TOP TEN perturbations for 40041_at (Homo sapiens)

Organism: Homo sapiens
Gene: 40041_at
Selected probe(set): 204162_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 40041_at (204162_at) across 6674 perturbations tested by GENEVESTIGATOR:

nutlin-3 (10uM); flagellin (500 ng/ml) study 1 (control vector) / flagellin study 4 (control vector; 500 ng/ml)

Relative Expression (log2-ratio):-6.5035443
Number of Samples:6 / 2
Experimental nutlin-3 (10uM); flagellin (500 ng/ml) study 1 (control vector)
Human breast adenocarcinoma cells MCF-7 expressing wild type p53, stably transfected with control empty vector pSUPER, treated with nutlin-3 (10 uM) for 45 hours followed by an additional 3 hours treatment of nutlin-3 (10uM) and flagellin (500 ng/ml). Cells were cultured in RPMI-1640 medium supplemented with 10% heat inactivated FBS and 50 U/ml of penicillin, 50 ug/ml of streptomycin. ATC code:---
Control flagellin study 4 (control vector; 500 ng/ml)
Human breast adenocarcinoma cells MCF-7 expressing wild type p53, stably transfected with control empty vector pSUPER, treated with DMSO 0.1% for 45 hours followed by an additional 3 hours with flagellin (500 ng/ml). Cells were cultured in RPMI-1640 medium supplemented with 10% heat inactivated FBS and 50 U/ml of penicillin, 50 ug/ml of streptomycin.

nutlin-3 study 2 (control vector; 10uM) / vehicle treated MCF-7-con cell sample

Relative Expression (log2-ratio):-5.874276
Number of Samples:6 / 3
Experimental nutlin-3 study 2 (control vector; 10uM)
Human breast adenocarcinoma cells MCF-7 expressing wild type p53, stably transfected with control empty vector pSUPER, treated with nutlin-3 (10 uM) for 48 hours. Cells were cultured in RPMI-1640 medium supplemented with 10% heat inactivated FBS and 50 U/ml of penicillin, 50 ug/ml of streptomycin. ATC code:---
Control vehicle treated MCF-7-con cell sample
Human breast adenocarcinoma cells MCF-7 expressing wild type p53 stably transfected with control empty vector pSUPER, vehicle treated with DMSO (0.1%) for 48 hours. Cells were cultured in RPMI-1640 medium supplemented with 10% heat inactivated FBS and 50 U/ml of penicillin, 50 ug/ml of streptomycin.

nutlin-3 (10uM); flagellin (500 ng/ml) study 1 (p53 shRNA) / nutlin-3 (10uM); flagellin (500 ng/ml) study 1 (control vector)

Relative Expression (log2-ratio):5.8015437
Number of Samples:3 / 6
Experimental nutlin-3 (10uM); flagellin (500 ng/ml) study 1 (p53 shRNA)
Human breast adenocarcinoma cells MCF-7 with depleted p53 (shRNA), treated with nutlin-3 (10 uM) for 45 hours followed by an additional 3 hours treatment of nutlin-3 (10 uM) and flagellin (500 ng/ml). Cells were stably transfected with vector pSUPER and expressing shRNA to p53. Cells were cultured in RPMI-1640 medium supplemented with 10% heat inactivated FBS and 50 U/ml of penicillin, 50 ug/ml of streptomycin. ATC code:---
Control nutlin-3 (10uM); flagellin (500 ng/ml) study 1 (control vector)
Human breast adenocarcinoma cells MCF-7 expressing wild type p53, stably transfected with control empty vector pSUPER, treated with nutlin-3 (10 uM) for 45 hours followed by an additional 3 hours treatment of nutlin-3 (10uM) and flagellin (500 ng/ml). Cells were cultured in RPMI-1640 medium supplemented with 10% heat inactivated FBS and 50 U/ml of penicillin, 50 ug/ml of streptomycin. ATC code:---

PD-0332991 study 4 (G1 arrest) / medium treated bronchial epithelial cell sample

Relative Expression (log2-ratio):-5.790118
Number of Samples:3 / 3
Experimental PD-0332991 study 4 (G1 arrest)
Bronchial epithelial cells (NHBE) treated with CDK4/6 inhibitor PD-0332991 (palbociclib) to arrest them in G1 phase for 8 hours. Therefore, cells were cultured in standard growth medium for 24 hours, followed by treatment with 1 μM PD-0332991 (non-toxic dose) for another 24 hours and then washed and treated with the same dose of PD-0332991 again for indicated timepoints. ATC code:---
Control medium treated bronchial epithelial cell sample
Bronchial epithelial cells (NHBE) cultured in standard growth medium for 2 x 24 hours, followed by culture in growth medium for another 8 hours.

