Significance Analysis of Microarrays
GI Stromal Tumors, Significant Genes
Top 20 Positive Significant Genes
PRKCQ protein kinase C, theta Hs.211593
KIAA1492 KIAA1492 protein Hs.91625
CA2 carbonic anhydrase II Hs.155097
PTP4A3 protein tyrosine phosphatase type IVA, member 3 Hs.43666
SPRY4 sprouty (Drosophila) homolog 4 Hs.285814
KIT v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog Hs.81665
KIAA0353 KIAA0353 protein Hs.10587
PROML1 prominin (mouse)-like 1 Hs.112360
SE57-1 CTCL tumor antigen se57-1 Hs.30315
AMPD3 adenosine monophosphate deaminase (isoform E) Hs.83918
KIAA0229 KIAA0229 protein Hs.20060
PLAT plasminogen activator, tissue Hs.274404
SFRP1 secreted frizzled-related protein 1 Hs.7306
EDN3 endothelin 3 Hs.1408
GUCY1A3 guanylate cyclase 1, soluble, alpha 3 Hs.75295
CTSL cathepsin L Hs.78056
BCHE butyrylcholinesterase Hs.1327
ABCB1 ATP-binding cassette, sub-family B (MDR/TAP), member 1 Hs.21330
PRKAR2B protein kinase, cAMP-dependent, regulatory, type II, beta Hs.77439
RBPMS RNA-binding protein gene with multiple splicing Hs.80248
Top 20 Negative Significant Genes
COL6A3 collagen, type VI, alpha 3 Hs.80988
PCOLCE procollagen C-endopeptidase enhancer Hs.202097
ADNP activity-dependent neuroprotective protein Hs.3657
GAS1 growth arrest-specific 1 Hs.65029
S100A10 S100 calcium-binding protein A10 Hs.119301
GAS1 growth arrest-specific 1 Hs.65029
COL1A2 collagen, type I, alpha 2 Hs.179573
JUN v-jun avian sarcoma virus 17 oncogene homolog Hs.78465
ADAM12 a disintegrin and metalloproteinase domain 12 Hs.8850
SEMA3C sema domain, immunoglobulin domain (Ig), short basic Hs.171921
CTSD cathepsin D (lysosomal aspartyl protease) Hs.79572
SRPX sushi-repeat-containing protein, X chromosome Hs.15154
AHNAK AHNAK nucleoprotein (desmoyokin) Hs.301417
PIM1 pim-1 oncogene Hs.81170
ZFHX1B zinc finger homeobox 1B Hs.34871
MAGP2 Microfibril-associated glycoprotein-2 Hs.300946
BIRC5 baculoviral IAP repeat-containing 5 (survivin) Hs.1578
FBLN2 fibulin 2 Hs.198862
PMP22 peripheral myelin protein 22 Hs.103724
COL1A2 collagen, type I, alpha 2 Hs.179573
Leiomyosarcoma, calponin positive group, Significant Genes
Top 20 Positive Significant Genes
MYPT2 myosin phosphatase, target subunit 2 Hs.130760
LMOD1 leiomodin 1 (smooth muscle) Hs.79386
MYH11 myosin, heavy polypeptide 11, smooth muscle Hs.78344
LAMA3 laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin) Hs.83450
SVIL supervillin Hs.154567
MYLK myosin, light polypeptide kinase Hs.211582
KCNMB1 potassium large conductance calcium-activated channel, subfamily M, beta member 1 Hs.93841
CNN1 calponin 1, basic, smooth muscle Hs.21223
ALDH1B1 aldehyde dehydrogenase 1 family, member B1 Hs.169517
ACTA2 actin, alpha 2, smooth muscle, aorta Hs.195851
RAB23 RAB23, member RAS oncogene family Hs.94769
MYRL2 myosin regulatory light chain 2, smooth muscle isoform Hs.9615
RAB23 RAB23, member RAS oncogene family Hs.94769
DNMT2 DNA (cytosine-5-)-methyltransferase 2 Hs.97681
GABRG2 gamma-aminobutyric acid (GABA) A receptor, gamma 2 Hs.7195
LOC81691 exonuclease NEF-sp Hs.177926
