Observatorio de I+D+i UPM

Memorias de investigación
Research Publications in journals:
Digital framework to build, visualize and analyze gene expression atlases with cellular resolution in zebrafish early embryogenesis
Year:2013
Research Areas
  • Electronic technology and of the communications
Information
Abstract
Gene expression atlases at the cellular level are a fundamental resource to quantify and understand embryogenesis multiscale processes in time and space.The automated reconstruction of prototypic atlases from multiple fluorescent in situ hybridization and nuclear counterstaining observed in 3D requires the development of dedicated computational strategies. Match-IT is an original tool requiring minimal human supervision to gather in a reference specimen, with resolution at the cellular level, gene expression patterns observed at various developmental stages from multiple fluorescent staining in different individuals with phenotypic variability. This framework was used to build a gene expression atlas for the zebrafish early embryogenesis from 51 different specimens, about 200,000 cell nuclei, 96 gene expression patterns for 9 different genes and 6 time cohorts spanning from 4 to 6.3 hpf (hours post fertilization). An interactive visualization application, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Automatic methods and tools are also proposed here to allow the assessment of gene expression at the single cell level and the automated identification, visualization and analysis of co-expression patterns and synexpression groups with their dynamics through developmental stages in a vertebrate early embryo.
International
Si
JCR
Si
Title
Nature Methods
ISBN
1548-7091
Impact factor JCR
19,276
Impact info
Datos JCR del año 2011
Volume
Journal number
From page
0
To page
0
Month
SIN MES
Ranking
Participants
  • Autor: Carlos Castro Gonzalez (UPM)
  • Autor: Miguel Angel Luengo Oroz (UPM)
  • Autor: Louise Duloquin ((Institut de Neurobiologie Alfred Fessard, CNRS)
  • Autor: Thierry Savy (Institut des Systèmes Complexes, École Polytechnique)
  • Autor: Barbara Rizzi (Institut de Neurobiologie Alfred Fessard, CNRS)
  • Autor: Sophie Desnoulez (Institut de Neurobiologie Alfred Fessard, CNRS)
  • Autor: Yannick Kergosien (Institut des Systèmes Complexes, École Polytechnique)
  • Autor: Maria Jesus Ledesma Carbayo (UPM)
  • Autor: Paul Bourgine (Institut des Systèmes Complexes, École Polytechnique)
  • Autor: Nadine Peyriéras (Institut de Neurobiologie Alfred Fessard, CNRS)
  • Autor: Andres de Santos Lleo (UPM)
Research Group, Departaments and Institutes related
  • Creador: Departamento: Ingeniería Electrónica
S2i 2020 Observatorio de investigación @ UPM con la colaboración del Consejo Social UPM
Cofinanciación del MINECO en el marco del Programa INNCIDE 2011 (OTR-2011-0236)
Cofinanciación del MINECO en el marco del Programa INNPACTO (IPT-020000-2010-22)