TOP TEN perturbations for 39804_at (Homo sapiens)
Organism: Homo sapiens
Gene: 39804_at
Selected probe(set): 209574_s_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array
Expression of 39804_at (209574_s_at) across 6674 perturbations tested by GENEVESTIGATOR:
EBNA2 overexpr. study 1 (4h) / control virus transfected EREB2-5 cell sample (24h)
Relative Expression (log2-ratio):4.825471Number of Samples:3 / 3
| Experimental | EBNA2 overexpr. study 1 (4h) |
| EREB2-5 cell line stably transfected with the chimeric Epstein-Barr virus-encoded nuclear antigen 2 (EBNA2) and control expression plasmid coding for bacterial chloramphenicol acetyltransferase (CAT) gene and . CAT was used as a negative control. Briefly, before the CAT and EBNA2 induction, cells were maintained in RPMI media and deprived of estrogen for 3 days before doxycycline and estrogen was added. Expression of EBNA2 was induced after addition of estrogen and expression of CAT was induced by the addition of doxycycline to a final concentration of 100 ng/mL medium. Doxycycline induced cells were harvested 4 hours after induction. Because EBNA2 is essential for the proliferation of EBV-infected cells, EREB2-5 cells grow only in the presence of estrogen. Before the preparation of RNA, NGFR cells were purified by MACS separation to enrich the cells with a transcriptional response to doxycycline. | |
| Control | control virus transfected EREB2-5 cell sample (24h) |
| EREB2-5 cell line stably transfected with control expression plasmid coding for bacterial chloramphenicol acetyltransferase (CAT) gene. CAT was used as a negative control. Briefly, before the CAT induction, cells were maintained in RPMI media and deprived of estrogen for 3 days before doxycycline was added. Expression of CAT was induced by the addition of doxycycline to a final concentration of 100 ng/mL medium. Doxycycline induced cells were harvested 24 hours after induction. Estrogen withdrawal leads to the inactivation of EBNA2, resulting in cell cycle arrest. Before the preparation of RNA, NGFR cells were purified by MACS separation to enrich the cells with a transcriptional response to doxycycline. |
EBNA2 overexpr. study 1 (24h) / EBNA2 overexpr. study 1 (4h)
Relative Expression (log2-ratio):-4.4441385Number of Samples:3 / 3
| Experimental | EBNA2 overexpr. study 1 (24h) |
| EREB2-5 cell line stably transfected with the chimeric Epstein-Barr virus-encoded nuclear antigen 2 (EBNA2) and control expression plasmid coding for bacterial chloramphenicol acetyltransferase (CAT) gene and . CAT was used as a negative control. Briefly, before the CAT and EBNA2 induction, cells were maintained in RPMI media and deprived of estrogen for 3 days before doxycycline and estrogen was added. Expression of EBNA2 was induced after addition of estrogen and expression of CAT was induced by the addition of doxycycline to a final concentration of 100 ng/mL medium. Doxycycline induced cells were harvested 24 hours after induction. Because EBNA2 is essential for the proliferation of EBV-infected cells, EREB2-5 cells grow only in the presence of estrogen. Before the preparation of RNA, NGFR cells were purified by MACS separation to enrich the cells with a transcriptional response to doxycycline. | |
| Control | EBNA2 overexpr. study 1 (4h) |
| EREB2-5 cell line stably transfected with the chimeric Epstein-Barr virus-encoded nuclear antigen 2 (EBNA2) and control expression plasmid coding for bacterial chloramphenicol acetyltransferase (CAT) gene and . CAT was used as a negative control. Briefly, before the CAT and EBNA2 induction, cells were maintained in RPMI media and deprived of estrogen for 3 days before doxycycline and estrogen was added. Expression of EBNA2 was induced after addition of estrogen and expression of CAT was induced by the addition of doxycycline to a final concentration of 100 ng/mL medium. Doxycycline induced cells were harvested 4 hours after induction. Because EBNA2 is essential for the proliferation of EBV-infected cells, EREB2-5 cells grow only in the presence of estrogen. Before the preparation of RNA, NGFR cells were purified by MACS separation to enrich the cells with a transcriptional response to doxycycline. |
zalypsis study 2 / untreated OPM1 cell sample
Relative Expression (log2-ratio):-3.9908257Number of Samples:2 / 2
| Experimental | zalypsis study 2 |
| OPM1 multiple myeloma cells treated in vitro with zalypsis (5 nM), a novel marine-derived compound with potent antimyeloma activity. Cells were harvested at the beginning of induction of cell death (15-20% cell death as assessed by Annexin V-FITC staining). ATC code:--- | |
| Control | untreated OPM1 cell sample |
| OPM1 multiple myeloma cells untreated. |
TGF-ß study 7 (12h) / rheumatoid arthritis study 10
Relative Expression (log2-ratio):3.5593395Number of Samples:3 / 6
| Experimental | TGF-ß study 7 (12h) |
