Computational identification of transcriptionally co-regulated genes, validation with the four ANT isoform genes
1 INRA, UMR 1019, Unité de Nutrition Humaine, 63122, St Genès-Champanelle, France
2 Université d'Auvergne, Unité de Nutrition Humaine, Clermont Université, BP 10448, 63000, Clermont-Ferrand, France
3 Institut des Neurosciences, Equipe Nanomédecine et Cerveau, Inserm U836, 38700, La Tronche, France
4 Université Joseph Fourier 1, Grenoble, 38041, France
5 Plate-forme Transcriptome et Protéome Cliniques, Institut de Biologie et Pathologie, CHU Grenoble, 38043, Grenoble, France
6 CNRS, 38042, Grenoble, France
BMC Genomics 2012, 13:482 doi:10.1186/1471-2164-13-482Published: 15 September 2012
Additional file 1:
ANT gene sequences in mammals. Mammalian ANT gene sequences selected for the 4 ANT isoforms in 24 mammals. Sequences were extracted from EnsEMBL database. Sequences in bold are sequences that do not contain undetermined bases in their promoter and are not too divergent from the corresponding human sequence.
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Additional file 2:
ANT gene models in mammals. Matrix families (i.e. V$MEF2), matrices (i.e. V$NRF2.01) and IUPAC strings from the four human ANTs gene promoters. For matrix families, an example of IUPAC string is shown. For matrices, only nucleotides (IUPAC) with high information content are presented (the matrix exhibits a high conservation at this position). For matrices, nucleotides in bold capital letters denote the core sequence used by MatInspector (defined as the highest, usually four, conserved consecutive positions) . The other nucleotides are from the flanking sequence. Motifs with an asterisk were identified from phylogenetic analyses. IUPAC nucleotide code: R (A or G); Y (C or T); S (G or C); W (A or T); K (G or T); M (A or C); B (C or G or T); D (A or G or T); H (A or C or T); V (A or C or G); N (any base).
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Additional file 3:
Scatter plots of the expression levels of genes with identical promoter models with the ANT promoters in different tissues.ANT1: average expression levels of the genes from Table 2 in the lung, skin and brain tissues versus their expression in muscle. ANT2: average expression levels of the genes from Table 3 in normal brain tissue versus their expression in glioblastoma. ANT3: average expression levels of the genes from Additional file 5 in normal brain tissue versus their expression in glioblastoma. ANT4: average expression levels of the genes from Table 4 in the lung, skin and brain tissues versus their expression in testis. Red diamonds correspond to over-expressed genes with at least a 1.5 fold changes between tissues.
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Additional file 4:
Genes co-regulated with the ANT3 gene. The full set of results obtained from the analysis with all constructed models of the ANT3 promoter regions were screened as described in Figure 1 either on the whole chromosome human sequences or the human promoter library (results with an asterisk). The gene in bold is shown overexpressed in microarrays. Gene IDs are with 15 numbers (ex. ENSG00000023228).
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Additional file 5:
Expression levels of genes that share promoter models with ANT genes in different tissues. Expression levels of genes that share promoter models with ANT promoters in different tissues. Data were obtained from hybridization experiments using Affymetrix genechips as described in material and methods. Y scale in log2 of the average values of the ratios. An average value of the ratios was also calculated for each gene whose expression was assessed by several probe sets.
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