DellaGattaData: Fragment dataset of 13 time-point mouse microarray time...
In gprege: Gaussian Process Ranking and Estimation of Gene Expression time-series
Description
Usage
Source
References
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
1
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.
gprege documentation built on Nov. 8, 2020, 7:48 p.m.
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Description Usage Source References
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
1 |
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.
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