PD-0332991 study 3 (G1 arrest) / medium treated bronchial epithelial cell sample

Relative Expression (log2-ratio):-5.7532907
Number of Samples:3 / 3
Experimental PD-0332991 study 3 (G1 arrest)
Bronchial epithelial cells (NHBE) treated with CDK4/6 inhibitor PD-0332991 (palbociclib) to arrest them in G1 phase for 6 hours. Therefore, cells were cultured in standard growth medium for 24 hours, followed by treatment with 1 μM PD-0332991 (non-toxic dose) for another 24 hours and then washed and treated with the same dose of PD-0332991 again for indicated timepoints. ATC code:---
Control medium treated bronchial epithelial cell sample
Bronchial epithelial cells (NHBE) cultured in standard growth medium for 2 x 24 hours, followed by culture in growth medium for another 6 hours.

nutlin-3 study 2 (p53 shRNA;10uM) / nutlin-3 study 2 (control vector; 10uM)

Relative Expression (log2-ratio):5.438733
Number of Samples:3 / 6
Experimental nutlin-3 study 2 (p53 shRNA;10uM)
Human breast adenocarcinoma cells MCF-7 with depleted p53 (shRNA), treated with nutlin-3 (10 uM) for 48 hours. Cells were stably transfected with vector pSUPER and expressing shRNA to p53. Cells were cultured in RPMI-1640 medium supplemented with 10% heat inactivated FBS and 50 U/ml of penicillin, 50 ug/ml of streptomycin. ATC code:---
Control nutlin-3 study 2 (control vector; 10uM)
Human breast adenocarcinoma cells MCF-7 expressing wild type p53, stably transfected with control empty vector pSUPER, treated with nutlin-3 (10 uM) for 48 hours. Cells were cultured in RPMI-1640 medium supplemented with 10% heat inactivated FBS and 50 U/ml of penicillin, 50 ug/ml of streptomycin. ATC code:---

PD-0332991 study 2 (G1 arrest) / medium treated bronchial epithelial cell sample

Relative Expression (log2-ratio):-5.2516565
Number of Samples:3 / 3
Experimental PD-0332991 study 2 (G1 arrest)
Bronchial epithelial cells (NHBE) treated with CDK4/6 inhibitor PD-0332991 (palbociclib) to arrest them in G1 phase for 4 hours. Therefore, cells were cultured in standard growth medium for 24 hours, followed by treatment with 1 μM PD-0332991 (non-toxic dose) for another 24 hours and then washed and treated with the same dose of PD-0332991 again for indicated timepoints. ATC code:---
Control medium treated bronchial epithelial cell sample
Bronchial epithelial cells (NHBE) cultured in standard growth medium for 2 x 24 hours, followed by culture in growth medium for another 4 hours.

pancreatic islet study 3 (expanded; PPRF) / normal pancreatic islet sample

Relative Expression (log2-ratio):5.220852
Number of Samples:2 / 7
Experimental pancreatic islet study 3 (expanded; PPRF)
Human pancreatic islets were isolated from a cadaveric donor. The population was 70% pure in mature islets, which was determined by dithizone staining. Islets cells were expanded according to Pharmaceutical Production Research Facility Protocol (PPRF) for 6 weeks. Expansion phase: Approximately 2,500 islet equivalents were seeded onto 75-cm2 fibronectin-coated tissue culture-treated flasks in a proprietary serum-free medium (PPRF medium). The serum-free PPRF medium was supplemented with 30% serum-free mesenchymal-conditioned medium. When the cell migration resulted in the formation of large-size colonies, the cells were harvested by trypsinization and replated into new tissue culture flasks. Once the cells reached near confluence (80–90%) in monolayer, they were trypsinized, counted, and subcultured at a density of 5,000 cells per cm2. Thereafter, cells were serially passaged using the same protocol.
Control normal pancreatic islet sample
Pancreatic islets were obtained from seven donors aged between 37 and 70 years and body mass index between 22 and 27. Functional islets were cultured in CMRL 1066 supplemented with 10% FCS, 1% glutamine, 5.6 mM glucose, 1 mM HEPES, 110 U/ml penicillin, and 110 g/ml streptomycin for 7 days or immediately processed after isolation.

metformin study 6 (1000uM) / vehicle (medium) treated hepatocyte sample

Relative Expression (log2-ratio):-5.0591183
Number of Samples:2 / 2
Experimental metformin study 6 (1000uM)
Hepatocytes treated with compound: metformin (1000uM; CHEMBL1431) for 24 hours. ATC code:
Control vehicle (medium) treated hepatocyte sample
Hepatocytes treated with vehicle (medium) for 24 hours.

PD-0332991 study 4 (cell cycle re-entry) / PD-0332991 study 4 (G1 arrest)

Relative Expression (log2-ratio):4.8617964
Number of Samples:3 / 3
Experimental PD-0332991 study 4 (cell cycle re-entry)
Bronchial epithelial cells (NHBE) treated with CDK4/6 inhibitor PD-0332991 (palbociclib) to arrest them in G1 phase but then re-cultured in growth medium for 8 hours to selectively allow them re-entry of cell cycle. Therefore, cells were cultured in standard growth medium for 24 hours, followed by treatment with 1 μM PD-0332991 (non-toxic dose) for another 24 hours and then washed and treated with growth medium again for indicated timepoints. ATC code:---
Control PD-0332991 study 4 (G1 arrest)
Bronchial epithelial cells (NHBE) treated with CDK4/6 inhibitor PD-0332991 (palbociclib) to arrest them in G1 phase for 8 hours. Therefore, cells were cultured in standard growth medium for 24 hours, followed by treatment with 1 μM PD-0332991 (non-toxic dose) for another 24 hours and then washed and treated with the same dose of PD-0332991 again for indicated timepoints. ATC code:---