TOP TEN perturbations for 38859_at (Homo sapiens)
Organism: Homo sapiens
Gene: 38859_at
Selected probe(set): 209889_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array
Expression of 38859_at (209889_at) across 6674 perturbations tested by GENEVESTIGATOR:
diabetes type 2 study 27 (LCM) / diabetes type 2 study 27 (enzymatic)
Relative Expression (log2-ratio):2.392768Number of Samples:34 / 19
| Experimental | diabetes type 2 study 27 (LCM) |
| Pancreatic islet samples obtained from type 2 diabetic (T2D) phenotyped pancreatectomized patients (PPP) and isolated by laser capture microdissection (LCM). Islets specimens were retrieved by LCM from snap-frozen surgical specimen from patients who underwent pancreatectomy for pancreatic diseases. Histopathology of the resected tissue did not reveal insulitis in any PPP. Patients age <18 years were excluded. Patients with type 2 diabetes had fasting glycemia ≥7.0 mmol/l; HbA1C ≥6.5% and history of diabetes for >1 year. | |
| Control | diabetes type 2 study 27 (enzymatic) |
| Pancreatic islet samples obtained from type 2 diabetic (T2D) patients and isolated by enzymatic digestion. Well-preserved islets were isolated by collagenase digestion of pancreas from brain-dead organ donors which suffered from type 2 diabetes. After 2±1 days of culture, islets were successfully hand-picked and processed for further analyses. Type 2 diabetes was diagnosed based on clinical history, treatment with glucose-lowering drugs, and lack of anti-GAD65 autoantibodies. |
HIF-1a/HIF-2a depletion study 1 (hypoxia; HK2) / HIF-1a/HIF-2a depletion study 1 (normoxia; AB81)
Relative Expression (log2-ratio):-2.3071547Number of Samples:3 / 3
| Experimental | HIF-1a/HIF-2a depletion study 1 (hypoxia; HK2) |
| Proximal tubule epithelial cell line HK-2 with shRNA-mediated stable knock-down of HIF-1a and HIF-2a (Hypoxia-inducible factor 1-alpha and Hypoxia-inducible factor 2-alpha) 24 hours after treatment with hypoxia (20% O2). HK-2 cells were cultured in DMEM/F-12 supplemented with 10% fetal calf serum (FCS), 1% ITS, hydrocortisone, and antibiotics. The cells were incubated at 37 °C. | |
| Control | HIF-1a/HIF-2a depletion study 1 (normoxia; AB81) |
| Human podocyte cells AB81 with shRNA-mediated stable knock-down of HIF-1a and HIF-2a (Hypoxia-inducible factor 1-alpha and Hypoxia-inducible factor 2-alpha) 24 hours after treatment with normoxia (20% O2). Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates. |
smoking study 82 (3R4F; 33puffs/l; 24h) / smoking study 82 (3R4F; 33puffs/l; 4h)
Relative Expression (log2-ratio):2.0273533Number of Samples:3 / 3
| Experimental | smoking study 82 (3R4F; 33puffs/l; 24h) |
| Normal human bronchial epithelial (NHBE) cells treated with an aqueous extract (AE) of 3R4F cigarette smoke (high concentration=33 puffs/l) for 24 hours. AE was generated by bubbling mainstream smoke from 3R4F reference cigarette through ice-cold PBS using Health Canada smoking regime (puff volume 55 ml, puff duration 2s, puff interval 30s, and 100% blocking of filter ventilation). | |
| Control | smoking study 82 (3R4F; 33puffs/l; 4h) |
| Normal human bronchial epithelial (NHBE) cells treated with an aqueous extract (AE) of 3R4F cigarette smoke (high concentration=33 puffs/l) for 4 hours. AE was generated by bubbling mainstream smoke from 3R4F reference cigarette through ice-cold PBS using Health Canada smoking regime (puff volume 55 ml, puff duration 2s, puff interval 30s, and 100% blocking of filter ventilation). |
T-ALL study 1 / normal bone marrow sample
Relative Expression (log2-ratio):1.9103813Number of Samples:174 / 74
| Experimental | T-ALL study 1 |
| Bone marrow samples of patients with T-ALL. | |
| Control | normal bone marrow sample |
| Non-leukemic and healthy bone marrow sample. |
tumor supernatant activation study 3 / untreated memory CD4 T-cell sample
Relative Expression (log2-ratio):-1.8833609Number of Samples:4 / 3
| Experimental | tumor supernatant activation study 3 |
| Memory (CD45RA-) CD4+ T cells isolated from peripheral blood of female healthy donors were incubated for 24 hours in 1:1 mix of tumor supernatant from primary invasive breast ductal carcinoma and X-VIVO 20 medium supplemented with antiCD3/CD28 beads, before harvest for RNA isolation. The tumor supernatant was prepared as followed: fresh surgical specimen was dissociated in X-VIVO 20 medium by GentleMACS dissociator and the resulting suspension was clarified by centrifugation for 15min at 13'000 g. ATC code:--- | |
