control_genes {scone} | R Documentation

## Data: Positive and Negative Control Genes

### Description

Sets of "positive" and "negative" control genes, useful arguments for `scone`.

### Details

These gene sets can be used as negative or positive controls, either for RUV factor normalization or for evaluation and ranking of the normalization workflows.

Gene set datasets are in the form of `data.frame`, with the first column containing the gene symbols and an (optional) second column containing additional information (such as cortical layer or cell cycle phase).

Note that the gene symbols follow the mouse conventions (i.e. capitalized) or the human conventions (i.e, all upper-case), based on the original publication. One can use the `toupper`, `tolower`, and `toTitleCase` functions to alter symbol conventions.

Mouse gene symbols in `cortical_markers` are transcribed from Figure 3 of Molyneaux et al. (2007): "laminar-specific expression of 66 genes within the neocortex."

Human gene symbols in `housekeeping` are derived from the list of "housekeeping" genes from the cDNA microarray analysis of Eisenberg and Levanon (2003): "[HK genes] belong to the class of genes that are EXPRESSED in all tissues." "... from 47 different human tissues and cell lines."

Human gene symbols in `housekeeping_revised` from Eisenberg and Levanon (2013): "This list provided ... is based on analysis of next-generation sequencing (RNA-seq) data. At least one variant of these genes is expressed in all tissues uniformly... The RefSeq transcript according to which we deemed the gene 'housekeeping' is given." Housekeeping exons satisfy "(i) expression observed in all tissues; (ii) low variance over tissues: standard-deviation [log2(RPKM)]<1; and (iii) no exceptional expression in any single tissue; that is, no log-expression value differed from the averaged log2(RPKM) by two (fourfold) or more." "We define a housekeeping gene as a gene for which at least one RefSeq transcript has more than half of its exons meeting the previous criteria (thus being housekeeping exons)."

Human gene symbols in `cellcycle_genes` from Macosko et al. (2015) and represent a set of genes marking G1/S, S, G2/M, M, and M/G1 phases.

### References

Molyneaux, B.J., Arlotta, P., Menezes, J.R. and Macklis, J.D.. Neuronal subtype specification in the cerebral cortex. Nature Reviews Neuroscience, 2007, 8(6):427-437.

Eisenberg E, Levanon EY. Human housekeeping genes are compact. Trends in Genetics, 2003, 19(7):362-5.

Eisenberg E, Levanon EY. Human housekeeping genes, revisited. Trends in Genetics, 2013, 29(10):569-74.

Macosko, E. Z., et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell, 2015, 161.5:1202-1214.

### Examples

    data(housekeeping)
    data(housekeeping_revised)
    data(cellcycle_genes)
    data(cortical_markers)

[Package scone version 1.18.0 Index]