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Figure 1 | BMC Genomics

Figure 1

From: Relationship between gene co-expression and probe localization on microarray slides

Figure 1

Pair Correlation as a Function of Chromosomal Separation. Co-expressed and co-localized gene pair distributions as a function of the pair chromosomal distance for the alpha factor arrested cell cycle dataset [15]. We defined co-expression by selecting gene pairs that have a correlation coefficient >0.7 across the time course experiments. The pair distance was measured in terms of the number of ORFs separating its individual genes (blue curve). The distribution of the chip co-localized pairs (red curve) was constructed using pairs constrained to chip distances smaller than 12.5% of the maximal possible pair distance. Both distributions are enriched at a small chromosomal distance and share short and long range periodicities of 2 and 22 ORFs. These periodicities are pure artifacts, whereas the enrichment is partially biological. The chip design is such that nearest neighbor genes on the chromosome are printed in different blocks on the microarray chips whereas next nearest neighbor genes are printed in the same vicinity on the chip. This is correlated with the short-range periodicity as reflected in the staggered pattern shown in Fig 1a. Legend for this figure: blue curve: pairs with correlation >0.7 red curve: pairs with slide spacing <12.5% maximal spacing

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