Spare canonical correlation analysis to identify cortical thickness related SNPs
Ontology highlight
ABSTRACT:
INSTRUMENT(S): -
ORGANISM(S): Homo Sapiens
SUBMITTER: Alzheimer's disease convergence research center
PROVIDER: PRJEB72796 | EVA | 2024-02-23
REPOSITORIES: EVA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| scca_igap_filt_344.vcf.csi | Other | |||
| scca_igap_filt_344.vcf.gz | Vcf | |||
| scca_igap_filt_344.vcf.gz.csi | Vcf |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
Project description:1. Determination of serum expression level of HOTTIP and EIF4EBP1(Eukaryotic translation initiation factor 4E-binding protein 1) .
2. Investigation of the SNP HOTTIP rs1859168 and it’s association with CRC susceptibility.
3. Determination of serum level of Interleukin -6 and its relation to other studied genes.
4. Correlation of the expression of these genes with various stages of CRC to determine the prognostic value of each of them.
| 2365471 | ecrin-mdr-crc
Project description:Analysis of gene-expression profiles by microarrays can be very useful to characterize new potential candidate genes, key regulatory networks, and to define phenotypes or molecular signatures to improve the diagnosis or classification of the disease. We have used this approach in the study of one of the major causes of allergic diseases in Mediterranean countries, the olive pollen response, in order to find differential molecular markers among five clinical groups, Non-allergic, Asymptomatic, Allergic but not to olive pollen, Non-treated, olive pollen allergic patients and Olive pollen allergic patients (under specific-immunotherapy). The results of gene-expression by principal components analysis (PCA) clearly showed five clusters of samples that correlated with the five clinical groups. Analysis of differential gene-expression by multiple testing, and functional analysis by KEGG and Gene-Ontology revealed differential genes and pathways among the 5 clinical groups. The study population comprised 28 subjects, selected from a previous immunological study (Aguerri et al. Eur. J. Inflammation 2012, in press), from Andalusia, who were recruited in 2 olive pollen exposure situations: during (April-June) and outside the pollen season (October-December). We established 5 groups, and 6 subjects from each group were selected for gene-expression analysis: Group 1, non-allergic subjects; Group 2, asymptomatic subjects (diagnosed with olive pollen allergy by skin testing, with no seasonal respiratory symptoms [rhinitis and/or asthma], and who consulted for adverse reaction to drugs); Group 3, patients who were allergic, but not to olive pollen; Group 4, non-treated olive pollenM-bM-^@M-^Sallergic; and Group 5, olive pollenM-bM-^@M-^Sallergic patients (receiving olive pollenM-bM-^@M-^Sspecific immunotherapy).The subjects were unrelated and recruited at the Allergy Service of 4 hospitals in Andalusia (Granada, JaM-CM-)n, Sevilla, and MM-CM-!laga). Olive pollenM-bM-^@M-^Sallergic patients fulfilled the following criteria: seasonal rhinitis and/or asthma from April to June, a positive skin prick test result for O. europaea pollen extract (ALK AbellM-CM-3, Madrid, Spain), and no previous immunotherapy. Informed consent was obtained from each subject. Ethical approval for the study was obtained from the Ethical and Research Committee of the participating hospitals. PBMCs were isolated from heparin-containing peripheral blood samples taken during and outside pollen season, by gradient centrifugation on Lymphoprep (Comercial Rafer, Zaragoza, Spain) following the manufacturerM-bM-^@M-^Ys instructions.
2013-02-28 | E-GEOD-37157 | biostudies-arrayexpress
Project description:To investigate the role and mechanism of ANXA2 in retinal neovascularization, we used interfering and overexpressing lentivirus to intervene in HREC cells, respectively. Divided into interference group (negative control group and positive interference group), overexpression group (negative control group, overexpression positive control group). The mechanism of action of annexin A2 in human retinal vascular endothelium was explored by real-time PCR to quantify the expression of molecular genes in samples.
2022-08-20 | GSE136120 | GEO
Project description:Abstract Background: Cerebral ischemia-reperfusion (I/R) frequently caused the late-onset neuronal damage. Breviscapine has a promote in autophagy of microvascular endothelial cells in I/R and it can inhibit the oxidative damage and apoptosis. However, the mediation mechanism of breviscapine on neuronal cell death is unclear. Methods: Firstly, transcriptome sequencing was performed on three groups of mice neuronal normal group (Control group), oxygen-glucose deprivation/reoxygenation group (OGD/R group) and breviscapine administration group (Therapy group). Differentially expressed genes (DEGs) between OGD/R and Control groups, and between Therapy and OGD/R groups were obtained by limma package. The N6-methyladenosine (m6A) methylation related DEGs were selected out by the Pearson correlation analysis. Then, prediction and confirmation of drug targets were performed by Swiss Target Prediction and UniProt Knowledgebase (UniProtKB) datebase, and key genes were obtained by Pearson correlation analysis between m6A-related DEGs and drug target genes. Next, gene set enrichment (GSEA) analysis and Ingenuity pathway analysis (IPA) were used to obtain the pathways of key genes. Finally, a circRNA-miRNA-mRNA network was constructed based on the mRNAs, circRNAs and miRNAs. Results: 2250 DEGs between OGD/R and Control groups and 757 DEGs between Therapy and OGD/R groups were selected out by differential analysis. A total of 7 m6A related DEGs including Arl4d, Gm10653, Gm1113, Kcns3, Olfml2a, Stk26 and Tfcp2l1 were obtained by Pearson correlation analysis. Four key genes (Tfcp2l1, Kcns3, Olfml2a and Arl4d) were acquired, and GSEA showed that these key genes were significantly participated in DNA repair, e2f targets and g2m checkpoint. IPA revealed that Tfcp2l1 played a significant role in human embryonic stem cell pluripotency. The circRNA-miRNA-mRNA network showed that the mmu_circ_0001258 regulated the Tfcp2l1 by mmu-miR-301b-3p. Conclusions: In conclusion, four key genes including Tfcp2l1, Kcns3, Olfml2a and Arl4d significantly associated with the treatment of OGD/R by breviscapine were acquired, which would provide a theoretical basis for clinical trials.
