TOP TEN perturbations for 39959_at (Homo sapiens)

Organism: Homo sapiens
Gene: 39959_at
Selected probe(set): 205890_s_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 39959_at (205890_s_at) across 6674 perturbations tested by GENEVESTIGATOR:

IFN-g study 3 / vehicle (DME) treated bronchial epithelial cell sample

Relative Expression (log2-ratio):7.923839
Number of Samples:2 / 17
Experimental IFN-g study 3
Bronchial epithelial cells (NHBE) treated with 100 ng/ml recombinant human interferon gamma (IFN-g; vendor: PeproTech / catalog number: 300-02 / catalog name: IFN-γ) for 6 hours. For treatment primary cells were seeded at a density of 50'000 cells/well in pre-coated rat tail collagen type I 96-well plates for 24 hours followed by 4 hours starvation. NHBE cells were isolated from different Caucasian, healthy and non-smoker donors from the airway located above the bifurcation of the lungs (tracheal/bronchial).
Control vehicle (DME) treated bronchial epithelial cell sample
Bronchial epithelial cells (NHBE) treated with vehicle (DME) for 6 hours. For treatment primary cells were seeded at a density of 50'000 cells/well in pre-coated rat tail collagen type I 96-well plates for 24 hours followed by 4 hours starvation. NHBE cells were isolated from different Caucasian, healthy and non-smoker donors from the airway located above the bifurcation of the lungs (tracheal/bronchial).

TNF-ɑ study 16 (12h) / rheumatoid arthritis study 10

Relative Expression (log2-ratio):7.4775696
Number of Samples:3 / 6
Experimental TNF-ɑ study 16 (12h)
Synovial fibroblast samples isolated from affected knee of patients with rheumatoid factor positive rheumatoid arthritis (RA) were stimulated by 10 ng/ml of TNF-ɑ in serum-free DMEM for 12 hours. 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 TNF-ɑ stimulation, fibroblasts were cultured for four passages in DMEM medium supplemented with antibiotics and 10% FCS. The RA was classified according to the criteria of the American College of Rheumatology. Average duration of RA: 11.5 ± 0.5 years. Patients were receiving non-steroidal antiinflammatory drugs. CRP: 38.1 ± 7.2 mg/l.
Control rheumatoid arthritis study 10
Synovial fibroblast samples isolated from affected knee of patients with rheumatoid factor positive rheumatoid arthritis (RA), classified according to the criteria of the American College of Rheumatology. Average duration of RA: 11.5 ± 0.5 years. Patients were receiving non-steroidal antiinflammatory drugs. CRP: 38.1 ± 7.2 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.

IFN-g study 9 (24h) / untreated epidermal keratinocyte sample

Relative Expression (log2-ratio):7.40012
Number of Samples:3 / 6
Experimental IFN-g study 9 (24h)
Primary keratinocytes treated with interferon gamma (IFN-g) for 24 hours. Monolayer normal human keratinocyte (NHK) cultures were established and used in the second or third passage. Cultures were grown to 40 or 80% confluence, or maintained to 4 days postconfluency. Cultures were starved of growth factors in nonsupplemented M154 medium for 24 hours, and afterwards stimulated with recombinant human IFN-g for 24 hours.
Control untreated epidermal keratinocyte sample
Untreated primary epidermal keratinocytes. Monolayer normal human keratinocyte (NHK) cultures were established and used in the second or third passage. Cultures were grown to 40 or 80% confluence, or maintained to 4 days postconfluency.

rheumatoid arthritis study 69 (TNF; 20h; 1ng/ml) / rheumatoid arthritis study 69 (untreated)

Relative Expression (log2-ratio):7.3921685
Number of Samples:6 / 6
Experimental rheumatoid arthritis study 69 (TNF; 20h; 1ng/ml)
Joint synovial fibroblast samples from patients with rheumatoid arthritis after treatment with 1ng/ml TNF for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and isolated from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.
Control rheumatoid arthritis study 69 (untreated)
Joint synovial fibroblast samples from patients with rheumatoid arthritis. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and prepared from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.

rheumatoid arthritis study 69 (TNF; 20h; 1ng/ml) / rheumatoid arthritis study 69 (TNF; IL-17A; baseline)