ACTG2 actin, gamma 2, smooth muscle, enteric Hs.78045
TAGLN transgelin Hs.75777
SH3D5 SH3-domain protein 5 (ponsin) Hs.108924
KIAA0751 KIAA0751 gene product Hs.153610
Top 20 Negative Significant Genes
PLAGL1 pleiomorphic adenoma gene-like 1 Hs.75825
ETV5 ets variant gene 5 (ets-related molecule) Hs.43697
DOC1 deleted in oral cancer (mouse, homolog) 1 Hs.3436
LOXL2 lysyl oxidase-like 2 Hs.83354
SPRY2 sprouty (Drosophila) homolog 2 Hs.18676
AMPD2 adenosine monophosphate deaminase 2 (isoform L) Hs.82927
HLA-DNA major histocompatibility complex, class II, DN alpha Hs.11135
ADD3 adducin 3 (gamma) Hs.324470
T1A-2 lung type-I cell membrane-associated glycoprotein Hs.135150
TCF4 transcription factor 4 Hs.326198
KIAA1500 KIAA1500 protein Hs.15420
ATRX alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog) Hs.96264
SSI-3 STAT induced STAT inhibitor 3 Hs.296176
MMP2 matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase) Hs.111301
CDH11 cadherin 11, type 2, OB-cadherin (osteoblast) Hs.75929
KIAA0808 KIAA0808 gene product Hs.184297
BMP7 bone morphogenetic protein 7 (osteogenic protein 1) Hs.170195
THY1 Thy-1 cell surface antigen Hs.125359
GOLPH2 golgi phosphoprotein 2 Hs.182793
FLJ10128 uveal autoantigen with coiled coil domains and ankyrin repeats Hs.49753
Leiomyosarcoma, calponin-negative group, Significant Genes
Top 20 Positive Significant Genes
AIM2 absent in melanoma 2 Hs.105115
MIG monokine induced by gamma interferon Hs.77367
PLEC1 plectin 1, intermediate filament binding protein, 500kD Hs.79706
LOXL1 lysyl oxidase-like 1 Hs.65436
COL7A1 collagen, type VII, alpha 1 (epidermolysis bullosa, dystrophic, dominant and recessive) Hs.1640
SCYA5 small inducible cytokine A5 (RANTES) Hs.241392
KCNN4 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 Hs.10082
CAPG capping protein (actin filament), gelsolin-like Hs.82422
KIAA0750 KIAA0750 gene product Hs.314434
SBBI42 BCM-like membrane protein precursor Hs.20450
MME membrane metallo-endopeptidase (neutral endopeptidase, enkephalinase, CALLA, CD10) Hs.1298
MTR 5-methyltetrahydrofolate-homocysteine methyltransferase Hs.82283
XAGE-1 XAGE-1 protein Hs.112208
HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 Hs.73931
SH3BGRL3 SH3 domain binding glutamic acid-rich protein like 3 Hs.109051
HLA-DRB1 major histocompatibility complex, class II, DR beta 1 Hs.180255
VEGFC vascular endothelial growth factor C Hs.79141
PLOD procollagen-lysine, 2-oxoglutarate 5-dioxygenase Hs.75093
HOMER-2B Homer, neuronal immediate early gene, 2 Hs.93564
Top 20 Negative Significant Genes
CDC2L1 cell division cycle 2-like 1 (PITSLRE proteins) Hs.183418
ABLIM actin binding LIM protein 1 Hs.158203
SILV silver (mouse homolog) like Hs.95972
LRP5 low density lipoprotein receptor-related protein 5 Hs.6347
KIAA0381 KIAA0381 protein Hs.100113
PBX1 pre-B-cell leukemia transcription factor 1 Hs.155691
KIAA1102 KIAA1102 protein Hs.202949
KIAA1238 KIAA1238 protein Hs.334806
ALS2CR3 amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3 Hs.154248
