Background
Methods
Tissue samples and RCC cell lines
RNA extraction and microarray experiments
Data preprocessing
Functional clustering analysis
RT-PCR
Singular value decomposition
Results
Patterns of gene expression alterations in RCC tissue samples
Accession number | Gene name* | Avg. fold-change |
---|---|---|
M95167 | Dopamine transporter (SLC6A3) | 55.6 |
HG3044-HT3742 | Fibronectin 1 1,2,4
| 44.2 |
U29195 | Neuronal pentraxin II (NPTX2) | 38.6 |
X51441 | Serum amyloid A (SAA) (_s_at)1
| 37.4 |
J03474 | Serum amyloid A (SAA)1
| 34.4 |
U90546 | Butyrophilin (BTF4) | 32.5 |
X51441 | Serum amyloid A (SAA) (_at)1
| 29.2 |
M77349 | Transforming growth factor-beta induced gene product (BIGH3)1,3,4
| 28.4 |
X51956 | Enolase2 (ENO2)2,4
| 26.2 |
U10485 | Lymphoid-restricted membrane protein (Jaw1) | 25.9 |
D88667 | Cerebroside sulfotransferase | 21.3 |
U17077 | BENE4
| 17.3 |
M10321 | von Willebrand factor (vWF)1,2,3
| 15.5 |
U45878 | Inhibitor of apoptosis protein 1 | 14.4 |
X06256 | Fibronectin receptor alpha subunit1
| 12.8 |
L27624 | Tissue factor pathway inhibitor-2 | 12.1 |
M20902 | Apolipoprotein C-I (VLDL)1,2,4
| 12.0 |
M24766 | Alpha-2 collagen type IV (COL4A2)1,4
| 11.8 |
X90908 | I-15P (I-BABP) | 11.7 |
M15796 | Cyclin4
| 11.5 |
U52101 | YMP | 11.4 |
X66839 | MaTu MN for p54/58N | 10.7 |
M35878 | Insulin-like growth factor-binding protein-31,2,4
| 10.0 |
U24577 | LDL-phospholipase A2 | 9.4 |
L34155 | Laminin-related protein (LamA3) | 9.2 |
M16591 | Hemopoietic cell protein-tyrosine kinase (HCK)4
| 9.1 |
U60644 | HU-K44
| 8.9 |
X91911 | RTVP-11,4
| 8.4 |
M94250 | Retinoic acid inducible factor (MK) | 6.6 |
X07743 | Pleckstrin (P47)4
| 6.3 |
X51405 | Carboxypeptidase E (EC 3.4.17.10) | 6.0 |
X02761 | Fibronectin 11,2,4
| 5.9 |
Accession number | Gene name* | Avg. fold change |
---|---|---|
M10050 | Liver fatty acid binding protein (FABP1)2
| 118.8 |
M11437 | Kininogen (KNG) (cds2)1,2,3
| 64.9 |
X91220 | Na/Cl electroneutral thiazide-sensitive cotransporter | 51.0 |
U02388 | Cytochrome P450 4F2 (CYP4F2)3
| 44.9 |
M95549 | Sodium/glucose cotransporter protein1
| 43.9 |
J05257 | Microsomal dipeptidase (MDP)1
| 42.0 |
L13258 | Renal Na/Pi-cotransporter1
| 36.1 |
M29874 | Cytochrome P450-IIB (hIIB1) | 26.7 |
M11437 | Kininogen (KNG) (cds1) 1,2,3
| 23.3 |
X53961 | Lactoferrin (LTF) | 23.0 |
U17418 | Parathyroid hormone-related peptide receptor1
| 21.1 |
D31628 | 4-hydroxyphenylpyruvic acid dioxygenase (HPD)1,3
| 15.6 |
D12620 | Cytochrome P-450LTBV | 13.9 |
M31153 | Steroid 17-alpha-hydroxylase | 13.5 |
M13149 | Histidine-rich glycoprotein1
| 13.4 |
HG2841-HT2969 | Albumin 3 | 12.9 |
M34276 | Plasminogen1,2,4
| 12.5 |
M21642 | Antithrombin III (ATIII) Utah gene4
| 11.9 |
J03258 | Vitamin D receptor | 11.0 |
L12760 | Phosphoenolpyruvate carboxykinase (PCK1)1,2,4
| 10.9 |
X92720 | Phosphoenolpyruvate carboxykinase (PCK1)1,2,4
| 10.9 |
U95090 | Chromosome 19 cosmid F19541
| 10.5 |
J03910 | Metallothionein-IG (MT1G)2,4
| 10.3 |
U01120 | Glucose-6-phosphatase | 9.3 |
L47726 | Phenylalanine hydroxylase (PAH) 2,3
| 9.2 |
L32961 | 4-aminobutyrate aminotransferase (GABAT) | 8.6 |
M76180 | Aromatic amino acid decarboxylase | 8.6 |
X59766 | Zn-alpha2-glycoprotein1,4
| 8.5 |
U21931 | Fructose-1,6-biphosphatase (FBP1)1
| 8.4 |
M15656 | Aldolase B (ALDOB)1,2
| 8.3 |
Y07755 | S100A2, exon 1, 2 and 31
| 7.8 |
U27333 | Alpha (1,3) fucosyltransferase (FUT6) | 7.7 |
X63359 | UDP glucuronosyltransferase1
| 7.6 |
X01630 | Argininosuccinate synthetase1,2,3,4
| 7.5 |
M24902 | Prostatic acid phosphatase | 6.8 |
HG3286-HT3463 | Crystallin, Alpha A1
| 6.7 |
X59065 | FGF, exon 3 | 6.5 |
D78011 | Dihydropyrimidinase1,3,4
| 6.0 |
L07548 | Aminoacylase-1 (ACY1)1,4
| 5.9 |
L05144 | Phosphoenolpyruvate carboxykinase (PCK1)1,2,4
| 5.7 |
U27326 | Alpha (1,3/1,4) fucosyltransferase (FUT3) | 5.7 |
U22961 | Similar to L-glycerol-3-phosphate:NAD oxidoreductase and albumin1
| 5.6 |
Patterns of gene expression alterations in RCC cell line
Fold change | RCC tissuea
| RCC tissueb
| RCC cell line |
---|---|---|---|
≥2 | 373 | 660 | 1472 |
≥5 | 74 | 143 | 541 |
≥10 | 23 | 47 | 300 |