TOP TEN perturbations for 39271_at (Homo sapiens)
Organism: Homo sapiens
Gene: 39271_at
Selected probe(set): 228521_s_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array
Expression of 39271_at (228521_s_at) across 6674 perturbations tested by GENEVESTIGATOR:
EBNA2 overexpr. study 1 (24h) / control virus transfected EREB2-5 cell sample (24h)
Relative Expression (log2-ratio):-2.0121555Number 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 | 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. |
colorectal cancer study 4 (recurring) / adjacent colon tissue (recurring)
Relative Expression (log2-ratio):-1.8881435Number of Samples:24 / 3
Experimental | colorectal cancer study 4 (recurring) |
LCM-tumor tissue samples of patients who received resection after diagnosis of primary colorectal cancer. Patients developed metastatic recurrence during follow-up after surgery. | |
Control | adjacent colon tissue (recurring) |
Histologically normal colon tissue samples from patients with primary colorectal cancer collected after resection. Tissue was further extracted using laser-capture microdissection (LCM). With metastatic recurrence after resection during follow-up. |
colorectal cancer study 4 (non-recurring) / adjacent colon tissue (non-recurring)
Relative Expression (log2-ratio):-1.8669453Number of Samples:76 / 18
Experimental | colorectal cancer study 4 (non-recurring) |
LCM-tumor tissue samples of patients who received resection after diagnosis of primary colorectal cancer. Patients did not develop metastatic recurrence during follow-up after surgery. | |
Control | adjacent colon tissue (non-recurring) |
Histologically normal colon tissue samples from patients with primary colorectal cancer collected after resection. Tissue was further extracted using laser-capture microdissection (LCM). No metastatic recurrence during follow-up. |
glioma study 17 (glioblastoma; unsorted) / non-tumor cortical tissue
Relative Expression (log2-ratio):1.8376961Number of Samples:2 / 4
Experimental | glioma study 17 (glioblastoma; unsorted) |
Brain cells isolated from high grade glioblastoma (grade IV). Tumor tissue was dissociated using enzymatic treatment and all cells were used for RNA isolation. | |
Control | non-tumor cortical tissue |
Cortical tissue obtained from patients with epilepsy, but without any manifested brain cancer. The tissue was dissociated using enzymatic treatment, but all brain cell types were used for analyses. |
endometriosis study 6 (minimal/mild endo.; pro. MCP) / normal endometrium tissue (pro. MCP)
Relative Expression (log2-ratio):1.7528191Number of Samples:12 / 20
Experimental | endometriosis study 6 (minimal/mild endo.; pro. MCP) |
Endometrial tissue samples from women with minimal or mild endometriosis and pelvic pain and/or infertility collected in the proliferative menstrual cycle phase (MCP). Endometriosis was diagnosed based on the revised American Fertility Society classification system. The MCP was determined by endometrial histology, confirmed by estradiol and progesterone serum levels and corroborated by 2 independent bioinformatics methods: clustering in unsupervised whole-transcriptome principal component analysis and cycle phase assignment classifier analysis. Patients with hormonal treatment within previous 3 months and presence of malignancy or major systemic disease were excluded. | |
Control | normal endometrium tissue (pro. MCP) |
Normal endometrial tissue samples from women collected in the proliferative menstrual cycle phase (MCP). The MCP was determined by endometrial histology, confirmed by estradiol and progesterone serum levels and corroborated by 2 independent bioinformatics methods: clustering in unsupervised whole-transcriptome principal component analysis and cycle phase assignment classifier analysis. |
EBNA2 overexpr. study 1 (24h) / EBNA2 overexpr. study 1 (4h)
Relative Expression (log2-ratio):-1.7440481Number 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. |
EBNA2 overexpr. study 1 (24h) / NOTCH2-IC overexpr. study 1 (24h)
Relative Expression (log2-ratio):-1.7262983Number 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 | NOTCH2-IC overexpr. study 1 (24h) |
EREB2-5 cell line stably transfected with expression plasmid coding for intracellular domain of NOTCH2 (NOTCH2-IC). The stably transfected cells were maintained in RPMI media and deprived of estrogen for 3 days, before doxycycline was added. Expression of NOTCH2-IC 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. |