| Control | untreated memory CD4 T-cell sample |
| Memory (CD45RA-) CD4+ T-cells were isolated from peripheral blood of healthy female donors and incubated in X-VIVO 20 medium for 24 hours, before harvest for RNA isolation. |
T-cell activation study 3 / resting CD4 T-lymphocyte (crude fraction) sample
Relative Expression (log2-ratio):-1.8620396Number of Samples:2 / 2
| Experimental | T-cell activation study 3 |
| CD4+ T-cell samples prepared from crude lymphocyte fraction. Cells were activated with anti-CD3/28 beads for 18hrs. | |
| Control | resting CD4 T-lymphocyte (crude fraction) sample |
| Resting CD4 T-lymphocytes prepared from crude lymphocyte fraction. |
stem cell differentiation study 50 (IRF2 shRNA; ASC; proerythroblast) / stem cell differentiation study 50 (mock shRNA; ASC; proerythroblast)
Relative Expression (log2-ratio):1.8236198Number of Samples:3 / 4
| Experimental | stem cell differentiation study 50 (IRF2 shRNA; ASC; proerythroblast) |
| Proerythroblast differentiated from IRF2 (interferon regulatory factor 2) shRNA transduced hematopoietic stem/progenitor cells (CD34+). CD34+ hematopoietic stem/progenitor cells (HSC) were transduced with lentivirus expressing shRNA targeting IRF2 gene with following differentiation to the erythroid lineage. HSCs were obtained from magnetically sorted G-CSF mobilized peripheral blood mononuclear cells of healthy donors. Cells were expanded in StemSpan SFEM medium supplied with Flt-3 ligand (100 ng/ml), SCF (100 ng/ml), IL-3 (20 ng/ml), IL-6 (20 ng/ml) and penicillin/streptomycin. Cells were harvested for total RNA extraction at the proerythroblast stage of differentiation. | |
| Control | stem cell differentiation study 50 (mock shRNA; ASC; proerythroblast) |
| Proerythroblast differentiated from control shRNA transduced hematopoietic stem/progenitor cells (CD34+). CD34+ hematopoietic stem/progenitor cells (HSC) were transduced with lentivirus expressing control shRNA with following differentiation to the erythroid lineage. HSCs were obtained from magnetically sorted G-CSF mobilized peripheral blood mononuclear cells of healthy donors. Cells were expanded in StemSpan SFEM medium supplied with Flt-3 ligand (100 ng/ml), SCF (100 ng/ml), IL-3 (20 ng/ml), IL-6 (20 ng/ml) and penicillin/streptomycin. Cells were harvested for total RNA extraction at the proerythroblast stage of differentiation. |
Langerhans cell histiocytosis study 2 (multisystem) / Langerhans cell histiocytosis study 2 (multifocal)
Relative Expression (log2-ratio):-1.8047466Number of Samples:2 / 2
| Experimental | Langerhans cell histiocytosis study 2 (multisystem) |
| Langerhans cell histiocytes (LCH, CD207+) samples isolated from LCH lesions of patients with multifocal, multisystem (disseminated) disease. Both patients received chemotherapy. Sites of LCH lesions: subj.ID:1 (skin, lungs, multiple skull, mastoid, gingiva), subj.ID:13 (mandible, skull, vertebrae, recurrent orbit, liver, spleen, pituitary gland). | |
| Control | Langerhans cell histiocytosis study 2 (multifocal) |
| Langerhans cell histiocytes (LCH, CD207+) samples isolated from LCH lesions of patients with multifocal (bone, skin lesions) disease. |
glioma study 17 (oligoastrocytoma; unsorted) / non-tumor cortical tissue
Relative Expression (log2-ratio):1.792489Number of Samples:2 / 4
| Experimental | glioma study 17 (oligoastrocytoma; unsorted) |
| Brain cells isolated from low grade oligoastrocytoma (grade II). 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. |
dendritic cell study 6 (gardiquimod; RN486) / dendritic cell study 6 (untreated)
Relative Expression (log2-ratio):-1.7826653Number of Samples:4 / 8
| Experimental | dendritic cell study 6 (gardiquimod; RN486) |
| Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors and treated with gardiquimod (TLR7 agonist) and RN486 (Bruton’s tyrosine kinase; BTK inhibitor) for 3 hours. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+. | |
| Control | dendritic cell study 6 (untreated) |
| Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+. |