2024-05-17 | E-MTAB-13017 | biostudies-arrayexpress
Project description:Genome-wide association studies (GWAS) have identified dozens of genomic loci, whose single nucleotide polymorphisms (SNPs) predispose to prostate cancer (PCa). However, the biological functions of these common genetic variants and the mechanisms to increase disease risk are largely unknown. We integrated chromatin-IP coupled sequencing (ChIP-seq) and microarray expression profiling in the TMPRSS2-ERG gene rearrangement positive DuCaP cell model with the NHGRI GWAS PCa risk SNPs catalog, in an attempt to identify disease susceptibility SNPs localized within functional androgen receptor binding sites (ARBSs). Among the 48 GWAS index SNPs and 2,702 linked SNPs defined by the 1000G project 104 were found to be localized in the AR ChIP-seq peaks. Of these risk SNPs, rs11891426 T/G in the 7th intron of its host gene melanophilin (MLPH) was found located within a putative auxiliary ARE motif, which we found enriched in the neighborhood of canonical ARE motifs. Exchange of T to G attenuated the transcriptional activity of the MLPH-ARBS in a reporter gene assay. The expression of MLPH protein in tissue samples from prostate cancer patients was significantly lower in those with the G compared to the T allele. Moreover, a significant positive correlation of AR and MLPH protein expression levels was also confirmed in tissue samples. These results unravel a hidden link between AR and a functional PCa risk SNP rs11891426, whose allele alteration affects androgen regulation of its host gene MLPH. This study shows the power of integrative studies to pin down functional risk SNPs and justifies further investigations.
2015-10-12 | GSE63693 | GEO
Project description: Not available
| S-EPMC10670923 | biostudies-literature
Project description:To obtain AIA_H related genes [the significant differentially expressed genes (DEGs) of AIA_H model group vs. Normal control group] and BHGZD therapeutic effect related genes [DEGs of BHGZD treatment group vs. AIA_H model group], the microarray analysis was carried out.
2021-12-03 | GSE189942 | GEO
Project description:Collagen VI-related muscular dystrophies (COL6RD) are a rare, inherited group of congenital muscular dystrophies. The phenotype spans from an early-onset, severe, and rapidly progressive clinical course in Ullrich congenital muscular dystrophy (UCMD), to a late-onset, mild and slowly progressive form in Bethlem muscular dystrophy (BM). COL6RD are caused by pathogenic variants in any of the three collagen type VI genes (COL6A1, COL6A2, COL6A3), which cause absence, reduction, mislocalization, or dysfunction of the collagen VI microfibrils in the skeletal muscle extracellular matrix (myomatrix), leading to yet incompletely understood downstream effects. Pathologic alterations in muscle biopsies of COL6RD varies, ranging from severely dystrophic changes, to mildly myopathic, represented by isolated myofiber atrophy. In this study, we aim to define the pathophysiologic events responsible for the histologic alterations of muscle and their progression in COL6RD. Aided by automated image analysis, we reviewed COL6RD patient muscle biopsies (n=22) and stratified them to three groups based on the degree of fibrosis and muscle fiber atrophy. Using microarray and RNA-Seq, we then performed global gene expression profiling on the same muscle biopsies and compared it with controls (n=14). Different histologic groups were characterized by similar transcriptional signatures predominantly featuring the upregulation of myomatrix component genes and downregulation of skeletal muscle and mitochondrion-specific genes. Our results also identified the TGFβ1 pathway in strong correlation with the development of COL6RD pathology at the histologic level, beginning early in the disease process, preceding fibrosis, and increasing in direct correlation with increased histologic severity. Overall, our study identifies COL6RD as a primary disorder of the myomatrix and posits dysregulation of TGFβ1-dependent pathways as a potential factor in pathogenesis of the disease.
2022-03-22 | GSE103972 | GEO
Project description:Correlation analysis between gut microbiota characteristics and melasma
| PRJNA885395 | ENA
Project description:To obtain AIA_H related genes [the significant differentially expressed genes (DEGs) of AIA_H model group vs. Normal control group] and BHGZD therapeutic effect related genes [DEGs of BHGZD treatment group vs. AIA_H model group], the microarray analysis was carried out.
2021-12-11 | GSE190522 | GEO