TY - GEN
T1 - Comparing and analysing gene expression patterns across animal species using 4DXpress
AU - Haudry, Yannick
AU - Ong, Chuang Kee
AU - Ettwiller, Laurence
AU - Berube, Hugo
AU - Letunic, Ivica
AU - Kapushesky, Misha
AU - Weeber, Paul Daniel
AU - Wang, Xi
AU - Gagneur, Julien
AU - Girardot, Charles
AU - Arendt, Detlev
AU - Bork, Peer
AU - Brazma, Alvis
AU - Furlong, Eileen
AU - Wittbrodt, Joachim
AU - Henrich, Thorsten
PY - 2008
Y1 - 2008
N2 - High-resolution spatial information on gene expression over time can be acquired through whole mount in-situ hybridisation experiments in animal model species such as fish, fly or mouse. Expression patterns of many genes have been studied and data has been integrated into dedicated model organism databases like ZFIN for zebrafish, MEPD for medaka, BDGP for drosophila or MGI for mouse. Nevertheless, a central repository that allows users to query and compare gene expression patterns across different species has not yet been established. For this purpose we have integrated gene expression data for zebrafish, medaka, drosophila and mouse into a central public repository named 4DXpress (http://ani.embl.de/4DXpress). 4DXpress allows to query anatomy ontology based expression annotations across species and quickly jump from one gene to the orthologs in other species based on ensembl-compara relationships. We have set up a linked resource for microarray data at ArrayExpress. In addition we have mapped developmental stages between the species to be able to compare corresponding developmental time phases. We have used clustering algorithms to classify genes based on their expression pattern annotations. To illustrate the use of 4DXpress we systematically analysed the relationships between conserved regulatory inputs and spatio-temporal gene expression derived from 4DXpress and found significant correlation between expression patterns of genes predicted to have similar regulatory elements in their promoters.
AB - High-resolution spatial information on gene expression over time can be acquired through whole mount in-situ hybridisation experiments in animal model species such as fish, fly or mouse. Expression patterns of many genes have been studied and data has been integrated into dedicated model organism databases like ZFIN for zebrafish, MEPD for medaka, BDGP for drosophila or MGI for mouse. Nevertheless, a central repository that allows users to query and compare gene expression patterns across different species has not yet been established. For this purpose we have integrated gene expression data for zebrafish, medaka, drosophila and mouse into a central public repository named 4DXpress (http://ani.embl.de/4DXpress). 4DXpress allows to query anatomy ontology based expression annotations across species and quickly jump from one gene to the orthologs in other species based on ensembl-compara relationships. We have set up a linked resource for microarray data at ArrayExpress. In addition we have mapped developmental stages between the species to be able to compare corresponding developmental time phases. We have used clustering algorithms to classify genes based on their expression pattern annotations. To illustrate the use of 4DXpress we systematically analysed the relationships between conserved regulatory inputs and spatio-temporal gene expression derived from 4DXpress and found significant correlation between expression patterns of genes predicted to have similar regulatory elements in their promoters.
UR - http://www.scopus.com/inward/record.url?scp=84863183397&partnerID=8YFLogxK
M3 - Conference contribution
AN - SCOPUS:84863183397
SN - 9781848161085
T3 - Series on Advances in Bioinformatics and Computational Biology
SP - 373
EP - 382
BT - Proceedings of 6th Asia-Pacific Bioinformatics Conference, APBC 2008
T2 - 6th Asia-Pacific Bioinformatics Conference, APBC 2008
Y2 - 14 January 2008 through 17 January 2008
ER -