DellaGattaData:
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)
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.