title: The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain.
abstract: We are developing a three-dimensional (3D) atlas of the human embryonic brain using anatomical landmarks and gene expression data to define major subdivisions through 12 stages of development [Carnegie Stages (CS) 12-23; approximately 26-56 days post conception (dpc)]. Virtual 3D anatomical models are generated from intact specimens using optical projection tomography (OPT). Using MAPAINT software, selected gene expression data, gathered using standard methods of in situ hybridization and immunohistochemistry, are mapped to a representative 3D model for each chosen Carnegie stage. In these models, anatomical domains, defined on the basis of morphological landmarks and comparative knowledge of expression patterns in vertebrates, are linked to a developmental neuroanatomic ontology. Human gene expression patterns for genes with characteristic expression in different vertebrates (e.g. PAX6, GAD65 and OLIG2) are being used to confirm and/or refine the human anatomical domain boundaries. We have also developed interpolation software that digitally generates a full domain from partial data. Currently, the 3D models and a preliminary set of anatomical domains and ontology are available on the atlas pages along with gene expression data from approximately 100 genes in the HUDSEN Human Spatial Gene Expression Database (http://www.hudsen.org). The aim is that full 3D data will be generated from expression data used to define a more detailed set of anatomical domains linked to a more advanced anatomy ontology and all of these will be available online, contributing to the long-term goal of the atlas, which is to help maximize the effective use and dissemination of data wherever it is generated.
authors.affiliation: Institute of Human Genetics, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, UK. j.m.kerwin@ncl.ac.uk
authors.forename: Janet
authors.initials: J
authors.lastname: Kerwin
authors.forename: Yiya
authors.initials: Y
authors.lastname: Yang
authors.forename: Paloma
authors.initials: P
authors.lastname: Merchan
authors.forename: Subrot
authors.initials: S
authors.lastname: Sarma
authors.forename: Jessica
authors.initials: J
authors.lastname: Thompson
authors.forename: Xunxian
authors.initials: X
authors.lastname: Wang
authors.forename: Juan
authors.initials: J
authors.lastname: Sandoval
authors.forename: Luis
authors.initials: L
authors.lastname: Puelles
authors.forename: Richard
authors.initials: R
authors.lastname: Baldock
authors.forename: Susan
authors.initials: S
authors.lastname: Lindsay
mesh_terms: D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism; D001921:Brain / Q000196:embryology* / Q000378:metabolism*; D001931:Brain Mapping / Q000379:methods; D003196:Computer Graphics; D030541:Databases, Genetic; D005136:Eye Proteins / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression / Q000502:physiology*; D020869:Gene Expression Profiling / Q000379:methods; D018507:Gene Expression Regulation, Developmental / Q000502:physiology*; D005968:Glutamate Decarboxylase / Q000235:genetics / Q000378:metabolism; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008959:Models, Neurological; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism; D000076104:Oligodendrocyte Transcription Factor 2; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors / Q000235:genetics / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D041622:Tomography, Optical / Q000379:methods; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D005136:Eye Proteins; D005968:Glutamate Decarboxylase; D018398:Homeodomain Proteins; D009419:Nerve Tissue Proteins; D000076104:Oligodendrocyte Transcription Factor 2; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors; D012097:Repressor Proteins; D014157:Transcription Factors; C405708:OLIG2 protein, human; C000605730:PAX6 protein, human; C401141:glutamate decarboxylase 2