Table 1.
Identification of genes most differentially expressed between the parental cell line and the over-expressing cell lines
| Changes in HMGA2 WT cells | Changes in HMGA2trunc cells | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Rank | Gene | Description | MA | qPCR | Rel. to EGFP* | Gene | Description | MA | qPCR | Rel. to EGFP* | |
| a) | 1 | CXCL6 | Chemokine (C-X-C motif) ligand 6 | -8.4 | -6.7 | -2.2 | CXCL6 | Chemokine (C-X-C motif) ligand 6 | -9.0 | -6.3 | -2.2 |
| 2 | IL8 | Interleukin 8 | -7.5 | -7.1 | -6.4 | HLA-DRA | Major histocompatibility complex class II antigen DRA | -8.7 | -8.1 | -7.2 | |
| 3 | CD24 | CD24 molecule | -7.1 | HLA-DPA1 | Major histocompatibility complex class II antigen DPA1 | -8.0 | -6.8 | -5.5 | |||
| 4 | C13orf33 | Chromosome 13 open reading frame 33 | -6.5 | ChGn | Chondroitin beta-1,4-N-acetylgalactosaminyltransferase | -6.5 | |||||
| 5 | PTGES | Prostaglandin E synthase | -6.3 | PKIB | cAMP-dependent protein kinase inhibitor 2 | -6,4 | -4.9 | -5.0 | |||
| 6 | ChGn | Chondroitin beta-1,4-N-acetylgalactosaminyltransferase | -5.6 | IFI44L | Interferon-induced protein 44-like | -6.2 | |||||
| 7 | IL6 | Interleukin 6 | -5.5 | LAMA4 | Laminin alpha chain | -6.2 | |||||
| 8 | PDE4D | cAMP-specific phosphodiesterase 4D | -5.2 | SLC38A5 | Solute carrier family 38, member 5 | -6.0 | |||||
| 9 | IL1RN | Interleukin 1 receptor antagonist | -5.1 | -4.4 | -3.0 | PTPRN2 | Protein tyrosine phosphatise, receptor type, N2 | -5.5 | |||
| 10 | CES1 | Carboxylesterase 1 | -5.1 | C13orf33 | Chromosome 13 open reading frame 33 | -5.4 | |||||
| 11 | KIAA1644 | KIAA1644 protein | -5.0 | -3.4 | -1.7 | n/a | Similar to Wnt-1 inducible signalling pathway protein 1 | -5.4 | |||
| 12 | SAMSN1 | SH3-SAM adaptor protein | -4.8 | IL1B | Interleukin1 beta | -5.3 | -4.3 | -2.2 | |||
| 13 | SERPIND1 | Serpin peptidase inhibitor, clade D, member 1 | -4.7 | F2RL1 | Coagulation factor II receptor-like 1 | -5.2 | |||||
| 14 | FAM5C | Familiy with sequence similarity 5,member C | -4.4 | CD74 | CD74 antigen-associated invariant chain | -5.2 | -5.4 | -4.3 | |||
| 15 | n/a | Transcribed sequence FLJ 26764 | -4.3 | IL1RN | Interleukin 1 receptor antagonist | -5.2 | -5.2 | -3.8 | |||
| b) | 1 | ZBED2 | Zinc finger BED domain-containing protein 2 | 5.3 | 4.5 | n/a | transcribed sequence FLJ33010 | 6.7 | |||
| 2 | SHROOM2 | Shroom family member 2 | 4.6 | CXCL12 | Chemokine (C-X-C motif) ligand 12 | 6.4 | 2.7 | 2.0 | |||
| 3 | FGF13 | Fibroblast growth factor 13 | 4.5 | 4.6 | 5.6 | PRSS7 | Serine protease 7 | 6.0 | |||
| 4 | BAI3 | Brain-specific angiogenesis inhibitor 3 | 4.5 | 4.4 | 5.4 | SULT1B1 | Sulfotransferase 1B1 | 5.8 | |||
| 5 | PLXNA4 | Plexin A4 | 4.4 | SSX1 | Synovial sarcoma, X breakpoint 1 | 4.9 | 9.6 | 10.2 | |||
| 6 | LCP1 | Lymphocyte cytosolic protein 1 | 4.1 | 3.9 | 2.1 | MMP3 | Matrix metalloproteinase-3 | 4.7 | |||
| 7 | C20orf197 | Chromosome 20 open reading frame 197 | 4.0 | CYB5R2 | Cytochrome b5 reductase 2 | 4.5 | |||||
| 8 | G0S2 | G0/S switch 2 | 3.7 | 5.6 | 5.4 | KISS1 | KiSS-1 metastasis-supressor | 4.5 | |||
| 9 | HDAC9 | Histone deacetylase 9 | 3.7 | 1.5 | EDN1 | Endothelin 1 | 4.5 | ||||
| 10 | SIGLEC15 | Sialic acid binding Ig-like lectin 15 | 3.7 | SYNE1 | Synaptic nuclear envelope protein 1 | 4.4 | |||||
| 11 | HCLS1 | Hematopoietic cell-specific Lyn substrate 1 | 3.6 | 2.5 | 3.6 | HAPLN1 | Hyaluronan and proteoglycan link protein 1 | 4.4 | |||
| 12 | LOC646340 | similar to Ankyrin repeat domain-containing protein 18A | 3.6 | n/a | transcribed sequence FLJ35091 | 4.4 | |||||
| 13 | GATA3 | GATA binding protein 3 | 3.5 | 3.6 | >10 | n/a | Similar to TATA box-binding protein-associated factor 1B | 4.3 | |||
| 14 | SH3BGRL2 | SH3 domain binding glutamic acid-rich protein like 2 | 3.5 | BAI3 | Brain-specific angiogenesis inhibitor 3 | 4.2 | 4.6 | 5.6 | |||
| 15 | PDE4B | cAMP-specific phospodiesterase 4B | 3.5 | n/a | Similar to cytochrome c oxidase I | 4.1 | |||||
The 15 most down- (a) and up-(b) regulated genes were ranked according to the expression fold change between transfectants and parental cells based on the microarray data. Changes in gene expression were validated by real time PCR using TaqMan assays, values in brackets are relative to those for the eGFP controls, for comparison. The expression level of each target gene was normalized for TBP expression and represented as fold induction over parental cells. Fold change ratios from both microarray (MA) and real-time assay (qPCR), including qPCR values (marked by an asterisk) calculated relative to those from eGFP only control cells, are shown.