GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle - PubMed (original) (raw)

GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle

Aurélie Lardenois et al. Database (Oxford). 2010.

Abstract

GermOnline 4.0 is a cross-species database portal focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. It is thus a source of information for life scientists as well as clinicians who are interested in gene expression and regulatory networks. The GermOnline gateway provides unlimited access to information produced with high-density oligonucleotide microarrays (3'-UTR GeneChips), genome-wide protein-DNA binding assays and protein-protein interaction studies in the context of Ensembl genome annotation. Samples used to produce high-throughput expression data and to carry out genome-wide in vivo DNA binding assays are annotated via the MIAME-compliant Multiomics Information Management and Annotation System (MIMAS 3.0). Furthermore, the Saccharomyces Genomics Viewer (SGV) was developed and integrated into the gateway. SGV is a visualization tool that outputs genome annotation and DNA-strand specific expression data produced with high-density oligonucleotide tiling microarrays (Sc_tlg GeneChips) which cover the complete budding yeast genome on both DNA strands. It facilitates the interpretation of expression levels and transcript structures determined for various cell types cultured under different growth and differentiation conditions. Database URL: www.germonline.org/

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Figures

Figure 1.

The Saccharomyces Genomics Viewer. (a) A heatmap summarizes the data for diploid MATa/α cells cultured in rich media (YPD and YPA) and sporulation medium (1–12 h). Data for the top (+) and bottom (−) strand of a region covering 10 000 bp including the GAL locus are shown as log2-transformed signals (blue and red indicating low and high values, respectively; the database report page contains a scale). Each column corresponds to an oligonucleotide probe on the tiling arrays and each line corresponds to a sample as indicated. Chromosomal co-ordinates are given. Protein coding genes are displayed in blue, and ncRNAs in purple. Transcripts are symbolized by grey boxes. Differentially expressed segments are given in green and meiosis-specific segments are shown in red. Vertical lines represent transcript boundaries. Vertical yellow and red bars represent known and predicted Middle Sporulation Element (MSE) transcription factor target motifs, respectively. (b) Graphical display of Ye6100 GeneChip expression data obtained for CDC10 in two diploid MATa/α wild-type strains (W303 and SK1) cultured in YPA and sporulation medium (W303 2, 4, 6, 8, 10, 12 h; SK1 1, 2, 3, 4, 6, 8, 10 h) as compared to sporulation-deficient controls (W303 MATa/a and SK1 _MAT_α/α) cultured in YPA and sporulation medium (W303 2, 4, 6 h; SK1 2, 4, 6, 8 h). YPA samples are given in blue. The dotted red line represents the empirical expression-cutoff as published in (30). Log2-transformed signals and percentiles are indicated on the x-axis. (c) The GAL10 locus is shown in its genomic context and the target sequence covered by the oligonucleotide probe set present on Ye6100 is given in green (OLIGO Ye6100).

Figure 2.

Display of genome annotation, ChIP-Chip and microarray expression data. (a) Ensembl genome annotation for CDC3 and neighbouring loci. Protein-coding genes are red rectangles. Chromosomal coordinates are given. Regulatory motifs investigated by Harbison et al. (33) are shown. (b) In vivo binding of selected transcription factors including Abf1 to the CDC3 (YLR314C) up-stream region in haploid MATa cells cultured in rich medium with glucose (YPD). (c) Abf1 binding in samples from fermenting (YPD, red), respiring (YPA, blue) and sporulating (SPII 4 h and 8 h, green) cells. Signals for the upstream gene (TAD3), the CDC3 promoter (iCDC3) and the CDC3 coding region are given for comparison. (d) CDC3 mRNA expression data in strains containing homozygous wild-type (ABF1) or temperature sensitive (ts, abf1-1) alleles as well as strains bearing one wild-type or ts and one galactose-inducible allele (ABF1/GAL-ABF1; abf1-1/GAL-ABF1) at three different temperatures during growth and sporulation as indicated. Log2 ratios and the percentiles are indicated on the x-axis in (b), (c) and (d). For more information about Abf1 see reference (31).

Figure 3.

Protein interaction data display. Different interaction data available for Ndt80 are shown as an example. For clarity, users can choose to display only proteins found using a specific method, such as pull-down or select all interactions. Hyperlinks lead to the corresponding GermOnline gene report page and PubMed entries.

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GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle - PubMed (original) (raw)