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Items: 14

1.

Vitamin-D Responsive SGPP2 Variants Associated with Lung Cell Expression and Lung Function

(Submitter supplied) Background: Vitamin D is associated with lung health in epidemiologi studies, but mechanisms mediating observed associations are poorly understood. This study explores mechanisms for an effect of vitamin D in lung through an in vivo gene expression study, an expression quantitative trait loci (eQTL) analysis in lung tissue, and a population-based cohort study of sequence variants. Methods: Microarray analysis investigated the association of gene expression in small airway epithelial cell with serum 25[OH]D in adult nonsmokers. more...
Organism:
Homo sapiens
Type:
Expression profiling by array; SNP genotyping by SNP array; Genome variation profiling by SNP array
Platforms:
GPL6804 GPL570
142 Samples
Download data: CEL, CHP
Series
Accession:
GSE44865
ID:
200044865

Analyze with GEO2R

2.

Genotype-Smoking Environment Interactions affecting eQTL in the Human Lung

(Submitter supplied) Background: Cases where genotype-phenotype relationships depend on environmental factors have been quantified for many complex diseases. Such genotype-environment interactions (GEI or GxE) may also affect expression Quantitative Trait Loci (eQTL) present in tissues critical for the manifestation of disease. To assess this hypothesis, we performed an analysis of eQTL-GEI resulting from an individual's smoking environment in the lung small airway epithelium (SAE). more...
Organism:
Homo sapiens
Type:
Expression profiling by array; SNP genotyping by SNP array
Platforms:
GPL570 GPL6804
180 Samples
Download data: CEL, CHP
Series
Accession:
GSE23087
ID:
200023087

Analyze with GEO2R

3.

Genetic Variability Modulation of SPOCK3 Gene Expression in the Human Small Airway Epithelium

(Submitter supplied) Testican 3 (coded for by SPOCK3), is an extracellular matrix heparan/chondroitin sulphate proteoglycan that possesses serine and cysteine protease inhibitor-like domains Based on the knowledge that serine proteases contribute to the destruction of the lung in cigarette smokers, but that only a fraction of smokers develop smoking-induced lung disease, we hypothesized that smokers expressed SPOCK3 at lower levels in the small airway epithelium, the initial site of smoking-induced disease, and further, that genetic variability modulates the expression of SPOCK3 in the airway epithelium. more...
Organism:
Homo sapiens
Type:
Expression profiling by array; SNP genotyping by SNP array; Genome variation profiling by SNP array
Platforms:
GPL570 GPL6804
212 Samples
Download data: CEL, CHP
Series
Accession:
GSE13932
ID:
200013932

Analyze with GEO2R

4.

CNV Polymorphisms Modulate the Expression of GST Subtypes in the Human Small Airway Epithelium and Alveolar Macrophages

(Submitter supplied) The glutathione S-transferase (GST) gene family codes for enzymes that detoxify xenobiotics by catalyzing the conjugation of xenobiotics to glutathione. Based on reports that inherited copy number variations (CNV) in the genome modulate some GST expression levels and with the knowledge that cigarette smoke contains >3000 xenobiotics, and that the small airway epithelium and alveolar macrophages are involved early in the pathogensis of smoking-induced lung disease, we asked: do germline CNVs modulate GST expression level in the small airway epithelium and alveolar macrophages? Affymetrix HG U133 Plus 2.0 microarrays were used to survey GST gene expression in the small airway epithelium and alveolar macrophages obtained by bronchoscopic brushings from current smokers (n=35) and nonsmokers (n=35). more...
Organism:
Homo sapiens
Type:
Expression profiling by array; Genome variation profiling by SNP array
Platforms:
GPL570 GPL6804
211 Samples
Download data: CEL, CHP
Series
Accession:
GSE20250
ID:
200020250

PubMed Full text in PMC Similar studies Analyze with GEO2R

5.

