Method
Simplified ontologies allowing comparison of developmental mammalian gene expression
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* Corresponding author: Adele Kruger adele@sanbi.ac.za
1 South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
2 Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
3 Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
Genome Biology 2007, 8:R229 doi:10.1186/gb-2007-8-10-r229
Published: 25 October 2007Additional files
Additional data file 1:
Genes for human and mouse grouped together if they are expressed in post-natal or developmental brain, respectively. The intersection between the human and mouse developmental brain genes represent those genes showing common expression in the two species. Subtracting genes commonly expressed in human and mouse post-natal brain determines those genes that show developmental restriction in either human, mouse or both species.
Format: EPS Size: 636KB Download file
Additional data file 2:
The table lists the Entrez Gene identifier and gene symbol of the 9,378 human-mouse orthologs found not to have an expression bias towards the embryonic and fetal stages of brain development. Genes were considered for analysis only if they have an ortholog, and if the ortholog also has expression evidence based on eVOC annotation.
Format: XLS Size: 1.7MB Download file
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Additional data file 3:
The table lists the HomoloGene group identifier, Human Entrez Gene identifier, Human Entrez gene symbol, Mouse Entrez Gene identifier, Mouse Entrez gene symbol and the correlation coefficient between the expression profiles of the genes in each species.
Format: XLS Size: 29KB Download file
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Additional data file 4:
The tissues represented are female reproductive system, heart, kidney, liver, lung, male reproductive system and stem cell for both post-natal and developmental expression. The table lists the HomoloGene group identifier, Entrez Gene identifier and Entrez gene symbol for human and mouse, as well as the species each row represents. Values in the table are 1 if the genes (in rows) are expressed in the given tissues (in columns) and 0 if the genes are not found to be expressed in the tissues.
Format: XLS Size: 50KB Download file
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