| Synovial fibroblast samples isolated from affected knee of patients with rheumatoid factor positive rheumatoid arthritis (RA) were stimulated by 10 ng/ml of TGF-ß in serum-free DMEM for 12 hours. Synovial fibroblasts were isolated from surgically obtained synovial membrane by trypsin/collagenase digestion, followed by negative purification using CD-14 Dynabeads® M-450. Before the TGF-ß stimulation, fibroblasts were cultured for four passages in DMEM medium supplemented with antibiotics and 10% FCS. The RA was classified according to the criteria of the American College of Rheumatology. Average duration of RA: 11.5 ± 0.5 years. Patients were receiving non-steroidal antiinflammatory drugs. CRP: 38.1 ± 7.2 mg/l. | |
| Control | rheumatoid arthritis study 10 |
| Synovial fibroblast samples isolated from affected knee of patients with rheumatoid factor positive rheumatoid arthritis (RA), classified according to the criteria of the American College of Rheumatology. Average duration of RA: 11.5 ± 0.5 years. Patients were receiving non-steroidal antiinflammatory drugs. CRP: 38.1 ± 7.2 mg/l. Synovial fibroblasts were isolated from surgically obtained synovial membrane by trypsin/collagenase digestion, followed by negative purification using CD-14 Dynabeads® M-450. The fibroblasts were than cultured for four passages in DMEM medium supplemented with antibiotics and 10% FCS. Prior RNA isolation, the fibroblasts were washed in serum free DMEM. |
precursor-B-ALL study 1 (t(1;19)(q23,q13)) / normal bone marrow sample
Relative Expression (log2-ratio):3.5532007Number of Samples:36 / 74
| Experimental | precursor-B-ALL study 1 (t(1;19)(q23,q13)) |
| Bone marrow samples of patients with precursor B-ALL (t(1;19)(q23,q13)/E2A-PBX1). | |
| Control | normal bone marrow sample |
| Non-leukemic and healthy bone marrow sample. |
CD44s overexpr. study 1 / normal HEK-293 cell sample
Relative Expression (log2-ratio):-3.2790065Number of Samples:3 / 3
| Experimental | CD44s overexpr. study 1 |
| Human embryonic kidney cell line HEK-293 transfected with pcDNA3.1(-) vector containing codon-optimized human CD44 sequence for expression. | |
| Control | normal HEK-293 cell sample |
| Untransfected, native human embryonic kidney cell line HEK-293 cell samples. |
TGF-β study 10 / untreated A549 cell sample
Relative Expression (log2-ratio):3.2137399Number of Samples:3 / 3
| Experimental | TGF-β study 10 |
| A549 cells were cultured for 2-3 weeks in the presence of 2ng/ml of TGF-β, to induce epithelial-mesenchymal transition (EMT). 24 hours prior analysis cells were re-seeded without TGF-β. | |
| Control | untreated A549 cell sample |
| A549 cells grown in standard media. |
B-CLL study 11 (rolipram) / rolipram study 4 (normal T-cell; 20uM)
Relative Expression (log2-ratio):3.1211166Number of Samples:4 / 4
| Experimental | B-CLL study 11 (rolipram) |
| Peripheral blood mononuclear cells (PBMCs) obtained from chronic lymphocytic leukemia (CLL) patients and in vitro treated with rolipram (20 uM, cyclic nucleotide phosphodiesterase (PDE4) inhibitor) for 4 hours. PBMCs' samples contained 90% CD19+ CD5+ B lineage CLL cells (B-CLL). Inclusion criteria: untreated CLL patients or at least 1 month after chemotherapy. Exclusion criteria: patients with active infections or other serious medical conditions or with white blood cell (WBC) counts of 15,000/l. ATC code:--- | |
| Control | rolipram study 4 (normal T-cell; 20uM) |
| MACS purified T-cells from healthy donor peripheral blood treated with rolipram (20 uM, cyclic nucleotide phosphodiesterase (PDE4) inhibitor) for 4 hours. ATC code:--- |
connective/soft tissue cancer study 1 (PDX; connective and soft tissue, pleomorphic rhabdomyosarcoma, adult type; primary) / connective/soft tissue cancer study 1 (PDX; connective and soft tissue, malignant peripheral nerve sheath tumor; primary)
Relative Expression (log2-ratio):-3.023284Number of Samples:2 / 3
| Experimental | connective/soft tissue cancer study 1 (PDX; connective and soft tissue, pleomorphic rhabdomyosarcoma, adult type; primary) |
| Patient-derived xenograft (PDX) samples generated in female athymic nude mice from patients with primary connective and soft tissue, pleomorphic rhabdomyosarcoma, adult type of the soft tissue (subcutaneously implanted). | |
| Control | connective/soft tissue cancer study 1 (PDX; connective and soft tissue, malignant peripheral nerve sheath tumor; primary) |
| Patient-derived xenograft (PDX) samples generated in female athymic nude mice from patients with primary connective and soft tissue, malignant peripheral nerve sheath tumor of the soft tissue (subcutaneously implanted). |
esophagus cancer study 1 (PDX; squamous cell carcinoma, NOS; metastatic) / esophagus cancer study 1 (PDX; squamous cell carcinoma, NOS; primary)
Relative Expression (log2-ratio):3.0214267Number of Samples:2 / 3
| Experimental | esophagus cancer study 1 (PDX; squamous cell carcinoma, NOS; metastatic) |
| Patient-derived xenograft (PDX) samples generated in female athymic nude mice from a metastasis of patients with primary squamous cell carcinoma, NOS of the oesophagus (subcutaneously implanted). Metastatic site of patient tumor sample is not reported. | |
| Control | esophagus cancer study 1 (PDX; squamous cell carcinoma, NOS; primary) |
| Patient-derived xenograft (PDX) samples generated in female athymic nude mice from patients with primary squamous cell carcinoma, NOS of the oesophagus (subcutaneously implanted). |