Yang Yu Similar Datasets
Project description:Antibody recognition of Trypanosoma cruzi conserved proteins was assessed by evaluating pools of patient IgG samples on microarrays of 400,000 peptides covering these proteins as 15-mers with an overlap of 13 amino acids.
2024-02-28 | GSE235074 | GEO
Project description:This study used SomaScan v 4.1 to profile>7000 proteins in human plasma KOREF1.
2025-11-25 | GSE310463 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE30721: Profiling proteome-scale antibody responses to M. tuberculosis proteins in sera of macaques infected with M. tuberculosis GSE30722: Profiling proteome-scale antibody responses to M. tuberculosis proteins in TB suspect's sera Refer to individual Series
2012-07-05 | E-GEOD-31368 | biostudies-arrayexpress
Project description:This study used SomaScan v 4.1 to profile>7000 proteins in maternal plasma and asses changes with gestational age and maternal characteristics. The study proposed models to estimate the expected protein abundance so that future datasets can be normalized agains these expected value to obtain Multiples of the Mean values.
2022-09-26 | GSE206454 | GEO
Project description:We performed genome-wide transcriptome and proteome analyses of the Fusarium fujikuroi wild type and ΔAREA and ΔAREB mutants under nitrogen limitation and excess. Microarray analysis revealed that each transcription factor regulates a total set of about 4200 genes under nitrogen limiting conditions with an enrichment of genes belonging to functional classes of primary/secondary metabolism, transporters, cell defense/virulence and transcription. Under nitrogen excess, AreA is not active as a transcriptional regulator, while AreB affects expression of about 4400 genes. Both transcription factors regulate a common set of about 2100 genes and most of the time work together either as positive or as negative regulators. Our proteomics analysis identified 446 AreA-regulated and 386 AreB-regulated proteins at nitrogen limitation and 138 AreA-regulated and 447 AreB-regulated proteins at nitrogen excess, respectively. Comparison of the proteome and transcriptome data indicates that many post-transcriptional regulations are facilitated by both GATA-factors, for example on enzymes involved in the TCA and glyoxylate cycle and the main glutamate/glutamine cycling.
2017-05-10 | GSE80480 | GEO
Project description:Different forms of N can affect plant metabolism. Differences can be observed at physiological and transcriptional levels comparing maize 4-day-old maize seedlings tretaed for three days with three different N forms: protein hydrolysates (SICIT2000 Spa), inorganic nitrogen (NH4H2PO4) or a mixture of free amino acids.
2017-04-26 | GSE89535 | GEO
Project description:To improve the power of mediation in high-throughput studies, here we introduce High-throughput mediation analysis (Hitman), which accounts for direction of mediation and applies empirical Bayesian linear modeling. We apply Hitman in a retrospective, exploratory analysis of the SLIMM-T2D clinical trial in which participants with type 2 diabetes were randomized to Roux-en-Y gastric bypass (RYGB) or nonsurgical diabetes/weight management, and fasting plasma proteome and metabolome were assayed up to 3 years. RYGB caused greater improvement in HbA1c, which was mediated by growth hormone receptor (GHR). GHR’s mediation is more significant than clinical mediators, including BMI. GHR decreases at 3 months postoperatively alongside increased insulin-like growth factor binding proteins IGFBP1/BP2; plasma GH increased at 1 year. Experimental validation indicates (1) hepatic GHR expression decreases in post-bariatric rats; (2) GHR knockdown in primary hepatocytes decreases gluconeogenic gene expression and glucose production. Thus, RYGB may induce resistance to diabetogenic effects of GH signaling.
2021-08-24 | GSE122279 | GEO
Project description:Recent work has bolstered the possibility that peripheral changes may be relevant to Alzheimer’s disease pathogenesis in the brain. While age-associated blood-borne proteins have been targeted to restore function to the aged brain, it remains unclear whether other dysfunctional systemic states can be exploited for similar benefits. Here we investigate whether APOE allelic variation or presence of brain amyloid are associated with plasma proteomic changes and the molecular processes associated with these changes. Using the SOMAscan assay, we measured 1,305 plasma proteins from 53 homozygous, APOE3 and APOE4 subjects without dementia. We investigated the relationship of either the APOE-ε4 allele or amyloid positivity with plasma proteome changes by linear mixed effects modeling and ontology-based pathway and module trait correlation analyses. APOE4 is associated with plasma protein differences linked to atherosclerosis, tyrosine kinase activity, cholesterol transport, extracellular matrix, and synaptogenesis pathways. Independent of APOE4, we found that subjects likely harboring brain amyloid exhibit plasma proteome signatures associated with AD-linked pathways, including neurovascular dysfunction. Our results indicate that APOE4 status or presence of brain amyloid are associated with plasma proteomic shifts prior to the onset of symptoms, suggesting that systemic pathways in certain risk contexts may be plausible targets for disease modification.
2025-02-19 | GSE275392 | GEO
Project description:Our objective was to identify the potential autoantibody markers in meningiomas using high-density human proteome arrays (~17,000 full-length recombinant human proteins). This study revealed the dysregulation of 489 and 104 proteins in grades I and II of meningioma, respectively, along with the enrichment of signalling pathways which play a major role in the manifestation of the disease. This study revealed the dysregulation of 489 and 104 proteins in grades I and II of meningioma, respectively, along with the enrichment of signalling pathways which play a major role in the manifestation of the disease. Autoantibody targets like IGHG4, CRYM, EFCAB2, STAT6, HDAC7A and CCNB1 were dysregulated across both grades.
2016-06-21 | GSE83507 | GEO
Project description:The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides was lacking. To this end, Akhilesh Pandey's lab reported a draft map of the human proteome based on high resolution Fourier transform mass spectrometry-based proteomics technology, which included an in-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells ( http://dx.doi.org/10.1038/nature13302 ). The profiling resulted in identification of proteins encoded by greater than 17,000 genes accounting for ~84% of the total annotated protein-coding genes in humans. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) complements available human genome and transcriptome data to accelerate biomedical research in health and disease. Pandey's lab and collaborators request that those considering use of this primary dataset for commercial purposes contact pandey@jhmi.edu. The full details of this study can be found in the PRIDE database: www.ebi.ac.uk/pride/archive/projects/PXD000561/. This ArrayExpress entry represents a top level summary of the metadata only which formed the basis of the reanalysis performed by Joyti Choudhary's team ( jc4@sanger.ac.uk ), results of which are presented in the Expression Atlas at EMBL-EBI : http://www.ebi.ac.uk/gxa/experiments/E-PROT-1.
2015-03-10 | E-PROT-1 | biostudies-arrayexpress