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Islet Scanone

This study analyzes cell cycle transcripts in islet cells using Islet Scan software, identifying outliers and skewness scores. The results are presented through LOD profiles, rainbow plots, and peak summaries. The data is sorted by transcript skew score and mice mean expression.

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Islet Scanone

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  1. Islet Scanone Brian S. Yandell 28 jan 2008

  2. Cell Cycle Transcripts • 217 probes, ~200 genes • Clustered by islet mlratio • LOD threshold ~5

  3. Outline • Summaries of LOD profiles • Rainbow plots of whole genome scans • Summary of peaks by chromosome • Check for outliers/skew • Skewness score to identify outliers

  4. Schema for Plots(illustrated with cell cycle module) • False-color image of scanone • Column = transcript • Row = genome position • Color = LOD score (red = 10+, blue = 0) • cM and Mb scale when examining 1 chr • Adapted from R/qtl’s plot.scantwo • Peak summary using +s sized by LOD • 1 peak per chr per transcript • Size of + proportional to LOD • Only transcripts that pass genome threshold • Max(LOD) > 5 or so

  5. Check for outliers/skew • skewness(x) > 10 suggests problems • Apply by transcript (skew = 0 for ideal normal) • High skew tends to identify outliers • Watch out for missing values • Index is rank order, plotted against skew • Sort transcripts (row = horizontal) by skew • Note 1 transcript with many extreme values • Transcript 10002725449 • Mean 1.989410 • Sort mice (column = vertical) by magnitude • Note mice at top with many extreme values • ID Mouse3373 Mouse3435 Mouse3513 • Mean 0.1069200 0.1959556 0.2474012

  6. Mice ordered by (signed) mean expression Transcripts ordered by skew score (>10)

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