TOP TEN perturbations for NM_000104 (Homo sapiens)

Organism: Homo sapiens
Gene: NM_000104
Selected probe(set): 202436_s_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of NM_000104 (202436_s_at) across 5392 perturbations tested by GENEVESTIGATOR:

hepatocyte (ESC) / Hep-G2

Relative Expression (log2-ratio):6.7319736
Number of Samples:8 / 9
Experimental hepatocyte (ESC)
Hepatocyte-like cells differentiated from embryonic stem cells (ESC)
Control 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:

chronic obstructive pulmonary disease study 3 / small airway epithelial cell sample (non-smoker)

Relative Expression (log2-ratio):5.8984804
Number of Samples:14 / 13
Experimental chronic obstructive pulmonary disease study 3
Small airway epithelial cells (10th to 12th order bronchi) obtained by bronchoscopy and brushing from smokers with chronic obstructive pulmonary disease (COPD).
Control small airway epithelial cell sample (non-smoker)
Small airway epithelial cells (10th to 12th order bronchi) obtained by bronchoscopy and brushing from normal non-smokers.

hair follicle keratinocyte study 1 (CD200-/CD49+) / hair follicle keratinocyte study 1 (CD200+/CD49+)

Relative Expression (log2-ratio):-5.881896
Number of Samples:3 / 3
Experimental hair follicle keratinocyte study 1 (CD200-/CD49+)
Primary hair follicle keratinocytes sample negative for CD200 and positive for CD49.
Control hair follicle keratinocyte study 1 (CD200+/CD49+)
Primary hair follicle keratinocytes sample positive for CD200 and CD49.

smoking study 30 / untreated tracheal epithelial cell sample (non-smoker)

Relative Expression (log2-ratio):5.8683987
Number of Samples:18 / 26
Experimental smoking study 30
Tracheal epithelial cells from healthy smokers. derived by tracheal brushing without conscious sedation. Tracheal epithelial cells were collected with a fiberoptic bronchoscope .Atropine 0.6 mg (IM) and 2.5 mL, 0.02% ipratropium was nebulized to decrease salivary and bronchial secretions. Topical anesthesia of the posterior pharynx and vocal cords was obtained by inhalation with 2 mL, 4% lidocaine followed by administering 1 spray of 20% benzocaine to the posterior pharynx. Unless there was a contraindication, the bronchoscope was introduced through the nostril after application of viscous 2% lidocaine with the patient sitting upright. Once the bronchoscope passed to the posterior pharynx, further topical anesthesia of the vocal cords and trachea was obtained with 1 mL aliquots of 1% lidocaine through the working port of the bronchoscope (maximum amount of lidocaine: 5 mg/kg body weight). After adequate topical anesthesia was obtained, a 2 mm cytology brush was advanced through the working channel of the bronchoscope and tracheal epithelial cells were obtained by gently gliding the brush back and forth 20 times on tracheal epithelium in at least five different locations.
Control untreated tracheal epithelial cell sample (non-smoker)
Untreated tracheal epithelial cells from healthy non-smokers, derived by tracheal brushing without conscious sedation. Tracheal epithelial cells were collected with a fiberoptic bronchoscope. Atropine 0.6 mg (IM) and 2.5 mL, 0.02% ipratropium was nebulized to decrease salivary and bronchial secretions. Topical anesthesia of the posterior pharynx and vocal cords was obtained by inhalation with 2 mL, 4% lidocaine followed by administering 1 spray of 20% benzocaine to the posterior pharynx. Unless there was a contraindication, the bronchoscope was introduced through the nostril after application of viscous 2% lidocaine with the patient sitting upright. Once the bronchoscope passed to the posterior pharynx, further topical anesthesia of the vocal cords and trachea was obtained with 1 mL aliquots of 1% lidocaine through the working port of the bronchoscope (maximum amount of lidocaine: 5 mg/kg body weight). After adequate topical anesthesia was obtained, a 2 mm cytology brush was advanced through the working channel of the bronchoscope and tracheal epithelial cells were obtained by gently gliding the brush back and forth 20 times on tracheal epithelium in at least five different locations.

sbPBS study 1 (direct treatment) / normal umbilical vein endothelial cell sample

Relative Expression (log2-ratio):5.8024416
Number of Samples:3 / 3
Experimental sbPBS study 1 (direct treatment)
Human umbilical vein endothelial cells (HUVEC) treated for 4 hours with smoke-bubbled PBS (sbPBS). Cells were cultured as monolayer on collagen A-coated cell culture plates, in standard endothelial growth medium. 1 day after confluency cells were starved overnight in endothelial growth medium containing 0.5% FCS and exposed to sbPBS for 4 hours. The aqueous cigarette smoke extract was produced from mainstream smoke (generated by a 20-port Borgwaldt smoking machine according to ISO standard 3308) from reference 3R4F cigarette bubbled through PBS (10 cigarettes/32 ml PBS). sbPBS was freshly prepared before experiment and was diluted in RPMI 1640 starving medium (0.5% FCS) to a final concentration of 0.09 puffs/ml. Primary cells were purchased from PromoCell. ATC code:---
Control normal umbilical vein endothelial cell sample
Human umbilical vein endothelial cells (HUVEC) cultured as monolayer on collagen A-coated cell culture plates, in standard endothelial growth medium. 1 day after confluency cells were starved overnight in HUVEC medium containing 0.5% FCS. Primary cells were purchased from PromoCell.

