Search results for "microarray"
showing 10 items of 401 documents
Neurobeachin (NBEA) is downregulated in blood cells from a patient with autism spectrum disorders (ASD)
2007
Identification of pathways involved in aneuploidy onset and its tolerance using a DNA microarray approach
2013
Genomic instability is a hallmark of the majority of human tumors explaining the heterogeneity shown by tumor cells. This phenomenon is often associated with chromosomal instability (CIN) and aneuploidy, a condition in which tumor cells lose or gain chromosomes. Previously, we showed that posttranscriptional silencing by RNAi of pRb1, DNMT12 and MAD2 is associated with aneuploidy in cultured human cells reinforcing the idea that there are several roads leading to aneuploidy. In the attempt to understand if a common molecular signature exists underlying aneuploidy and its tolerance in tumor cells, we induced aneuploidy in human fibroblasts (IMR90) by depleting Rb, MAD2 and DNMT1 genes and an…
Identification of molecular markers involved in cellular response to aneuploidy in normal and tumor cells
2020
Dal trascrittoma all’interattoma di miRNA: identificazione sperimentale e bioinformatica delle interazioni funzionali miRNA:mRNA
2013
I miRNA, piccole molecole endogene di RNA non codificante, regolano l’espressione genica attraverso la degradazione dei messaggeri (mRNA) o l’inibizione della traduzione. I miRNA maturi interagiscono con le proteine del complesso RISC (RNA-induced silencing complex) tra cui le proteine Argonaute (Ago), capaci di legare direttamente i miRNA e di mediare la regolazione dell’espressione genica in seguito alla interazione del miRNA con il proprio mRNA target. Un singolo miRNA può legare diversi mRNA e ciascun mRNA può essere regolato da diversi miRNA. La maggior parte dei software di predizione oggi disponibili individuano i putativi target di singoli miRNA ignorando caratteristiche di tipo glo…
A MULTI-LAYER MODEL TO STUDY GENOME-SCALE POSITIONS OF NUCLEOSOMES
2007
The positioning of nucleosomes along chromatin has been implicated in the regulation of gene expression in eukaryotic cells, because packaging DNA into nucleosomes affects sequence accessibility. In this paper we propose a new model (called MLM) for the identification of nucleosomes and linker regions across DNA, consisting in a thresholding technique based on cut-set conditions. For this purpose we have defined a method to generate synthetic microarray data fully inspired from the approach that has been used by Yuan et al. Results have shown a good recognition rate on synthetic data, moreover, the $MLM$ shows a good agreement with the recently published method based on Hidden Markov Model …
Speeding up the Consensus Clustering methodology for microarray data analysis
2010
Abstract Background The inference of the number of clusters in a dataset, a fundamental problem in Statistics, Data Analysis and Classification, is usually addressed via internal validation measures. The stated problem is quite difficult, in particular for microarrays, since the inferred prediction must be sensible enough to capture the inherent biological structure in a dataset, e.g., functionally related genes. Despite the rich literature present in that area, the identification of an internal validation measure that is both fast and precise has proved to be elusive. In order to partially fill this gap, we propose a speed-up of Consensus (Consensus Clustering), a methodology whose purpose…
Adaptive Techniques for Microarray Image Analysis with Related Quality Assessment
2007
We propose novel techniques for microarray image analysis. In particular, we describe an overall pipeline able to solve the most common problems of microarray image analysis. We pro- pose the microarray image rotation algorithm (MIRA) and the statis- tical gridding pipeline (SGRIP) as two advanced modules devoted to restoring the original microarray grid orientation and to detecting, the correct geometrical information about each spot of input mi- croarray, respectively. Both solutions work by making use of statis- tical observations, obtaining adaptive and reliable information about each spot property. They improve the performance of the microarray image segmentation pipeline (MISP) we rec…
proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis
2012
Abstract Background Throughout the metazoan lineage, typically gonadal expressed Piwi proteins and their guiding piRNAs (~26-32nt in length) form a protective mechanism of RNA interference directed against the propagation of transposable elements (TEs). Most piRNAs are generated from genomic piRNA clusters. Annotation of experimentally obtained piRNAs from small RNA/cDNA-libraries and detection of genomic piRNA clusters are crucial for a thorough understanding of the still enigmatic piRNA pathway, especially in an evolutionary context. Currently, detection of piRNA clusters relies on bioinformatics rather than detection and sequencing of primary piRNA cluster transcripts and the stringency …
ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis.
2015
Background: Cluster analysis is one of the most well known activities in scientific investigation and the object of research in many disciplines, ranging from statistics to computer science. It is central to the life sciences due to the advent of high throughput technologies, e.g., classification of tumors. In particular, in cluster analysis, it is of relevance to assess cluster quality and to predict the number of clusters in a dataset, if any. This latter task is usually performed via internal validation measures. Despite their potentially important role, both the use of classic internal validation measures and the design of new ones, specific for microarray data, do not seem to have grea…
Molecular mechanisms of sorafenib action in liver cancer cells.
2012
Sorafenib, a multikinase inhibitor, recently received FDA approval for the treatment of advanced hepatocellular carcinoma (HCC). However, as the clinical application of sorafenib evolves, there is increasing interest in defining the mechanisms underlying its anti-tumor activity. Considering that this specific inhibitor could target unexpected molecules depending on the biologic context, a precise understanding of its mechanism of action could be critical to maximize its treatment efficacy, while minimizing adverse effects. Two human HCC cell lines (HepG2 and Huh7), carrying different biological and genetic characteristics, were used in this study to examine the intracellular events leading …