Search results for "transcriptome"
showing 10 items of 610 documents
Assessing the reliability of gene expression measurements in very-low-numbers of human monocyte-derived macrophages
2019
Abstract Tumor-derived primary cells are essential for in vitro and in vivo studies of tumor biology. The scarcity of this cellular material limits the feasibility of experiments or analyses and hence hinders basic and clinical research progress. We set out to determine the minimum number of cells that can be analyzed with standard laboratory equipment and that leads to reliable results, unbiased by cell number. A proof-of-principle study was conducted with primary human monocyte-derived macrophages, seeded in decreasing number and constant cell density. Gene expression of cells stimulated to acquire opposite inflammatory states was analyzed by quantitative PCR. Statistical analysis indicat…
Identification and visualisation of differential isoform expression in RNA-seq time series
2017
AbstractAs sequencing technologies improve their capacity to detect distinct transcripts of the same gene and to address complex experimental designs such as longitudinal studies, there is a need to develop statistical methods for the analysis of isoform expression changes in time series data. Iso-maSigPro is a new functionality of the R package maSigPro for transcriptomics time series data analysis. Iso-maSigPro identifies genes with a differential isoform usage across time. The package also includes new clustering and visualization functions that allow grouping of genes with similar expression patterns at the isoform level, as well as those genes with a shift in major expressed isoform. T…
Disparity between Inter-Patient Molecular Heterogeneity and Repertoires of Target Drugs Used for Different Types of Cancer in Clinical Oncology
2020
Inter-patient molecular heterogeneity is the major declared driver of an expanding variety of anticancer drugs and personalizing their prescriptions. Here, we compared interpatient molecular heterogeneities of tumors and repertoires of drugs or their molecular targets currently in use in clinical oncology. We estimated molecular heterogeneity using genomic (whole exome sequencing) and transcriptomic (RNA sequencing) data for 4890 tumors taken from The Cancer Genome Atlas database. For thirteen major cancer types, we compared heterogeneities at the levels of mutations and gene expression with the repertoires of targeted therapeutics and their molecular targets accepted by the current guideli…
Transcriptome analysis of Phoenix canariensis Chabaud in response to Rhynchophorus ferrugineus Olivier attacks
2015
Red Palm Weevil (RPW, Rhynchophorus ferrugineus Olivier) threatens most palm species worldwide. Until now, no studies have analyzed the gene regulatory networks of Phoenix canariensis (Chabaud) in response to RPW attacks. The aim of this study was to fill this knowledge gap. Providing this basic knowledge is very important to improve its management.Results: A deep transcriptome analysis was performed on fully expanded leaves of healthy non-infested trees and attacked trees at two symptom stages (middle and late infestation). A total of 54 genes were significantly regulated during middle stage. Pathway enrichment analysis showed that phenylpropanoid-related pathways were induced at this stag…
A ceRNA approach may unveil unexpected contributors to deletion syndromes, the model of 5q- syndrome.
2015
In genomic deletions, gene haploinsufficiency might directly configure a specific disease phenotype. Nevertheless, in some cases no functional association can be identified between haploinsufficient genes and the deletion-associated phenotype. Transcripts can act as microRNA sponges. The reduction of transcripts from the hemizygous region may increase the availability of specific microRNAs, which in turn may exert in-trans regulation of target genes outside the deleted region, eventually contributing to the phenotype. Here we prospect a competing endogenous RNA (ceRNA) approach for the identification of candidate genes target of epigenetic regulation in deletion syndromes. As a model, we an…
Transcriptome Fingerprint of Bovine 2-Cell Stage Blastomeres Is Directly Correlated with the Individual Developmental Competence of the Corresponding…
2012
To date, gene expression profiles of bovine preimplantation embryos have only been indirectly related to developmental potential due to the invasive nature of such procedures. This study sought to find a direct correlation between transcriptome fingerprint of blastomeres of bovine 2-cell stage embryos with developmental competence of the corresponding sister blastomeres. Isolated blastomeres were classified according to the sister blastomere's development into three groups: two groups displayed developmental incompetency, including those blastomeres whose corresponding sister blastomeres either stopped cleaving after separation (2CB) or were blocked after two additional cleavages before emb…
Transcriptomic Signature of Trophoblast Differentiation in a Human Embryonic Stem Cell Model1
2011
Identification of genes involved in trophoblast differentiation is of great interest in understanding cellular and molecular mechanisms involved in placental development and is relevant clinically to fetal development, fertility, and maternal health. Herein, we investigated differentiation of human embryonic stem cells (hESCs) down the trophoblast lineage by culture with bone morphogenetic protein 4 (BMP4) over a 10-day period. Within 2 days, the stemness markers POU5F1 and NANOG were markedly down-regulated, followed temporally by up-regulation of the CDX2, KRT7, HLA-G, ID2, CGA, and CGB trophoblast markers. To understand, on a global scale, changes in the transcriptome during the differen…
CellLineNavigator: a workbench for cancer cell line analysis
2012
The CellLineNavigator database, freely available at http://www.medicalgenomics.org/celllinenavigator, is a web-based workbench for large scale comparisons of a large collection of diverse cell lines. It aims to support experimental design in the fields of genomics, systems biology and translational biomedical research. Currently, this compendium holds genome wide expression profiles of 317 different cancer cell lines, categorized into 57 different pathological states and 28 individual tissues. To enlarge the scope of CellLineNavigator, the database was furthermore closely linked to commonly used bioinformatics databases and knowledge repositories. To ensure easy data access and search abili…
The transcriptomes of columnar and standard type apple trees (Malus x domestica) - a comparative study.
2011
Columnar apple trees (Malus x domestica) provide several economic advantages due to their specific growth habit. The columnar phenotype is the result of the dominant allele of the gene Co and is characterized by thick stems with short internodes and reduced lateral branching. Co is located on chromosome 10 and often appears in a heterozygous state (Co/co). The molecular explanation of columnar growth is not well established. Therefore, we studied the transcriptomes of columnar and standard type apple trees using 454 and Illumina next generation sequencing (NGS) technologies. We analyzed the transcriptomes of shoot apical meristems (SAMs) because we expect that these organs are involved in f…
Stress responses in citrus peel: Comparative analysis of host responses to Huanglongbing disease and puffing disorder
2015
Abstract A comparison between transcriptomic responses to puffing disorder and Huanglongbing disease was conducted to decipher differences and similarities in gene and pathway regulation induced by abiotic (puffing) and biotic stresses (Huanglongbing) in citrus peel tissues. We functionally analyzed two previously published datasets: the first obtained for the study of puffing disorder using an Affymetrix citrus microarray and the second consisting of a deep sequencing analysis of symptomatic responses to Huanglongbing disease. Transcriptomic data were mined using bioinformatic tools to highlight genes and pathways playing a key role in modulating responses to different types of stress in c…