Relative Expression (log2-ratio):7.253162
Number of Samples:6 / 6
Experimental rheumatoid arthritis study 69 (TNF; 20h; 1ng/ml)
Joint synovial fibroblast samples from patients with rheumatoid arthritis after treatment with 1ng/ml TNF for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and isolated from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.
Control rheumatoid arthritis study 69 (TNF; IL-17A; baseline)
Joint synovial fibroblast samples at baseline from patients with rheumatoid arthritis before treatment with 1ng/ml TNF and/or IL-17 for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and prepared from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.

osteoarthritis study 46 (TNF; 20h; 1ng/ml) / osteoarthritis study 46 (TNF; IL-17; baseline)

Relative Expression (log2-ratio):6.701955
Number of Samples:6 / 6
Experimental osteoarthritis study 46 (TNF; 20h; 1ng/ml)
Joint synovial fibroblast samples from patients with osteoarthritis after treatment with 1ng/ml TNF for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and isolated from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.
Control osteoarthritis study 46 (TNF; IL-17; baseline)
Joint synovial fibroblast samples at baseline from patients with osteoarthritis before treatment with 1ng/ml TNF and/or IL-17 for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and prepared from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.

influenza virus study 11 (A/H5N3) / influenza virus study 4 (A/H1N1)

Relative Expression (log2-ratio):6.4719877
Number of Samples:3 / 3
Experimental influenza virus study 11 (A/H5N3)
Human carcinoma cell line A549 infected with influenza A virus subtype influenza virus A/duck/Malaysia/F119/3/1997(H5N3). Samples were taken 10 hours post-infection.
Control influenza virus study 4 (A/H1N1)
Human carcinoma cell line A549 infected with influenza A virus subtype A/WSN/33 (H1N1). Samples were taken 10 hours post-infection.

B. burgdorferi study 1 (IFN-g) / unstimulated HUVEC sample

Relative Expression (log2-ratio):6.375639
Number of Samples:2 / 2
Experimental B. burgdorferi study 1 (IFN-g)
Human umbilical vein endothelial cells (HUVEC) were stimulated with both Interferon-gamma (IFN-g) and Borrelia burgdorferi.
Control unstimulated HUVEC sample
Unstimulated human umbilical vein endothelial cells.

osteoarthritis study 46 (TNF; 20h; 1ng/ml) / osteoarthritis study 46 (untreated)

Relative Expression (log2-ratio):6.357903
Number of Samples:6 / 6
Experimental osteoarthritis study 46 (TNF; 20h; 1ng/ml)
Joint synovial fibroblast samples from patients with osteoarthritis after treatment with 1ng/ml TNF for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and isolated from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.
Control osteoarthritis study 46 (untreated)
Joint synovial fibroblast samples from patients with osteoarthritis. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and prepared from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.

cutaneous T-cell lymphoma study 1 (tumor phase) / normal skin tissue

Relative Expression (log2-ratio):6.223012
Number of Samples:4 / 8
Experimental cutaneous T-cell lymphoma study 1 (tumor phase)
Lesional skin biopsies from patients with cutaneous T-cell lymphoma in the tumor phase (extranodal).
Control normal skin tissue
Skin biopsies from healthy individuals.

Organism: Homo sapiens
Gene: 39959_at
Selected probe(set): 203146_s_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 39959_at (203146_s_at) across 6674 perturbations tested by GENEVESTIGATOR:

CNS cancer study 1 (PDX; glioma, malignant, NOS; primary) / CNS cancer study 1 (PDX; ependymoma, NOS; primary)

Relative Expression (log2-ratio):-4.8377676
Number 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).

medulloblastoma study 2 / non-tumor brain tissue

Relative Expression (log2-ratio):-3.8139772
Number of Samples:4 / 9
Experimental medulloblastoma study 2
Primary tumor tissue sample from the infratentorial brain of pediatric patients with large-cell anaplastic medulloblastoma.
Control non-tumor brain tissue
Histologically normal brain tissue at rapid autopsy from patients who died from atypical teratoid/rhabdoid tumor.

dengue fever study 10 (DF) / normal naive CD8 T cell sample

Relative Expression (log2-ratio):-3.3284626
Number of Samples:3 / 5
Experimental dengue fever study 10 (DF)
Activated CD8 T cells derived from peripheral blood mononuclear cells (PBMCs) of Thai individuals with Dengue fever (DF) characterized by the WHO 1997. FACS-sorted CD3+, CD8+, CD45RA+, and CCR7+ naive CD8 T subtype cells were used for analysis.
Control normal naive CD8 T cell sample
Normal naive CD8 T cells derived from peripheral blood mononuclear cells (PBMCs) of healthy Thai individuals. FACS-sorted CD3+, CD8+, CD45RA+, and CCR7+ naive CD8 T subtype cells were used for analysis.

