RTN.data: Pre-processed datasets for the RTN package.

In RTN: RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Description

Datasets used to demonstrate RTN main functions.

Format

tniData, tnaData, and tfsData

Details

The tniData and tnaData datasets were extracted, pre-processed and size-reduced from Fletcher et al. (2013) and Curtis et al. (2012). They consist of two lists used in the RTN vignettes for demonstration purposes only. The tniData list contains the 'expData', 'rowAnnotation' and 'colAnnotation' R objects, while the tnaData list contains the 'phenotype', 'phenoIDs' and 'hits' R objects.

The tfsData consists of a list with gene annotation for human transcription factors (TFs), compiled from 6 resources (Lambert et. al 2018; Carro et al. 2010; Vaquerizas et al. 2009; D. L. Fulton et al. 2009; Yusuf et al. 2012; and Ravasi et al. 2010), and provided here in the form of 'data frame' objects that include ENTREZ and HGNC gene symbol annotation.

The pksData consists of a list with gene annotation for human protein kinases, retrived from the Swiss-Prot Protein Knowledgebase (https://www.uniprot.org/docs/pkinfam), release 2020_02 of 22-Apr-2020.

tniData$expData

a named gene expression matrix with 120 samples (a subset from the Fletcher2013b).

tniData$rowAnnotation

a data.frame of characters with gene annotation (a subset from the Fletcher2013b).

tniData$colAnnotation

a data.frame of characters with sample annotation (a subset from the Fletcher2013b).

tnaData$phenotype

a named numeric vector with differential gene expression data.

tnaData$phenoIDs

a data.frame of characters with probe ids matching a secundary annotation source (e.g. Probe-to-ENTREZ).

tnaData$hits

a character vector with genes differentially expressed.

tfsData$Lambert2018

a data.frame listing TFs from Lambert et. al (2018).

tfsData$Yusuf2012

a data.frame listing TFs from Yusuf et al. (2012).

tfsData$Carro2010

a data.frame listing TFs from Carro et al. (2010).

tfsData$Ravasi2010

a data.frame listing TFs from Ravasi et al. (2010).

tfsData$Fulton2009

a data.frame listing TFs from Fulton et al. (2009).

tfsData$Vaquerizas2009

a data.frame listing TFs from Vaquerizas et al. (2009).

tfsData$all

a data.frame listing all TFs.

pksData$pkinfam2020

a data.frame listing human protein kinases.

References

Carro, M.S. et al., The transcriptional network for mesenchymal transformation of brain tumors. Nature, 463(7279):318-325, 2010.

Curtis C. et al., The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature, 486(7403):346-352, 2012.

Fletcher, M.N.C. et al., Master regulators of FGFR2 signalling and breast cancer risk. Nature Communications, 4:2464, 2013.

Fulton, D.L. et al., TFCat: the curated catalog of mouse and human transcription factors. Genome Biology, 10(3):R29, 2009.

Lambert, S.A. et al., The Human Transcription Factors. Cell, 172(4):650-665, 2018.

Ravasi, T. et al., An atlas of combinatorial transcriptional regulation in mouse and man. Cell, 140(5):744-752, 2010.

Vaquerizas, J.M. et al., A census of human transcription factors: function, expression and evolution. Nature Reviews Genetics, 10(4):252-263, 2009.

Yusuf, D. et al., The Transcription Factor Encyclopedia. Genome Biology, 13(3):R24, 2012.

Examples

    data(tniData)
    data(tnaData)
    data(tfsData)
    data(pksData)

RTN documentation built on Nov. 12, 2020, 2:02 a.m.