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For all tasks, male and female mice in the 129B6 genetic background were generated from heterozygous matings and all tests used mutant mice with their respective wild type littermates as controls.
Apoe−/− mice, which were on the C57BL/6 genetic background, were generated from breeding pairs purchased from the Jackson Laboratory, Bar Harbor, ME.
Cx3cr1 −/− /Ccl2 −/− mouse strains on C57BL/6 background were generated from Cx3cr1 −/− mice (Combadiere et al, 2003) and Ccl2 −/− mice (from B. Rollins, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA).
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Shh+/– mice on a C57BL/6J genetic background were generated as previously described, and were obtained from Cyagen Biosciences (Santa Clara, CA, USA).
Dgat1−/− mice (C57BL/6J background) were generated as described [ 8].
E1-DN mice in FVB background were generated previously [ 31].
HBx transgenic mice (C57B/6 background) were generated as described.
Background data were generated from 500-bp upstream sequences from the TSSs of rice genes, of which the gene expression ratio was between 0.8 and 1.2.
Raw data with a global background subtraction were generated from GenePix pro 6.0.
For each spatial pattern in Simu 1 and Simu 2, counts Y i were generated as follows: Counts in all background areas were generated from a Poisson distribution with mean E i.
In fdrMotif search, for each input sequence 10 background sequences were generated from a 4th-order Markov model and an upper boundary of false discovery rate (FDR) of 0.15 as suggested by fdrMotif was adopted to control FDR.
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