | 0.68 | 0.159 | 0.23 | H007802_01 | CGI-134 protein | AK002008 (external link) | 3385 | LOC51023 (external link) |
| 3 | 0.245 | 0.05 | 0.20 | H006006_01 | Human Ig rearranged lambda-chain mRNA, subgroup VL3, V-J region, partial cds |
L21961 (external link) | 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 selected subset | Expected in selected subset | Observed/Expected |
| 5198 | structural molecule activity | 5 | 2.35 | 2.13 |
Biological Process
| GO id | GO classification | Observed in selected subset | Expected in selected subset | Observed/Expected | |
| 6811 | ion transport | 5 | 1.81 | 2.76 | |
| 48513 | organ development | 6 | 2.78 | 2.16 | |
| 9887 | organogenesis | 6 | 2.78 | 2.16 |
