DellaGattaData {gprege} | R Documentation

## Fragment dataset of 13 time-point mouse microarray time series of gene expression ratios and and a ranking list of TP63 targets suggested by TSNI.

### Description

exprs_tp63_RMA

  100 gene reporters of 13 time-points mouse Affymetrix microarray gene expression coming from a study on primary mouse keratinocytes with an induced activation of the TRP63 transcription factor (GEO-accession number:GSE10562, see Source section), where a reverse-engineering algorithm was developed (TSNI: time-series network identification) to infer the direct targets of TRP63 (Della Gatta et.al. 2008). The data has been processed using `rma` (affy) and the profiles are centred (zero-mean) across the timepoints.

DGatta_labels_byTSNI, DGatta_labels_byTSNItop100

  a ranking list suggested based by TSNI is provided. The inferred direct targets were biologically confirmed by correlation with ChIP-Seq binding regions; therefore the list is used as a noisy ground truth. See Source section.

genesymbols

  Names of the genes that the transcipt_IDs (in exprs_tp63_RMA) correspond to.

gpregeOutput

  Its field 'rankingScores' contains log-marginal likelihood ratios, used as ranking scores, for each gene reporter in exprs_tp63_RMA. This is the output from a run of gprege on the full DellaGatta dataset (see demTp63Gp1.R) and stored here for convenience.

### Usage

      data(FragmentDellaGattaData)

### Source

GEO: http://www.ncbi.nlm.nih.gov/geo/, TSNI ranking: genome.cshlp.org/content/suppl/2008/05/05/gr.073601.107.DC1/DellaGatta_SupTable1.xls

### References

Della Gatta G, et al. Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering. Genome Research 2008, 18(6):939.

[Package gprege version 1.36.0 Index]