CSMD1 shows complex somatic alterations in esophageal squamous cell carcinoma based on a pilot integrated analysis

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
SNP genotyping by SNP array; Genome variation profiling by SNP array
Platforms:
GPL3718 GPL3720 GPL6804
152 Samples
Download data: CEL
Series
Accession:
GSE74705
ID:
200074705

PubMed Full text in PMC Similar studies

6.

CSMD1 shows complex somatic alterations in esophageal squamous cell carcinoma based on a pilot integrated analysis [Affy_SNP5]

(Submitter supplied) Since ESCC is a complex and heterogeneous disease, it is increasingly important that analyses combine the evaluation of alterations in DNA, including somatic copy number alterations (SCNA), which distinguished from germ line copy number variants, allelic imbalance and LOH, and RNA, including those that occur in both mRNA and miRNA on the same specimen. Thus, in order to better understand their potential interactions in the development of cancers, in the present study, we studied alterations at DNA level as well as expression of mRNA and target miRNA in tumors and their matched normal tissues from 56 ESCC cases on a candidate tumor suppressor gene CSMD1 to characterize there alterations in this gene for import insights into the cellular detect that cause the complex disease, ESCC.
Organism:
Homo sapiens
Type:
SNP genotyping by SNP array; Genome variation profiling by SNP array
Platform:
GPL6804
72 Samples
Download data: CEL
Series
Accession:
GSE74703
ID:
200074703

PubMed Full text in PMC Similar studies

7.

Genomic landscape of somatic alterations in esophageal squamous cell carcinoma and gastric cancer

(Submitter supplied) Gastric cancer and esophageal cancer are the 2nd and 6th leading causes of cancer death worldwide. We analyzed DNA copy numbers for 73 ESCC (43 SNP5.0 and 30 500K SNP) with the Affymetrix SNP arrays . Our analyses implicated potential driver mutations involving the following genes: mutations in TP53, BRCA2, NOTCH2, CTNNB1, and LEPREL2; amplification of CCND1, FGF3/4/19, and MYC; and deletion of CDKN2A/B.
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array
Platform:
GPL6804
90 Samples
Download data: CEL, TXT
Series
Accession:
GSE43470
ID:
200043470

PubMed Full text in PMC Similar studies

8.

Affymetrix SNP array data for squamous cell carcinoma of base of tongue and healthy individuals samples

(Submitter supplied) Base of tongue squamous cell carcinoma (BTSCC) is a common tumor of oropharynx worldwide. In addition, BTSCC is a lethal disease and its treatment results in significant disability. Considerable importance is given in lifestyle, particularly tobacco and alcohol use, in cases of BTSCC. It was postulated that BTSCC arises if the ability to metabolize carcinogens, to repair DNA damage and to control cell signaling and cell cycle are defective in individuals with continued exposure to benzo(a)pyrene, ethanol and acetaldehyde. more...
Organism:
Homo sapiens
Type:
SNP genotyping by SNP array
Platform:
GPL6804
98 Samples
Download data: CEL, TXT
Series
Accession:
GSE46812
ID:
200046812

PubMed Full text in PMC Similar studies

9.

eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors

(Submitter supplied) Motivation: Identification of eQTL, the genetic loci that contribute to heritable variation in gene expression, can be obstructed by factors that produce variation in expression profiles if these factors are unmeasured or hidden from direct analysis. Methods: We have developed a method for Hidden Expression Factor analysis (HEFT) that identifies individual and pleiotropic effects of eQTL in the presence of hidden factors. more...
Organism:
Homo sapiens
Type:
Expression profiling by array; SNP genotyping by SNP array
Platforms:
GPL6804 GPL570
232 Samples
Download data: CEL, CHP, TXT
Series
Accession:
GSE40364
ID:
200040364

PubMed Full text in PMC Similar studies Analyze with GEO2R

10.