ABLIM actin binding LIM protein 1 Hs.158203
MN1 meningioma (disrupted in balanced translocation) 1 Hs.268515
TBL1 transducin (beta)-like 1 Hs.76536
EPHX2 epoxide hydrolase 2, cytoplasmic Hs.113
MEIS3 Meis (mouse) homolog 3 Hs.117313
ADD3 adducin 3 (gamma) Hs.324470
HSA277165 hairless protein  Hs.272367
RPP30 ribonuclease P (30kD) Hs.139120
C5ORF4 chromosome 5 open reading frame 4 Hs.10235
SFRP1 secreted frizzled-related protein 1 Hs.7306
PRDX2 peroxiredoxin 2 Hs.146354
Synovial Sarcoma Significant Genes
Top 20 Positive Significant Genes
CRABP1 cellular retinoic acid-binding protein 1 Hs.7678
PRAME preferentially expressed antigen in melanoma Hs.30743
COL2A1 collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital) Hs.81343
KCNQ2 potassium voltage-gated channel, KQT-like subfamily, member 2 Hs.4975
COL9A2 collagen, type IX, alpha 2 Hs.37165
TGFB2 transforming growth factor, beta 2 Hs.169300
NPTX2 neuronal pentraxin II Hs.3281
APBA2 amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like) Hs.26468
ENC1 ectodermal-neural cortex (with BTB-like domain) Hs.104925
ZNF161 zinc finger protein 161 Hs.6557
NOGOR nogo receptor Hs.30868
CPA3 carboxypeptidase A3 (mast cell) Hs.646
TGFB2 transforming growth factor, beta 2 Hs.169300
ATSV axonal transport of synaptic vesicles Hs.259873
NOE1 olfactomedin related ER localized protein Hs.74376
ENC1 ectodermal-neural cortex (with BTB-like domain) Hs.104925
ZIC2 Zic family member 2 (odd-paired Drosophila homolog) Hs.132863
RGS6 regulator of G-protein signalling 6 Hs.3221
ECEL1 endothelin converting enzyme-like 1 Hs.26880
KIAA1547 KIAA1547 protein Hs.31305
Top 20 Negative Significant Genes
P8 p8 protein (candidate of metastasis 1) Hs.8603
CGI-44 CGI-44 protein; sulfide dehydrogenase like (yeast) Hs.8185
RNF15 ring finger protein 15 Hs.59545
CASP1 caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase) Hs.2490
RARRES3 retinoic acid receptor responder (tazarotene induced) 3 Hs.17466
UCP2 uncoupling protein 2 (mitochondrial, proton carrier) Hs.80658
AIF1 allograft inflammatory factor 1 Hs.76364
CYBB cytochrome b-245, beta polypeptide (chronic granulomatous disease) Hs.88974
RNASE6 ribonuclease, RNase A family, k6 Hs.23262
IL16 interleukin 16 (lymphocyte chemoattractant factor) Hs.82127
CD4 CD4 antigen (p55) Hs.17483
C7 complement component 7 Hs.78065
ARHGDIB Rho GDP dissociation inhibitor (GDI) beta Hs.83656
HLA-DMA major histocompatibility complex, class II, DM alpha Hs.77522
LGALS9 lectin, galactoside-binding, soluble, 9 (galectin 9) Hs.81337
ITGB2 integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit) Hs.83968
IFI35 interferon-induced protein 35 Hs.50842
CTSS cathepsin S Hs.181301
KIAA1268 KIAA1268 protein Hs.152925
FER1L3 fer-1 (C.elegans)-like 3 (myoferlin) Hs.234680
Liposarcoma Significant Genes
Top 20 Positive Significant Genes
TNA tetranectin (plasminogen-binding protein) Hs.65424
DLL4 delta-like 4 homolog (Drosophila) Hs.3736
HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 Hs.1376
SELENBP1 selenium binding protein 1 Hs.334841
