TOP TEN perturbations for 38946_at (Homo sapiens)
Organism: Homo sapiens
Gene: 38946_at
Selected probe(set): 206547_s_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array
Expression of 38946_at (206547_s_at) across 6674 perturbations tested by GENEVESTIGATOR:
bone cancer study 1 (PDX; chondrosarcoma, NOS; primary) / bone cancer study 1 (PDX; myxoid chondrosarcoma; primary)
Relative Expression (log2-ratio):5.511628Number of Samples:2 / 2
| Experimental | bone cancer study 1 (PDX; chondrosarcoma, NOS; primary) |
| Patient-derived xenograft (PDX) samples generated in female athymic nude mice from patients with primary chondrosarcoma, NOS of the bone (subcutaneously implanted). | |
| Control | bone cancer study 1 (PDX; myxoid chondrosarcoma; primary) |
| Patient-derived xenograft (PDX) samples generated in female athymic nude mice from patients with primary myxoid chondrosarcoma of the bone (subcutaneously implanted). |
NOTCH2-IC overexpr. study 1 (72h) / NOTCH2-IC overexpr. study 1 (0h)
Relative Expression (log2-ratio):5.03057Number of Samples:3 / 3
| Experimental | NOTCH2-IC overexpr. study 1 (72h) |
| 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 were induced immediately after estrogen withdrawal. The 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 72 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. | |
| Control | NOTCH2-IC overexpr. study 1 (0h) |
| 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. Cells were harvested directly after estrogen depletion period of 3 days (0 hours). 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) / control virus transfected EREB2-5 cell sample (24h)
Relative Expression (log2-ratio):4.9374485Number 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. |
stem cell differentiation study 59 (iDRG; 12d) / stem cell differentiation study 59 (8d)
Relative Expression (log2-ratio):4.8602686Number of Samples:4 / 4
| Experimental | stem cell differentiation study 59 (iDRG; 12d) |
| Immature dorsal root ganglia neurons (iDRGs) obtained by differentiation of WA09 embryonic stem cells. WA09 cells were differentiated for 8 days and subsequently cryopreserved. After thawing, cells were further differentiated for 4 days. Further details are described in the paper. | |
| Control | stem cell differentiation study 59 (8d) |
| WA09 embryonic stem cell samples differentiated for 8 days. Further details are described in the paper. |
EBNA2 overexpr. study 1 (4h) / control virus transfected EREB2-5 cell sample (24h)
Relative Expression (log2-ratio):4.8478975Number 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. |
NOTCH2-IC overexpr. study 1 (72h) / control virus transfected EREB2-5 cell sample (72h)
Relative Expression (log2-ratio):4.777604Number of Samples:3 / 3
| Experimental | NOTCH2-IC overexpr. study 1 (72h) |
| 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 were induced immediately after estrogen withdrawal. The 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 72 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. | |
| Control | control virus transfected EREB2-5 cell sample (72h) |
| 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, the stably transfected cells were maintained in RPMI media and were induced immediately after estrogen withdrawal. The expression of CAT was induced by the addition of doxycycline to a final concentration of 100 ng/mL medium. Doxycycline induced cells were harvested 72 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. |
male infertility study 1 (juvenile; Ad-) / normal testicular lobules tissue (mJS10)
Relative Expression (log2-ratio):-4.6583424Number of Samples:2 / 8
| Experimental | male infertility study 1 (juvenile; Ad-) |
| Human testicular lobules biopsy samples isolated from prepubescent patients with undescended testes. Testes of these children contained very low level of A-dark (Ad-) spermatogonial cells. | |
| Control | normal testicular lobules tissue (mJS10) |
| Biopsies of human testicular lobules isolated from fertile vasectomized adult men with normal spermatogenesis. Histological analysis classified samples as mJS10 (modified Johnsen score 10). |
NOTCH1-IC overexpr. study 2 (72h) / control virus transfected EREB2-5 cell sample (72h)
Relative Expression (log2-ratio):4.6325865Number of Samples:2 / 3
| Experimental | NOTCH1-IC overexpr. study 2 (72h) |
| EREB2-5 cell line stably transfected with expression plasmid coding for intracellular domain of NOTCH1 (NOTCH1-IC). The stably transfected cells were maintained in RPMI media and were induced immediately after estrogen withdrawal. The expression of NOTCH1-IC was induced by the addition of doxycycline to a final concentration of 100 ng/mL medium. Doxycycline induced cells were harvested 72 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. | |
| Control | control virus transfected EREB2-5 cell sample (72h) |
| 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, the stably transfected cells were maintained in RPMI media and were induced immediately after estrogen withdrawal. The expression of CAT was induced by the addition of doxycycline to a final concentration of 100 ng/mL medium. Doxycycline induced cells were harvested 72 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. |
stem cell differentiation study 59 (iDRG; 12d) / normal embryonic stem cell sample (WA09)
Relative Expression (log2-ratio):4.5303154Number of Samples:4 / 4
| Experimental | stem cell differentiation study 59 (iDRG; 12d) |
| Immature dorsal root ganglia neurons (iDRGs) obtained by differentiation of WA09 embryonic stem cells. WA09 cells were differentiated for 8 days and subsequently cryopreserved. After thawing, cells were further differentiated for 4 days. Further details are described in the paper. | |
| Control | normal embryonic stem cell sample (WA09) |
| Undifferentiated WA09 embryonic stem cell samples. |
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, leiomyosarcoma, NOS; primary)
Relative Expression (log2-ratio):4.52071Number 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, leiomyosarcoma, NOS; primary) |
| Patient-derived xenograft (PDX) samples generated in female athymic nude mice from patients with primary connective and soft tissue, leiomyosarcoma, NOS of the soft tissue (subcutaneously implanted). |