colorectal cancer study 25 / adjacent colon tissue
Relative Expression (log2-ratio):-1.700593Number of Samples:94 / 17
Experimental | colorectal cancer study 25 |
Human primary colorectal carcinoma sample. | |
Control | adjacent colon tissue |
Normal colon tissue samples adjacent to tumor from patients with colorectal cancer. |
uterine/pelvic pathology study 2 (pro. MCP) / normal endometrium tissue (pro. MCP)
Relative Expression (log2-ratio):1.6348581Number of Samples:15 / 20
Experimental | uterine/pelvic pathology study 2 (pro. MCP) |
Endometrial tissue samples collected from women with uterine/pelvic pathology in the proliferative menstrual cycle phase (MCP). The group contained cycling women 20 – 50 years old with symptomatic uterine fibroids, pelvic organ prolapse, and adenomyosis. The MCP was determined by endometrial histology, confirmed by estradiol and progesterone serum levels and corroborated by 2 independent bioinformatics methods: clustering in unsupervised whole-transcriptome principal component analysis and cycle phase assignment classifier analysis. Patients with hormonal treatment within previous 3 months and presence of malignancy or major systemic disease were excluded. | |
Control | normal endometrium tissue (pro. MCP) |
Normal endometrial tissue samples from women collected in the proliferative menstrual cycle phase (MCP). The MCP was determined by endometrial histology, confirmed by estradiol and progesterone serum levels and corroborated by 2 independent bioinformatics methods: clustering in unsupervised whole-transcriptome principal component analysis and cycle phase assignment classifier analysis. |
connective/soft tissue cancer study 1 (PDX; connective and soft tissue, leiomyosarcoma, NOS; metastatic) / connective/soft tissue cancer study 1 (PDX; connective and soft tissue, clear cell sarcoma, NOS; metastatic)
Relative Expression (log2-ratio):-1.6313353Number of Samples:2 / 2
Experimental | connective/soft tissue cancer study 1 (PDX; connective and soft tissue, leiomyosarcoma, NOS; metastatic) |
Patient-derived xenograft (PDX) samples generated in female athymic nude mice from a metastasis of patients with primary connective and soft tissue, leiomyosarcoma, NOS of the soft tissue (subcutaneously implanted). Metastatic site of patient tumor sample is not reported. | |
Control | connective/soft tissue cancer study 1 (PDX; connective and soft tissue, clear cell sarcoma, NOS; metastatic) |
Patient-derived xenograft (PDX) samples generated in female athymic nude mice from a metastasis of patients with primary connective and soft tissue, clear cell sarcoma, NOS of the soft tissue (subcutaneously implanted). Metastatic site of patient tumor sample is not reported. |
Organism: Homo sapiens
Gene: 39271_at
Selected probe(set): 206560_s_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array
Expression of 39271_at (206560_s_at) across 6674 perturbations tested by GENEVESTIGATOR:
glioma study 16 (LN-229) / normal astrocyte sample
Relative Expression (log2-ratio):7.183628Number of Samples:2 / 3
Experimental | glioma study 16 (LN-229) |
Human glioma cell line LN229 was cultured in DMEM supplemented with 10% FCS (fetal calf serum) and antibiotics at 37°C and 5% CO2. | |
Control | normal astrocyte sample |
Normal brain astrocytes. Clonetics normal human astrocytes (NHA) from Cambrex (primary-derived cultures) and cultured according to the manufacturer's recommendations. |
esophagus cancer study 1 (PDX; squamous cell carcinoma, NOS; metastatic) / esophagus cancer study 1 (PDX; squamous cell carcinoma, NOS; primary)
Relative Expression (log2-ratio):4.6003294Number 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). |
esophagus cancer study 1 (PDX; adenocarcinoma, NOS; metastatic) / esophagus cancer study 1 (PDX; adenocarcinoma, NOS; primary)
Relative Expression (log2-ratio):4.409109Number of Samples:2 / 8
Experimental | esophagus cancer study 1 (PDX; adenocarcinoma, NOS; metastatic) |
Patient-derived xenograft (PDX) samples generated in female athymic nude mice from a metastasis of patients with primary adenocarcinoma, NOS of the oesophagus (subcutaneously implanted). Metastatic site of patient tumor sample is not reported. | |
Control | esophagus cancer study 1 (PDX; adenocarcinoma, NOS; primary) |
Patient-derived xenograft (PDX) samples generated in female athymic nude mice from patients with primary adenocarcinoma, NOS of the oesophagus (subcutaneously implanted). |
