Web-based analysis of the mouse transcriptome using Genevestigator - PubMed (original) (raw)

Web-based analysis of the mouse transcriptome using Genevestigator

Oliver Laule et al. BMC Bioinformatics. 2006.

Abstract

Background: Gene function analysis often requires a complex and laborious sequence of laboratory and computer-based experiments. Choosing an effective experimental design generally results from hypotheses derived from prior knowledge or experimentation. Knowledge obtained from meta-analyzing compendia of expression data with annotation libraries can provide significant clues in understanding gene and network function, resulting in better hypotheses that can be tested in the laboratory.

Description: Genevestigator is a microarray database and analysis system allowing context-driven queries. Simple but powerful tools allow biologists with little computational background to retrieve information about when, where and how genes are expressed. We manually curated and quality-controlled 3110 mouse Affymetrix arrays from public repositories. Data queries can be run against an annotation library comprising 160 anatomy categories, 12 developmental stage groups, 80 stimuli, and 182 genetic backgrounds or modifications. The quality of results obtained through Genevestigator is illustrated by a number of biological scenarios that are substantiated by other types of experimentation in the literature.

Conclusion: The Genevestigator-Mouse database effectively provides biologically meaningful results and can be accessed at https://www.genevestigator.ethz.ch.

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Figures

Figure 1

Figure 1

Validation of expression profiles. The results shown were calculated from 2138 arrays of type MG-U74Av2 (12 K). Similar results can be obtained using arrays of type Mouse430 2.0 (40 K) for categories available in both array types. For each gene, the signal intensity value indicated in each category is the average signal intensity value (of the corresponding probe set) from all arrays within this category. Average signal intensity values are available throughout all shown categories for all probe sets represented on the 12 K array. A. Anatomy expression profiles of genes shown in the literature to be preferentially expressed in muscle and heart (Mm.234274) or in retina (Mm.2965, Mm.39200, Mm.8008, Mm.20422). B1-B3. Development expression profiles of three genes previously shown to be expressed in oocytes and up to the 8-cell stage (Mm.28010), between E7.5 and E8.5 (Mm.197), and in adult mouse but low in embryo or newborn mice (Mm.3485). Developmental stages are defined as pre-natal (given in Theiler stages (TS); a: TS-1 to 2, b: TS-3 to 5, c: TS-6 to 9, d: TS-10 to 13, e: TS-14 to 18, f: TS-19 to 23, g: TS-24 to 27) or post-natal (given in days after birth; h: 0–3, i: 4–15, j: 16–63, k: 64–255, l: > 256). C and D. Response of Sirt1 (Mm.351459) to a set of stimuli (C) and to genetic modifications (D). Only treatments or mutations inducing strong up or down regulation are shown. Effects described in the text are highlighted. These precompiled responses are log-ratios from the average signal intensity values of treatment versus control samples from a variety of experiments and tissues.

Figure 2

Figure 2

Identification of marker genes. Hierarchical cluster of the top 30 genes preferentially or specifically expressed in the heart. Results were calculated from 2138 arrays of type MG-U74Av2 (12 K).

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