atypical teratoid/rhabdoid tumor study 1 / non-tumor brain tissue

Relative Expression (log2-ratio):-3.23285
Number of Samples:20 / 9
Experimental atypical teratoid/rhabdoid tumor study 1
Primary tumor tissue sample from the brain of pediatric patients with atypical teratoid/rhabdoid tumor (AT/RT).
Control non-tumor brain tissue
Histologically normal brain tissue at rapid autopsy from patients who died from atypical teratoid/rhabdoid tumor.

dengue fever study 10 (DHF) / normal naive CD8 T cell sample

Relative Expression (log2-ratio):-3.1633043
Number of Samples:2 / 5
Experimental dengue fever study 10 (DHF)
Activated CD8 T cells derived from peripheral blood mononuclear cells (PBMCs) of Thai individuals with Dengue hemorrhagic fever (DF) characterized by the WHO 1997. FACS-sorted CD3+, CD8+, HLA_DR+, and CD38+ effector CD8 T subtype cells were used for analysis.
Control normal naive CD8 T cell sample
Normal naive CD8 T cells derived from peripheral blood mononuclear cells (PBMCs) of healthy Thai individuals. FACS-sorted CD3+, CD8+, CD45RA+, and CCR7+ naive CD8 T subtype cells were used for analysis.

CNS cancer study 1 (PDX; glioma, malignant, NOS; primary) / CNS cancer study 1 (PDX; glioblastoma, NOS; primary)

Relative Expression (log2-ratio):-2.9047098
Number of Samples:2 / 3
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; 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).

stem cell differentiation study 59 (iDRG; 15d) / stem cell differentiation study 59 (8d)

Relative Expression (log2-ratio):2.8912706
Number of Samples:4 / 4
Experimental stem cell differentiation study 59 (iDRG; 15d)
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 7 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.

Langerhans cell histiocytosis study 1 / normal myeloid dendritic cell sample

Relative Expression (log2-ratio):-2.8862734
Number of Samples:7 / 3
Experimental Langerhans cell histiocytosis study 1
Langerhans cell histiocytes (LCH) were isolated from LCH lesions of patients undergoing surgery. All patients had single system disease, five patients had bone lesion, one had skin lesion and one had mucosal manifestation. Langerhans cells histiocytes were purified by FACS as CD1a+ / CD270 + population with > 95% purity.
Control normal myeloid dendritic cell sample
Normal myeloid dendritic cells were isolated from peripheral blood of healthy adult donors. Myeloid dendritic cells were defined as HLA-DR+ / CD11c + / BDCA1+ / BDCA3- population.

stem cell differentiation study 59 (iDRG; 15d) / stem cell differentiation study 59 (iDRG; 9d)

Relative Expression (log2-ratio):2.871334
Number of Samples:4 / 4
Experimental stem cell differentiation study 59 (iDRG; 15d)
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 7 days. Further details are described in the paper.
Control stem cell differentiation study 59 (iDRG; 9d)
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 1 day. Further details are described in the paper.

memory B cell study 1 (CD27high) / memory B cell study 1 (undivided)

Relative Expression (log2-ratio):-2.831705
Number of Samples:6 / 6
Experimental memory B cell study 1 (CD27high)
CD27 enriched proliferating human memory B cells expressing high level of CD27 (marker of antibody secretion) activated with CpG oligodeoxynucleotide (10 ng/ml), recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml), recombinant human BAFF (75 ng/ml) in PC-L medium (IMDM medium, lacromin (50mg/ml), insulin (5mg/ml), penicillin/streptomycin, gentamicin (15mg/ml), normocin (0.1% v/v), 10% FCS) for 80 hours.
Control memory B cell study 1 (undivided)
CD27 enriched undivided human memory B cells (expressing low level of CD27) activated with CpG oligodeoxynucleotide (10 ng/ml), recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml), recombinant human BAFF (75 ng/ml) in PC-L medium (IMDM medium, lacromin (50mg/ml), insulin (5mg/ml), penicillin/streptomycin, gentamicin (15mg/ml), normocin (0.1% v/v), 10% FCS) for 80 hours.