HumanDataExamples: Human Transcription Factor data and Bladder cancer dataset.

In CoRegNet: CoRegNet : reconstruction and integrated analysis of co-regulatory networks

Description

Internal datasets for the use of the package containing : A list of 2020 Human Transcription Factors in EntrezGene or Official Gene Symbol (HUGO) from the FANTOM consortium (Ravasi et al, 2010), A gene expression and copy number dataset of bladder cancer, Datasets of human TF protein interactions and regulatory interactions.

Usage

data(HumanTF)
data(HumanTF_entrezgene)
data(CIT_BLCA_EXP)
data(CIT_BLCA_CNV)
data(CIT_BLCA_Subgroup)
data(ENCODE_sub)
data(CHEA_sub)
data(STRING_sub)
data(HIPPIE_sub)

Format

HumanTF

A character vector of Official (HUGO) gene symbols

HumanTF_entrezgene

A character vector of EntrezGene

CIT_BLCA_EXP

A matrix of bladder cancer gene expression from the CIT program. Only contains the 1000 genes with highest standard deviation. rownames : genes, colnames : samples. (from Rebouissou et al. 2014)

CIT_BLCA_CNV

A matrix of bladder cancer DNA copy number aberrations from the CIT program. Only contains the TF and the tumor samples of CIT_BLCA_EXP. rownames : TF, colnames : samples.

CIT_BLCA_Subgroup

A data.frame with sample name in first column and classification from the TCGA in the second column.

CIT_BLCA_smallGRN

An example CoRegNet object.

ENCODE_sub

A data.frame of regulatory interactions from the ENCODE project.

CHEA_sub

A data.frame of regulatory interactions from the ChEA2 database. (http://amp.pharm.mssm.edu/ChEA2)

STRING_sub

A data.frame of Protein interaction between TF from the STRING database. (http://string.embl.de)

HIPPIE_sub

A data.frame of Protein interaction between TF from the HIPPIE database. (http://cbdm.mdc-berlin.de/tools/hippie)

References

Rebouissou S, Bernard-Pierrot I, de Reynies A, Lepage M-L, Krucker C, Chapeaublanc E, Herault A, Kamoun A, Caillault A, Letouze E, Elarouci N, Neuzillet Y, Denoux Y, Molinie V, Vordos D, Laplanche A, Maille P, Soyeux P, Ofualuka K, Reyal F, et al (2014) EGFR as a potential therapeutic target for a subset of muscle-invasive bladder cancers presenting a basal-like phenotype. Science Translational Medicine 6: 244ra91-244ra91

Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci , Daub et al (2010) An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man. Cell 140: 744-752

Kou Y, Chen EY, Clark NR, Duan Q, Tan CM and Ma ayan A (2013) ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome. In ... pp 416-430. Berlin, Heidelberg: Springer Berlin Heidelberg

Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, Mering von C and Jensen LJ (2012) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research 41: D808-D815

Schaefer MH, Fontaine J-F, Vinayagam A, Porras P, Wanker EE and Andrade-Navarro MA (2012) HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores. PLoS ONE 7: e31826

Examples

data(HumanTF)
head(HumanTF)
data(HumanTF_entrezgene)
head(HumanTF_entrezgene)

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: shiny
Loading required package: arules
Loading required package: Matrix

Attaching package: 'arules'

The following objects are masked from 'package:base':

    abbreviate, write

[1] "ABL1"  "PARP1" "AEBP1" "AES"   "NR0B1" "AHR"  
[1] "25"  "142" "165" "166" "190" "196"

CoRegNet documentation built on Nov. 8, 2020, 5:06 p.m.