UAP1 UDP-N-acteylglucosamine pyrophosphorylase 1 Hs.21293
POR P450 (cytochrome) oxidoreductase Hs.167246
DMRT2 doublesex and mab-3 related transcription factor 2 Hs.59506
RNASE1 ribonuclease, RNase A family, 1 (pancreatic) Hs.78224
TNXB tenascin XB Hs.169886
CPZ carboxypeptidase Z Hs.78068
APOA1 apolipoprotein A-I Hs.93194
CLDN5 claudin 5 (transmembrane protein deleted in velocardiofacial syndrome) Hs.110903
PALM paralemmin Hs.78482
SERPINB2 serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2 Hs.75716
WNT2 wingless-type MMTV integration site family member 2 Hs.89791
GPRC5B G protein-coupled receptor, family C, group 5, member B Hs.242407
DEPP decidual protein induced by progesterone Hs.93675
STC1 stanniocalcin 1 Hs.25590
PRSC1 protease, cysteine, 1 (legumain) Hs.18069
WNT2 wingless-type MMTV integration site family member 2 Hs.89791
Top 20 Negative Significant Genes
RAI RelA-associated inhibitor Hs.324051
APLP1 amyloid beta (A4) precursor-like protein 1 Hs.74565
INHBA inhibin, beta A (activin A, activin AB alpha polypeptide) Hs.727
HSPC150 HSPC150 protein similar to ubiquitin-conjugating enzyme Hs.5199
FGF11 fibroblast growth factor 11 Hs.31339
CHML choroideremia-like (Rab escort protein 2) Hs.170129
FZD1 frizzled (Drosophila) homolog 1 Hs.94234
KIAA1488 KIAA1488 protein Hs.9414
NRP2 neuropilin 2 Hs.17778
HXB hexabrachion (tenascin C, cytotactin) Hs.289114
PIR121 p53 inducible protein Hs.258503
CRABP1 cellular retinoic acid-binding protein 1 Hs.7678
ETV4 ets variant gene 4 (E1A enhancer-binding protein, E1AF) Hs.77711
LOC54557 hypothetical protein Hs.143330
SLC5A3 solute carrier family 5 (inositol transporters), member 3 Hs.324787
ARHGEF5 Rho guanine nucleotide exchange factor (GEF) 5 Hs.334
TRPS1 trichorhinophalangeal syndrome I Hs.26102
MEF-2 myelin gene expression factor 2 Hs.44268
CSRP2 cysteine and glycine-rich protein 2 Hs.10526
Malignant Fibrous Histiocytoma Significant Genes
Top 20 Positive Significant Genes
SFRP4 secreted frizzled-related protein 4 Hs.105700
GRO1 GRO1 oncogene (melanoma growth stimulating activity, alpha) Hs.789
SCYA2 small inducible cytokine A2 (monocyte chemotactic protein 1, homologous to mouse Sig-je) Hs.303649
BST1 bone marrow stromal cell antigen 1 Hs.169998
COL6A3 collagen, type VI, alpha 3 Hs.80988
LIF leukemia inhibitory factor (cholinergic differentiation factor) Hs.2250
GARP glycoprotein A repetitions predominant Hs.151641
GNA15 guanine nucleotide binding protein (G protein), alpha 15 (Gq class) Hs.73797
SAA1 serum amyloid A1 Hs.332053
LOX lysyl oxidase Hs.102267
CTGF connective tissue growth factor Hs.75511
SRPX sushi-repeat-containing protein, X chromosome Hs.15154
MME membrane metallo-endopeptidase (neutral endopeptidase, enkephalinase, CALLA, CD10) Hs.1298
CTGF connective tissue growth factor Hs.75511
SCYA7 small inducible cytokine A7 (monocyte chemotactic protein 3) Hs.251526
PLAU plasminogen activator, urokinase Hs.77274
THBS2 thrombospondin 2 Hs.108623
KIAA0118 KIAA0118 protein Hs.184627
TIMP1 tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor) Hs.5831
