tmod-data: Default gene expression module data

Description Details References See Also Examples

Description

Gene expression module data from Chaussabel et al. (2008) and Li et al. (2014)

Details

The tmod package includes one data set of class tmod which can be loaded with data(tmod). This data set is derived from two studies (see package vignette for details). By default, enrichment analysis with tmod uses this data set; however, it is not loaded into user workspace by default.

References

Chaussabel, Damien, Charles Quinn, Jing Shen, Pinakeen Patel, Casey Glaser, Nicole Baldwin, Dorothee Stichweh, et al. 2008. "A Modular Analysis Framework for Blood Genomics Studies: Application to Systemic Lupus Erythematosus." Immunity 29(1):150-64.

Li, Shuzhao, Nadine Rouphael, Sai Duraisingham, Sandra Romero-Steiner, Scott Presnell, Carl Davis, Daniel S Schmidt, et al. 2014. "Molecular Signatures of Antibody Responses Derived from a Systems Biology Study of Five Human Vaccines." Nature Immunology 15(2):195-204.

See Also

tmod-class, modmetabo

Examples

1
2
3
4
5
# list of first 10 modules
data(tmod)
tmod
tmod$MODULES[1:10, ]
tmod[1:10]

Example output

For tmod user guide, type `tmodUserGuide()'
An object of class "tmod"
	606 modules, 12712 genes
             ID                                   Title           Category
LI.M0     LI.M0                      targets of FOSL1/2         TF targets
LI.M1.0 LI.M1.0  integrin cell surface interactions (I) molecular function
LI.M1.1 LI.M1.1 integrin cell surface interactions (II) molecular function
LI.M2.0 LI.M2.0                extracellular matrix (I)           location
LI.M2.1 LI.M2.1               extracellular matrix (II)           location
LI.M2.2 LI.M2.2              extracellular matrix (III)           location
LI.M3     LI.M3       regulation of signal transduction          signaling
LI.M4.0 LI.M4.0            cell cycle and transcription biological process
LI.M4.1 LI.M4.1                          cell cycle (I) biological process
LI.M4.2 LI.M4.2                   PLK1 signaling events          signaling
        Annotated
LI.M0         Yes
LI.M1.0       Yes
LI.M1.1       Yes
LI.M2.0       Yes
LI.M2.1       Yes
LI.M2.2       Yes
LI.M3         Yes
LI.M4.0       Yes
LI.M4.1       Yes
LI.M4.2       Yes
                                                                              URL
LI.M0     http://www.interactivefigures.com/meni/btm416_annotation/btmdata/M0.htm
LI.M1.0 http://www.interactivefigures.com/meni/btm416_annotation/btmdata/M1.0.htm
LI.M1.1 http://www.interactivefigures.com/meni/btm416_annotation/btmdata/M1.1.htm
LI.M2.0 http://www.interactivefigures.com/meni/btm416_annotation/btmdata/M2.0.htm
LI.M2.1 http://www.interactivefigures.com/meni/btm416_annotation/btmdata/M2.1.htm
LI.M2.2 http://www.interactivefigures.com/meni/btm416_annotation/btmdata/M2.2.htm
LI.M3     http://www.interactivefigures.com/meni/btm416_annotation/btmdata/M3.htm
LI.M4.0 http://www.interactivefigures.com/meni/btm416_annotation/btmdata/M4.0.htm
LI.M4.1 http://www.interactivefigures.com/meni/btm416_annotation/btmdata/M4.1.htm
LI.M4.2 http://www.interactivefigures.com/meni/btm416_annotation/btmdata/M4.2.htm
                Source SourceID original.ID   B
LI.M0   Li et al. 2013       LI          M0  12
LI.M1.0 Li et al. 2013       LI        M1.0  29
LI.M1.1 Li et al. 2013       LI        M1.1  12
LI.M2.0 Li et al. 2013       LI        M2.0  30
LI.M2.1 Li et al. 2013       LI        M2.1  45
LI.M2.2 Li et al. 2013       LI        M2.2  14
LI.M3   Li et al. 2013       LI          M3  47
LI.M4.0 Li et al. 2013       LI        M4.0 335
LI.M4.1 Li et al. 2013       LI        M4.1 145
LI.M4.2 Li et al. 2013       LI        M4.2  34
An object of class "tmod"
	10 modules, 455 genes

tmod documentation built on Oct. 23, 2020, 6:12 p.m.