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Although a huge amount of mammalian genomic data does become publicly available, …

Biology Articles » Bioinformatics » Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells » Figures

- Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells

mcith_btm430f1.gif Figure 1 An overview of the web-based query interface and retrieval system for the RefDIC server. A user can submit various types of query to view gene expression profiles and to retrieve the experimental raw data, such as CEL files, from the web interface.

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mcith_btm430f2.gif Figure 2 (A) Box and whisker plot of mean hybridization signal intensities for probe set categories A, B and C on Mouse430_2 across 119 samples. The expression level for each was calculated using the gcRMA algorithm. (B) Similarity of expression patterns between probe-set pairs to which the same gene was assigned, though into different categories. The numerals in each element of the triangular matrix represent the average Pearson's correlation coefficients (r) for the expression patterns across the samples between the probe-set pairs. (C) Distribution of Pearson's correlation coefficients between the mRNA and protein levels in the 166 genes when the probe sets in category A were used (black bar) and when those in categories B or C were used (white bar).

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mcith_btm430f3.gif Figure 3 (A) A query form for visualization of mRNA profiling data. Users can search and retrieve the mRNA profiling data for genes of interest with various types of query (i.e. gene symbol, gene/protein name, accession number of mRNA or protein sequences, GO terms or Pfam domain name). (B) When the users submit a query, the RefDIC server returns the list of genes available for visualization. Users can select the genes/probe sets, cell types or data processing type that they want to view.

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mcith_btm430f4.GIF Figure 4 (A) A snapshot of the mRNA profile view. The mRNA levels for the probe sets are represented as a heat map of the different mouse samples. The top and second rows of the heat map represent the types of cell or organ, respectively. The red and green colors in the heat map show high and low mRNA levels, respectively. In this case, three probe sets (1426165_a_at, 1430192_at and 1449839_at) are mapped to caspase 3. When users click the probe set name shown this figure, they can view the genomic positions of these probe sets (inset). (B) Two examples of visualization of mRNA and protein levels: ornithine aminotransferase (left panel) and peroxiredoxin 3 (right panel) are shown. The levels of both mRNA and protein are represented by the relative values in log2 space.

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