113993 SH3BGRL3 SH3 domain binding glutamic acid-rich protein like 3 Hs.109051
Top 20 Negative Significant Genes
BRPF3 bromodomain and PHD finger containing, 3 Hs.42179
INADL PDZ domain protein (Drosophila inaD-like) Hs.321197
ITM3 integral membrane protein 3 Hs.111577
WRB tryptophan rich basic protein Hs.198308
BRPF3 bromodomain and PHD finger containing, 3 Hs.42179
CA11 carbonic anhydrase XI Hs.22777
TCF-3 HMG-box transcription factor TCF-3 Hs.102367
COL4A5 collagen, type IV, alpha 5 (Alport syndrome) Hs.169825
FBXL2 f-box and leucine-rich repeat protein 2 Hs.6092
TCF-3 HMG-box transcription factor TCF-3 Hs.102367
CDKN1C cyclin-dependent kinase inhibitor 1C (p57, Kip2) Hs.106070
KIAA0657 KIAA0657 protein Hs.6654
DKFZP564O0423 DKFZP564O0423 protein Hs.5028
KIAA1705 KIAA1705 protein Hs.7076
TP53 tumor protein p53 (Li-Fraumeni syndrome) Hs.1846
BCL2 B-cell CLL/lymphoma 2 Hs.79241
PC4 activated RNA polymerase II transcription cofactor 4 Hs.74861
CAP2 adenylyl cyclase-associated protein 2 Hs.296341
GNAS1 guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1 Hs.273385
SDCCAG33 serologically defined colon cancer antigen 33 Hs.284217
Schwannoma Significant Genes
Top 20 Positive Significant Genes
NRXN1 neurexin 1 Hs.22998
S100B S100 calcium-binding protein, beta (neural) Hs.83384
TITF1 thyroid transcription factor 1 Hs.197764
L1CAM L1 cell adhesion molecule
ADORA3 adenosine A3 receptor Hs.258
STHM sialyltransferase Hs.288215
APOC2 apolipoprotein C-II Hs.75615
KIAA1260 neuroligin Hs.21107
ST14 suppression of tumorigenicity 14 (colon carcinoma, matriptase, epithin) Hs.56937
TREM2 triggering receptor expressed on myeloid cells 2 Hs.44234
PHRET1 PH domain containing protein in retina 1 Hs.8124
GPM6B glycoprotein M6B Hs.5422
SERPINA5 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5 Hs.76353
GFAP glial fibrillary acidic protein Hs.1447
AD037 AD037 protein Hs.318715
NRXN3 neurexin 3 Hs.22269
PLP1 proteolipid protein 1 (Pelizaeus-Merzbacher disease, spastic paraplegia 2, uncomplicated) Hs.1787
SEMA3B sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B Hs.82222
Top 20 Negative Significant Genes
SLC7A2 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 Hs.153985
TBX3-iso TBX3-iso protein Hs.267182
MFAP2 microfibrillar-associated protein 2 Hs.83551
ADCY1 adenylate cyclase 1 (brain) Hs.259768
FBLN1 fibulin 1 Hs.79732
MLLT4 myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4 Hs.100469
KIAA1462 KIAA1462 protein Hs.46901
KIAA1130 KIAA1130 protein Hs.21035
RBM9 RNA binding motif protein 9 Hs.5011
EGFR epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog) Hs.77432
FBN2 fibrillin 2 (congenital contractural arachnodactyly) Hs.79432
MLLT4 myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4 Hs.100469
DPEP1 dipeptidase 1 (renal) Hs.109
P311 P311 protein Hs.142827
CD9P-1 CD9 partner 1 Hs.300591
GAS1 growth arrest-specific 1 Hs.65029
ASS argininosuccinate synthetase Hs.160786
HOXD8 homeo box D8 Hs.301963
SLUG slug (chicken homolog), zinc finger protein Hs.93005