Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1149538 | ENA |
REPOSITORIES: ENA
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Project description:Effective therapies for kidney transplant antibody-mediated rejection (ABMR) (Mayer et al, 2024) will require accurate diagnoses plus assessment of ABMR activity, and the new tests that were used to show treatment effects in the clinical trial such as donor-derived cell-free DNA (dd-cfDNA) and molecular biopsy analysis (MMDx) could be useful. ). In a partial correlation network, all four tests were correlated, in a hierarchy of inter-test correlations: MMDx ABMR > dd-cfDNA > histology ABMR > and DSA. Surprisingly, DSA correlated at least as strongly with MMDx ABMR as with histologic ABMR, even though DSA is not used in MMDx. When expressed in the same six rejection classes, MMDx diagnosed ABMR more frequently than histology. When histology disagreed with MMDx ABMR, dd-cfDNA, and DSA correlated more strongly with MMDx assessment. However, histology also detected ABMR lesions in some cases that MMDx called no rejection, correlating with subthreshold molecular ABMR activity and dd-cfDNA and DSA (AJT 25:72-87, 2024). Thus, the four-way inter-test correlations extend below current thresholds for diagnosing ABMR. Molecular rejection predicted outcomes better than histologic rejection in Trifecta, confirmed in the earlier INTERCOMEX study. These results map a network of four ABMR-related tests that can add precision to ABMR assessment in trials and clinical management and highlight the need to establish the clinical significance of subthreshold ABMR activity.
2025-07-23 | GSE288273 | GEO
Project description:Salmo trutta Raw sequence reads from dd-RAD sequencing
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Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.
2024-09-02 | MODEL2408160001 | BioModels
Project description:Validation of the RT-qPCR test by comparison with the 4-gene microarray test and the original random forest-based CMS (consensus molecular subtypes) classifier
2017-08-01 | GSE85043 | GEO
Project description:Digital dermatitis (DD) causes lameness in dairy cattle. To detect quantitative trait loci (QTL) associated with DD, genome-wide association studies (GWAS) were performed using high density single nucleotide polymorphism (SNP) genotypes and binary case/control, quantitative (average number of FW per hoof trimming record), and recurrent (cases with 2 DD episodes vs. controls) phenotypes from cows across four dairies (controls n = 129 vs. FW n = 85). Linear mixed model (LMM) and random forest (RF) approaches identified top SNPs, which were used as predictors in Bayesian regression models to assess SNP predictive value. The LMM and RF analyses identified a QTL on BTA1 for the binary phenotype and on BTA2 for the quantitative phenotype. The binary and recurrent LMM GWASs also detected a QTL on BTA2 that was at a different position than the QTL from the quantitative phenotype analysis. The QTL on BTA1 lacked apparent candidate genes, whereas both QTL on BTA2 included genes associated with immune response and wound healing. Although larger sample sizes are necessary to reaffirm these small effect loci amidst a strong environmental effect, the sample cohort used in this study was sufficient for estimating SNP effects with high predictive value.
2020-12-07 | GSE159157 | GEO
Project description:Purpose: The goal of this study is to evaluate transcriptional regulation of the accumulation of phenols and anthocyanins in young leaves of subtropical forest tree species by using NGS-derived RNA-seq. Methods: Leaf mRNA profiles of subtropical tree Schima superba and Cryptocarya concinna grown under contasting light were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. FPKM produced by RSEM are provided. Results: Assemblies of the sequence data yielded 61,618 and 64,413 unigenes for Schima superba and Cryptocarya concinna,respectively. Overall,75.14% and 66.46% of the unigenes were annotated in the protein database Nonredundant protein (Nr), Nonredundant nucleotide (Nt), Swiss-Prot、Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG) and Gene Ontology (GO) for S. superba and C concinna,respectively.A total of 3896, 3488 and 266 genes were differentially expressed in full light-exposed young leaf (FLY), low light-exposed young leaf (LYL) and low light-exposed mature leaf (LML) relative to low light-exposed mature leaf (FML) of S. superba, respectively, and 2097, 2047 and 211 genes were differentially expressed in the corresponding leaves of C. concinna. Conclusions: Our study represents the first detailed analysis of transcriptomes in young and mature leaves of dorminant trees from a subtropical forest in China, with biologic replicates, generated by RNA-seq technology. Photosynthesis-related genes and phenol pathways-related genes were extensively down- and up-regulated in young versus mature leaves of the two species.
2018-10-01 | GSE104004 | GEO