CNS cancer study 1 (PDX; glioma, malignant, NOS; primary) / CNS cancer study 1 (PDX; ependymoma, NOS; primary)
Relative Expression (log2-ratio):-4.3497143Number of Samples:2 / 2
Experimental | CNS cancer study 1 (PDX; glioma, malignant, NOS; primary) |
Patient-derived xenograft (PDX) samples generated in female athymic nude mice from patients with primary glioma, malignant, NOS of the central nervous system (subcutaneously implanted). | |
Control | CNS cancer study 1 (PDX; ependymoma, NOS; primary) |
Patient-derived xenograft (PDX) samples generated in female athymic nude mice from patients with primary ependymoma, NOS of the central nervous system (subcutaneously implanted). |
CNS cancer study 1 (PDX; glioblastoma, NOS; primary) / CNS cancer study 1 (PDX; ependymoma, NOS; primary)
Relative Expression (log2-ratio):-4.2071342Number of Samples:3 / 2
Experimental | CNS cancer study 1 (PDX; glioblastoma, NOS; primary) |
Patient-derived xenograft (PDX) samples generated in female athymic nude mice from patients with primary glioblastoma, NOS of the central nervous system (subcutaneously implanted). | |
Control | CNS cancer study 1 (PDX; ependymoma, NOS; primary) |
Patient-derived xenograft (PDX) samples generated in female athymic nude mice from patients with primary ependymoma, NOS of the central nervous system (subcutaneously implanted). |
expO skin cancer study 1 (squamous cell carcinoma, NOS; metastatic) / expO skin cancer study 1 (malignant melanoma, NOS; metastatic)
Relative Expression (log2-ratio):-3.8035154Number of Samples:2 / 9
Experimental | expO skin cancer study 1 (squamous cell carcinoma, NOS; metastatic) |
Metastatic tumor tissue samples obtained from patients with primary squamous cell carcinoma (NOS) of the skin. | |
Control | expO skin cancer study 1 (malignant melanoma, NOS; metastatic) |
Metastatic tumor tissue samples obtained from patients with primary malignant melanoma (NOS) of the skin. |
pancreatic cancer study 3 (ipmn) / normal pancreas tissue
Relative Expression (log2-ratio):3.403698Number of Samples:3 / 6
Experimental | pancreatic cancer study 3 (ipmn) |
Intraductal papillary mucinous neoplasm from patients with pancreatic cancer. | |
Control | normal pancreas tissue |
Normal human pancreatic tissue. |
basal cell carcinoma study 6 (primary) / melanoma study 34 (primary)
Relative Expression (log2-ratio):-3.0838623Number of Samples:15 / 14
Experimental | basal cell carcinoma study 6 (primary) |
Primary tumor tissue from the skin of patients with primary basal cell carcinoma (BCC). | |
Control | melanoma study 34 (primary) |
Primary tumor tissue from the skin of patients with primary cutaneous melanoma (PCM). PCM consisted of 2 thin melanomas (< 1 mm; T1), 3 intermediate-thickness melanomas (1–4 mm; T2-3), and 9 thick melanomas (> 4 mm; T4). |
breast cancer study 5 / normal mammary gland tissue
Relative Expression (log2-ratio):-2.8424273Number of Samples:20 / 7
Experimental | breast cancer study 5 |
Breast non-BLC (sporadic basal-like cancer) tumor samples. | |
Control | normal mammary gland tissue |
Normal breast tissue samples. |
bronchial epithelial cell differentiation study 1 (day28) / bronchial epithelial cell differentiation study 1 (subconfluent)
Relative Expression (log2-ratio):2.8390036Number of Samples:3 / 3
Experimental | bronchial epithelial cell differentiation study 1 (day28) |
Differentiated normal human bronchial epithelial cell (NHBE) cultured for 28 days in an air-liquid interface (ALI) system. At this time point cells were fully differentiated and formed a polarized, pseudostratified mucociliary epithelium. In order to generate the ALI culture, undifferentiated cells were grown under submerged conditions in bronchial air-liquid interface (B-ALI) growth basal medium supplemented with expansion media. When cells reached confluency (after 3-5 days), an air-liquid interface culture (ALI system) was created by removing the apical medium and replacing the medium of the basal compartment with B-ALI differentiation medium. During the 28 days culture medium was replaced every 48 hour. | |
Control | bronchial epithelial cell differentiation study 1 (subconfluent) |
Subconfluent undifferentiated normal human bronchial epithelial cell (NHBE) cultured for 1-2 days under submerged conditions in bronchial air-liquid interface (B-ALI) growth basal medium supplemented with expansion media. At this time point cells still grew dispersed in the culture insert and covered 70% of the insert. |