Scheetz2006: Gene expression in the mammalian eye

In pbreheny/hdrm: High-Dimensional Regression Modeling

Gene expression in the mammalian eye

Description

In this study, laboratory rats (Rattus norvegicus) were studied to learn about gene expression and regulation in the mammalian eye. Inbred rat strains were crossed and tissue extracted from the eyes of 120 animals from the F2 generation. Microarrays were used to measure levels of RNA expression in the isolated eye tissues of each subject.

Of the 31,000 different probes, 18,976 were detected at a sufficient level to be considered “expressed” in the mammalian eye. For the purposes of this analysis, we treat one of those genes, Trim32, as the outcome. Trim32 is known to be linked with a genetic disorder called Bardet-Biedl Syndrome (BBS): the mutation (P130S) in Trim32 gives rise to BBS. For this reason, Trim32 is also sometimes called Bbs11.

Format

• y: Gene expression measurement for Trim32

• X: Gene expression measurements for remaining genes

Dimensions

• n = 120

• p = 18,975

Annotation

• The object fData contains the associated gene names, gene symbols, and chromosome locations for the (mapped) probes in X. Rows of fData correspond to columns of X, and are named accordingly.

References

Scheetz TE, Kim K-YA, Swiderski RE, Philp AR, Braun TA, Knudtson KL, Dorrance AM, DiBona GF, Huang J, Casavant TL, Sheffield VC and Stone EM (2006). Regulation of gene expression in the mammalian eye and its relevance to eye disease. Proceedings of the National Academy of Sciences, 103: 14429-14434.

pbreheny/hdrm documentation built on May 24, 2024, 9:30 p.m.