Search results for " transcriptomic."

Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects

2016

BACKGROUND: Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the origin of IBPs in insects and other arthropods. RESULTS: Our study shows that the last common ancestor of insects (Hexapoda) already possessed a substantial numbe…

FUNCTIONAL GENOMIC APPROACHES TO ELUCIDATE BIOTIC AND ABIOTIC STRESS RESPONSES IN PLANTS

ITCH E3 ubiquitin ligase downregulation compromises hepatic degradation of branched-chain amino acids

2022

Objective: Metabolic syndrome, obesity, and steatosis are characterized by a range of dysregulations including defects in ubiquitin ligase tagging proteins for degradation. The identification of novel hepatic genes associated with fatty liver disease and metabolic dysregulation may be relevant to unravelling new mechanisms involved in liver disease progression Methods: Through integrative analysis of liver transcriptomic and metabolomic obtained from obese subjects with steatosis, we identified itchy E ubiquitin protein ligase (ITCH) as a gene downregulated in human hepatic tissue in relation to steatosis grade. Wild-type or ITCH knockout mouse models of non-alcoholic fatty liver disease (N…

Gaining Insight into Exclusive and Common Transcriptomic Features Linked with Biotic Stress Responses in Malus

2017

Identifying key information in transcriptomic data is very important, especially when the “omic” study deals with plant responses to stresses in field conditions where a high number of variables and disturbing factors may affect the analysis. In this meta-analysis we collected 12 transcriptomic works in Malus in order to identify which key genes, proteins, gene categories are involved in general plant pathological conditions and those features linked with exclusive biotic stress responses. Those genes that are only related with molecular responses to pathogen attacks and those linked with other plant physiological processes were identified. A pipeline composed by pathway and gene set enrich…

Novel insights in the genetics of HCC recurrence and advances in transcriptomic data integration.

2011

Background & Aims: In approximately 70% of patients with hepatocellular carcinoma (HCC) treated by resection or ablation, disease recurs within 5 years. Although gene expression signatures have been associated with outcome, there is no method to predict recurrence based on combined clinical, pathology, and genomic data (from tumor and cirrhotic tissue). We evaluated gene expression signatures associated with outcome in a large cohort of patients with early stage (Barcelona-Clinic Liver Cancer 0/A), single-nodule HCC and heterogeneity of signatures within tumor tissues. Methods:We assessed 287 HCC patients undergoing resection and tested genome-wide expression platforms using tumor (n = 287)…

Transcriptional changes through menstrual cycle reveal a global transcriptional derepression underlying the molecular mechanism involved in the windo…

2021

The human endometrium is a dynamic tissue that only is receptive to host the embryo during a brief time in the middle secretory phase, called the window of implantation (WOI). Despite its importance, regulation of the menstrual cycle remains incompletely understood. The aim of this study was to characterize the gene cooperation and regulation of menstrual cycle progression, to dissect the molecular complexity underlying acquisition of endometrial receptivity for a successful pregnancy, and to provide the scientific community with detailed gene co-expression information throughout the menstrual cycle on a user-friendly web-tool database. A retrospective gene co-expression analysis was perfor…

Deciphering transcriptional regulation mechanisms underlining fruit development and ripening in Vitis vinifera

2019

BACKGROUND: Grapes (Vitis vinifera ) are an important woody crop cultivated in a broad range of environmental conditions. Grapefruit development is a physiological process whose molecular regulatory networks are still not sufficiently investigated. OBJECTIVE: The primary aim of the work was to identify which key genes, molecular mechanisms and networks were involved in fruit ripening and development through a comparison of available transcriptomic data at different stages during grape development and ripening. Secondly, we aimed at identifying among these fruit-related genes, which genes play also a functional role in other developmental and physiological processes in reproductive tissues (…

Análisis transcriptómico del daño por frío en fruto de melocotón

2016

En la industria hortofrutícola las bajas temperaturas se utilizan para retrasar la maduración y el decaimiento de los frutos. A pesar de tener un uso extendido, los frutos de melocotón sometidos a almacenamiento prolongado en frío (CS) a menudo desarrollan una forma de daño por frío (CI) genéticamente controlada llamada harinosidad (mealiness/woolliness [WLT]): un desorden textural de la pulpa del fruto caracterizado por la perdida de suculencia Aunque durante el frío se han observado algunas alteraciones microscópicas, los síntomas visibles o macroscópicos de daño se desarrollan, no obstante, cuando los frutos se transfieren a temperatura ambiente (temperaturas de simulación de vida útil, …

Integrative Gene Expression and Metabolic Analysis Tool IgemRNA

2022

ABSTRACTGenome scale metabolic modelling is widely used technique to research metabolism impacts on organism’s properties. Additional omics data integration enables a more precise genotype-phenotype analysis for biotechnology, medicine and life sciences. Transcriptome data amounts rapidly increase each year. Many transcriptome analysis tools with integrated genome scale metabolic modelling are proposed. But these tools have own restrictions, compatibility issues and the necessity of previous experience and advanced user skills. We have analysed and classified published tools, summarized possible transcriptome pre-processing, and analysis methods and implemented them in the new transcriptome…

Transcriptome and metabolome analysis of citrus fruit to elucidate puffing disorder.

2014

a b s t r a c t A systems-level analysis reveals details of molecular mechanisms underlying puffing disorder in Citrus fruit. Flavedo, albedo and juice sac tissues of normal fruits and fruits displaying symptoms of puffing disorder were studied using metabolomics at three developmental stages. Microarrays were used to compare normal and puffed fruits for each of the three tissues. A protein-protein interaction network inferred from previous work on Arabidopsis identified hub proteins whose transcripts show significant changes in expression. Glycolysis, the backbone of primary metabolism, appeared to be severely affected by the disorder, based on both transcriptomic and metabolomic results. …