Titre :

Latent network-based representations for large-scale gene expression data analysis

Auteur(s) :

Dhifli, Wajdi [Auteur]
Université de Lille
Puig, Julia [Auteur]
Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé [CREATIS]
Modeling & analysis for medical imaging and Diagnosis [MYRIAD]
Dispot, Aurélien [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Elati, Mohamed [Auteur correspondant]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]

Titre de la revue :

BMC Bioinformatics

Pagination :

466

Éditeur :

BioMed Central

Date de publication :

2019-02-04

ISSN :

1471-2105

Mot(s)-clé(s) en anglais :

Latent signals
Network-based transformations
Gene expression
Gene perturbation
Regulator activity

Discipline(s) HAL :

Sciences du Vivant [q-bio]
Informatique [cs]

Résumé en anglais : [en]

AbstractBackground: With the recent advancements in high-throughput experimental procedures, biologists are gathering huge quantities of data. A main priority in bioinformatics and computational biology is to provide system ...
Lire la suite >AbstractBackground: With the recent advancements in high-throughput experimental procedures, biologists are gathering huge quantities of data. A main priority in bioinformatics and computational biology is to provide system level analytical tools capable of meeting an ever-growing production of high-throughput biological data while taking into account its biological context. In gene expression data analysis, genes have widely been considered as independent components. However, a systemic view shows that they act synergistically in living cells, forming functional complexes and more generally a biological system.Results: In this paper, we propose LATNET , a signal transformation framework that, starting from an initial large-scale gene expression data, allows to generate new representations based on latent network-based relationships between the genes. LATNET aims to leverage system level relations between the genes as an underlying hidden structure to derive the new transformed latent signals. We present a concrete implementation of our framework, based on a gene regulatory network structure and two signal transformation approaches, to quantify latent network-based activity of regulators, as well as gene perturbation signals. The new gene/regulator signals are at the level of each sample of the input data and, thus, could directly be used instead of the initial expression signals for major bioinformatics analysis, including diagnosis and personalized medicine.Conclusion: Multiple patterns could be hidden or weakly observed in expression data. LATNET helps in uncovering latent signals that could emphasize hidden patterns based on the relations between the genes and, thus, enhancing the performance of gene expression-based analysis algorithms. We use LATNET for the analysis of real-world gene expression data of bladder cancer and we show the efficiency of our transformation framework as compared to using the initial expression data.Lire moins >

Langue :

Anglais

Vulgarisation :

Non

Projet ANR :

Adaptive Automated Scientific Laboratory

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL