TOP TEN perturbations for 39841_at (Homo sapiens)

Organism: Homo sapiens
Gene: 39841_at
Selected probe(set): 230748_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 39841_at (230748_at) across 6673 perturbations tested by GENEVESTIGATOR:

stem cell differentiation study 46 (BMP4, inhibitors) / normal embryonic stem cell sample (WA09)

Relative Expression (log2-ratio):5.3701124
Number of Samples:3 / 3
Experimental stem cell differentiation study 46 (BMP4, inhibitors)
Extraembryonic cells differentiated from WA09 cells in chemically defined medium supplemented with BMP4 and inhibitors of activin and FGF2. Differentiation was performed in the absence of feeders cells and serum. Cells were first grown on fibronection-coated plates in CDM supplemented with activin (10 ng/ml) and FGF2 (12 ng/ml) for two days and then in CDM supplemented with BMP4 (10 ng/ml), an inhibitor of Alk4/5/7 receptors (type I Activin receptor-like kinase), SB431542 (10uM), and an inhibitor of FGF receptors, SU5402 (10uM), for 3-4 days.
Control normal embryonic stem cell sample (WA09)
WA09 embryonic stem cells cultivated in chemically defined medium (CDM). Cells were first grown on fibronection-coated plates in CDM supplemented with activin (10 ng/ml) and FGF2 (12 ng/ml) for two days and then further cultivated in CDM alone for 3-4 days. CDM consists of 50% Iscove’s Modified Dulbecco’s Medium and 50% F12 Ham´s nutrient mixture. It is devoid of serum and supplemented with insulin (7 ug/ml), transferrin (15 ug/ml), monothioglycerol (450 uM) and serum albumin (5 mg/ml).

pancreatic islet study 3 (re-differentiated; PPRF; 6d) / pancreatic islet study 3 (expanded; PPRF)

Relative Expression (log2-ratio):5.112878
Number of Samples:2 / 2
Experimental pancreatic islet study 3 (re-differentiated; PPRF; 6d)
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 for 6 weeks and re-differentiated for 6 days according to Pharmaceutical Production Research Facility (PPRF) Protocol. Re-differentiation phase: For induction of expanded cells to differentiate into islet-like cell clusters, the cells were seeded into 60 mm ultra-low attachment dishes in serum-free CMRL-1066 supplemented with 4 mM L-glutamine, 1% BSA, insulin (10 g/ml), transferrin (5.5 g/ml), sodium selenite (6.7ng/ml), and 1% antibiotic antimycotic solution at a density of 6.0 x 10EXP6 cells per dish. The induction medium was further added with islet neogenesis-associated protein (INGAP) peptide at a concentration of 1.0 ug/ml.
Control 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.

TGF-ß study 8 (4h) / osteoarthritis study 6

Relative Expression (log2-ratio):5.005975
Number of Samples:3 / 6
Experimental TGF-ß study 8 (4h)
Synovial fibroblast samples isolated from affected knee of patients with osteoarthritis (OA) were stimulated by 10 ng/ml of TGF-ß in serum-free DMEM for 4 hours. Average duration of OA: 4.4 ± 0.6 years, all patients were rheumatoid factor negative. Patients were receiving non-steroidal antiinflammatory drugs. CRP: 13.2 ± 2.9 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. Before the TGF-ß stimulation, fibroblasts were cultured for four passages in DMEM medium supplemented with antibiotics and 10% FCS.
Control osteoarthritis study 6
Synovial fibroblast samples isolated from affected knee of patients with osteoarthritis (OA). Average duration of OA: 4.4 ± 0.6 years, all patients were rheumatoid factor negative. Patients were receiving non-steroidal antiinflammatory drugs. CRP: 13.2 ± 2.9 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.

uterine/pelvic pathology study 2 (pro. MCP) / uterine/pelvic pathology study 2 (late se MCP)

Relative Expression (log2-ratio):-4.9115877
Number of Samples:15 / 2
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 uterine/pelvic pathology study 2 (late se MCP)
Endometrial tissue samples collected from women with uterine/pelvic pathology in the late secretory 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.

F. tularensis study 1 (novicida) / uninfected peripheral blood monocyte sample

Relative Expression (log2-ratio):-4.8607855
Number of Samples:4 / 6
Experimental F. tularensis study 1 (novicida)
Peripheral blood monocytes infected with the Francisella tularensis subspecies novicida isolate U112 (100 MOI) for 24 hours.
Control uninfected peripheral blood monocyte sample
Peripheral blood monocytes uninfected.

connective/soft tissue cancer study 1 (PDX; connective and soft tissue, sarcoma, NOS; metastatic) / connective/soft tissue cancer study 1 (PDX; connective and soft tissue, clear cell sarcoma, NOS; metastatic)

Relative Expression (log2-ratio):-4.800727
Number of Samples:3 / 2
Experimental connective/soft tissue cancer study 1 (PDX; connective and soft tissue, 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, sarcoma, 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.

Hep-G2 / HepaRG

Relative Expression (log2-ratio):4.763612
Number of Samples:9 / 12
Experimental Hep-G2
Human primary cancer cell line derived from the liver of a patient with hepatocellular carcinoma. Synonyms:HEP-G2; Hep G2; HEP G2; HepG2; HEPG2 Cellosaurus code:
Control HepaRG
Immortalized cancer cell line derived from female patient with hepatocellular carcinoma. Cells can be induced to differentiate into hepatocyte-like cells by exposure to DMSO. Synonyms:Hepa-RG Cellosaurus code:

esophageal squamous cell carcinoma study 1 / normal esophageal epithelium sample

Relative Expression (log2-ratio):-4.6939354
Number of Samples:8 / 18
Experimental esophageal squamous cell carcinoma study 1
Esophageal squamous cell carcinoma (ESCC) biopsy samples from chemotherapy-naive patients with histological grading G1 (well differentiated) and UICC stage II and III, which undergone esophagectomy.
Control normal esophageal epithelium sample
Histologically normal esophageal squamous cell epithelium biopsy samples from patients that were investigated for esophageal pain, but diagnosed as healthy.

VTX-2337 study 1 / 3M-055 study 1

Relative Expression (log2-ratio):-4.630636
Number of Samples:3 / 3
Experimental VTX-2337 study 1
Peripheral blood monocytes isolated from healthy donors. Cells were treated overnight with 1uM VTX-2337 drug, which represents a TLR8 (Toll-like receptor 8) agonist with potential immunostimulating and antineoplastic activities.
Control 3M-055 study 1
Peripheral blood monocytes isolated from healthy donors. Cells were treated overnight with 1uM 3M-055 drug, which represents a TLR7 (Toll-like receptor 7) agonist.

Barrett's esophagus study 3 / normal esophageal epithelium sample

Relative Expression (log2-ratio):-4.61086
Number of Samples:17 / 18
Experimental Barrett's esophagus study 3
Esophageal epithelium samples from areas with Barrett's esophagus metaplasia which were recovered by laser capture microdissection.
Control normal esophageal epithelium sample
Histologically normal esophageal squamous cell epithelium biopsy samples from patients that were investigated for esophageal pain, but diagnosed as healthy.