Modulation of Cystatin A Expression in Human Airway Epithelium Related to Genotype, Smoking COPD and Lung Cancer

(Submitter supplied) Cystatin A (gene: CSTA), is up-regulated in non-small-cell lung cancer (NSCLC) and dysplastic vs normal human bronchial epithelium. In the context that chronic obstructive pulmonary disease (COPD), a small airway epithelium (SAE) disorder, is independently associated with NSCLC (especially squamous cell carcinoma, SCC), but only occurs in a subset of smokers, we hypothesized that genetic variation, smoking and COPD modulate CSTA gene expression levels in SAE, with further up-regulation in SCC. more...
Organism:
Homo sapiens
Type:
Expression profiling by array; SNP genotyping by SNP array
Platforms:
GPL570 GPL6804
342 Samples
Download data: CEL, CHP, TXT
Series
Accession:
GSE22047
ID:
200022047

PubMed Full text in PMC Similar studies Analyze with GEO2R

11.

Emergence of Non-Random Chromosomal Alterations (Trisomy 7 and 20) Derived from Diploid Human Colonic Epithelial Cells

(Submitter supplied) Aneuploidy from chromosomal instability is frequently detected in the vast majority of sporadic colorectal cancer patients and is believed to be an early driving force in disease progression. Despite this observation, the cellular advantages conferred by these cytogenetic alterations are poorly understood. We have isolated and immortalized non-transformed human colonic epithelial cells (HCECs) from non-cancerous biopsy tissue from a previous CRC patient undergoing routine colonoscopy. more...
Organism:
Homo sapiens
Type:
SNP genotyping by SNP array; Genome variation profiling by SNP array
Platform:
GPL6804
2 Samples
Download data: CEL, TXT
Series
Accession:
GSE24092
ID:
200024092

PubMed Full text in PMC Similar studies

12.

Meningioma initiating cells (MICs) derived from primary tumors

(Submitter supplied) The majority of meningiomas are benign tumors associated with favorable outcomes; however, the less common aggressive variants with unfavorable outcomes often recur and may be due to sub-populations of less-differentiated cells residing within the tumor. These sub-populations of tumor cells, termed tumor-initiating cells, may be isolated from heterogeneous tumors when sorted or cultured in defined medium designed for enrichment of the tumor-initiating cells. more...
Organism:
Homo sapiens
Type:
SNP genotyping by SNP array; Genome variation profiling by SNP array; Expression profiling by array
Platforms:
GPL6804 GPL6947
6 Samples
Download data: CEL, CHP, TXT
Series
Accession:
GSE22577
ID:
200022577

PubMed Full text in PMC Similar studies Analyze with GEO2R

13.

Identification of novel SNP candidates associated with chemo-responsiveness in colorectal cancers

(Submitter supplied) Identificaiton of novel single-nucleotide polymorphism (SNP) candidates associated with chemo-responsiveness in colorectal cancers using microarray Response rates of 104 colorectal cancer patients to established regiments (FL, CAPE, FLOX, FLIRI) were evaluated by histoculture drug response assay. Affymetrix SNP 5.0 chips were used to determine genotypes of the same colorectal cancer patients. SNPs associated with chemosensitivity to standard regimens were identified by genome-wide association study. more...
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array
Platform:
GPL6804
104 Samples
Download data: CEL, CHP
Series
Accession:
GSE16718
ID:
200016718

PubMed Full text in PMC Similar studies

14.

Identification of novel gene amplification events in breast cancer

(Submitter supplied) To identify novel gene amplification events that may contribute to breast cancer progression, we examined copy number variation in 161 primary breast cancer samples using the Affymetrix 250K_Nsp and 250K_Sty microarrays or the Affymetrix SNP5.0 microarray.
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array; SNP genotyping by SNP array
Platforms:
GPL3720 GPL3718 GPL6804
203 Samples
Download data: CEL, CHP
Series
Accession:
GSE16619
ID:
200016619

PubMed Full text in PMC Similar studies

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