sbPBS study 1 (indirect treatment) / normal umbilical vein endothelial cell sample

Relative Expression (log2-ratio):5.7137585
Number of Samples:3 / 3
Experimental sbPBS study 1 (indirect treatment)
Human umbilical vein endothelial cells (HUVEC) treated for 4 hours with supernatant from human monocytic cell line (MONO-MAC-6) exposed to smoke-bubbled PBS (sbPBS). HUVEC cells were cultured as monolayer on collagen A-coated cell culture plates, in standard endothelial growth medium. 1 day after confluency cells were starved overnight in endothelial growth medium containing 0.5% FCS and treated for 4 hours with supernatant from MONO-MAC-6 cells exposed to sbPBS. Prior to supernatant collection MONO-MAC-6 cells were starved for 2 hours in RPMI 1640 medium (containing 0.5% FCS) and exposed for 2 hours with sbPBS. The aqueous cigarette smoke extract was produced from mainstream smoke (generated by a 20-port Borgwaldt smoking machine according to ISO standard 3308) from reference 3R4F cigarette bubbled through PBS (10 cigarettes/32 ml PBS). sbPBS was freshly prepared before experiment and was diluted in RPMI 1640 starving medium (0.5% FCS) to a final concentration of 0.09 puffs/ml. HUVEC Primary cells were purchased from PromoCell, MONO-MAC-6 cells from Prof. Ziegler-Heitbrock (University of Leicester, UK). ATC code:---
Control normal umbilical vein endothelial cell sample
Human umbilical vein endothelial cells (HUVEC) cultured as monolayer on collagen A-coated cell culture plates, in standard endothelial growth medium. 1 day after confluency cells were starved overnight in HUVEC medium containing 0.5% FCS. Primary cells were purchased from PromoCell.

smoking study 75 / normal alveolar macrophage sample

Relative Expression (log2-ratio):5.7123194
Number of Samples:15 / 15
Experimental smoking study 75
Alveolar macrophages obtained from current smokers by bronchoscopy with bronchoalveolar lavage after pre-treatment with 360mcg albuterol. Macrophages were sorted by flow cytometry using forward scatter and autofluorescence characteristics to 98 ? 2% purity. All subjects had lower lung function than healthy control donors. Subject inclusion criteria: age 30 to 65 and current smoking of at least 10 cigarettes per day (mean 1.4 ? 0.7 packs/d), with a history of at least 10 pack-years (mean 47 ? 27). Two smokers had mild COPD (GOLD class 1) and five subjects had moderate COPD (GOLD class 2). Five smokers had mild reductions in diffusing capacity for CO (60?80% of predicted), suggestive of mild emphysema. Exclusion criteria: FEV1/FVC<0.4, methacholine PC20 <1 mg/mL, history of asthma, recent upper respiratory tract, history of home oxygen use, or admission to an intensive care unit for respiratory failure. Subject characteristics: age 51 ? 8 years, FEV1 prebronchodilator 80 ? 15% predicted, FEV1/FVC prebronchodilator 0.62 ? 0.12, FEV1 post-bronchodilator 84 ? 16% predicted, FEV1/FVC post-bronchodilator 0.67 ? 0.14 (mean ? SD), PC20, mg/dl methacholine 11 (1.6, 48) (median (interquartile range)).
Control normal alveolar macrophage sample
Alveolar macrophages obtained from non-smoking healthy donors by bronchoscopy with bronchoalveolar lavage after pre-treatment with 360mcg albuterol. Macrophages were sorted by flow cytometry using forward scatter and autofluorescence characteristics to 98 ? 2% purity. Subject inclusion criteria: age 30 to 65 years, no history of lung disease and a history of <10 pack-years of smoking with no smoking in the previous 10 years. Subject characteristics: age 41 ? 8 years, FEV1 prebronchodilator 104 ? 12% predicted, FEV1/FVC prebronchodilator 0.80 ? 0.06, FEV1 post-bronchodilator 107 ? 12% predicted, FEV1/FVC post-bronchodilator 0.83 ? 0.05 (mean ? SD), PC20, mg/dl methacholine 64 (64, 64) (median (interquartile range)).

glioma study 16 (LN-229) / normal astrocyte sample

Relative Expression (log2-ratio):-5.574374
Number 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.

glioma study 16 (LN-215) / normal astrocyte sample

Relative Expression (log2-ratio):-5.5519667
Number of Samples:2 / 3
Experimental glioma study 16 (LN-215)
Human glioma cell line LN215 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.

smoking study 68 (24h) / sham-exposed buccal epithelial organotypic tissue

Relative Expression (log2-ratio):5.452299
Number of Samples:3 / 2
Experimental smoking study 68 (24h)
Human buccal epithelial organotypic culture 24 hours after exposure at the air-liquid interface to 40.7% (vol/vol) cigarette smoke of 4 cigarettes (one 3R4F conventional reference cigarette at the time, 1h interval). Cigarettes smoke was diluted with air (0.16 L/min). Organotypic culture consisted of epithelial cells derived from a healthy non-smoker 46 years old male, cultured to form multilayered, highly differentiated human buccal phenotype model.
Control sham-exposed buccal epithelial organotypic tissue
Human buccal epithelial organotypic culture 24 hours after exposure at the air-liquid interface to humidified air (4 exposure, 1h interval) Organotypic culture consisted of epithelial cells derived from a healthy non-smoker 46 years old male, cultured to form multilayered, highly differentiated human buccal phenotype model.