TCsimData: Simulated time-course gene expression data set

In splineTimeR: Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

Description

Simulated data set of gene expression temporal profiles of 2000 genes. Data contain expression values in 8 time points after applying 2 differrent types of perturbation/treatment ("T1" and "T2").

Usage

data(TCsimData)

Format

An object of class ExpressionSet with 2000 observations per time point and perturbation/treatment. Phenotypic data of the object (pData(TCsimData)) contain 4 columns with the following variables:

SampleName

names of the samples

Time

time points when samples were collected

Treatment

types of treatment

Replicate

names of replicates

Details

Simulation experiments were conducted using GeneNetWeaver (GNW), an open-source simulator for the DREAM challenges. The in silico expression data were simulated based on the network structure of a 2000-gene sub-network from the Reactome functional interaction network. The sub-network was converted to a dynamical network model without autoregulatory interactions (self-loops). The data were simulated based on the "ODEs" model. Two types of time-series experiments were chosen: "Time Series as in DREAM4" and "Multifactorial". Gene expression data were simulated for 48 time points after perturbations. For more details see GNW User Manual.

The names of "Time Series as in DREAM4" and "Multifactorial" simulation experiments were changed to "T1" and "T2", respectively. From the generated data sets, eight time points are provided (1, 4, 8, 16, 24, 32, 40 and 48). The numbers correspond to the same time units after perturbation (e.g. minutes, hours, days, ect.). Replicates for both time-course experiments were generated by the addition of the normally distributed random errors with a standard deviation of 0.05 to the expression values for each time point. Subsequently, the entire dataset was normalized between 0 and 1.

Value

An object of class ExpressionSet.

References

Marbach, D., Schaffter, T., Mattiussi, C., and Floreano, D. (2009). Generating realistic in silico gene networks for performance assessment of reverse engineering methods. Journal of Computational Biology 2(16), 229-239.

Schaffter, T., Marbach, D., and Roulet G. (2010). GNW User Manual. http://gnw.sourceforge.net

Reactome project. Reactome Functional Interaction Network. Retrieved September 25, 2015 from http://www.reactome.org/

Examples

data(TCsimData)
pData(TCsimData)
head(exprs(TCsimData),3)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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    decompose, spectrum

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

    union

Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: GSEABase
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Attaching package: 'S4Vectors'

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    expand.grid

Loading required package: XML
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Attaching package: 'graph'

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

    addNode

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    degree, edges, intersection

Loading required package: gtools

Attaching package: 'gtools'

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    permute

Loading required package: splines
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   SampleName Time Treatment Replicate
1      T1_1_A    1        T1         A
2      T1_4_A    4        T1         A
3      T1_8_A    8        T1         A
4     T1_16_A   16        T1         A
5     T1_24_A   24        T1         A
6     T1_32_A   32        T1         A
7     T1_40_A   40        T1         A
8     T1_48_A   48        T1         A
9      T1_1_B    1        T1         B
10     T1_4_B    4        T1         B
11     T1_8_B    8        T1         B
12    T1_16_B   16        T1         B
13    T1_24_B   24        T1         B
14    T1_32_B   32        T1         B
15    T1_40_B   40        T1         B
16    T1_48_B   48        T1         B
17     T2_1_A    1        T2         A
18     T2_4_A    4        T2         A
19     T2_8_A    8        T2         A
20    T2_16_A   16        T2         A
21    T2_24_A   24        T2         A
22    T2_32_A   32        T2         A
23    T2_40_A   40        T2         A
24    T2_48_A   48        T2         A
25     T2_1_B    1        T2         B
26     T2_4_B    4        T2         B
27     T2_8_B    8        T2         B
28    T2_16_B   16        T2         B
29    T2_24_B   24        T2         B
30    T2_32_B   32        T2         B
31    T2_40_B   40        T2         B
32    T2_48_B   48        T2         B
           T1_1_A    T1_4_A    T1_8_A   T1_16_A   T1_24_A   T1_32_A   T1_40_A
CBLB    0.2694519 0.2298501 0.2264346 0.3098134 0.2334534 0.2769527 0.2421014
PIK3AP1 0.4117338 0.3979743 0.3913873 0.3949694 0.4735874 0.3647500 0.4070117
CD19    0.1535824 0.1485299 0.1560007 0.1600164 0.1497391 0.1614824 0.1569213
          T1_48_A    T1_1_B    T1_4_B    T1_8_B   T1_16_B   T1_24_B   T1_32_B
CBLB    0.2742864 0.3104223 0.2693839 0.2090408 0.2212945 0.2216139 0.3365579
PIK3AP1 0.4242660 0.4144012 0.5171295 0.4217347 0.3688333 0.5634921 0.3439404
CD19    0.1625378 0.1402525 0.1284667 0.1459046 0.1614579 0.1708511 0.1639174
          T1_40_B   T1_48_B    T2_1_A    T2_4_A    T2_8_A   T2_16_A   T2_24_A
CBLB    0.3043460 0.2749473 0.3034619 0.2849250 0.3427918 0.3495445 0.3994772
PIK3AP1 0.4445268 0.4207147 0.4581445 0.4372855 0.4609360 0.4629310 0.4707800
CD19    0.1023661 0.1933537 0.1759513 0.1889277 0.1819394 0.2070384 0.2323579
          T2_32_A   T2_40_A   T2_48_A    T2_1_B     T2_4_B    T2_8_B   T2_16_B
CBLB    0.3837768 0.4153516 0.4690617 0.2643894 0.25235257 0.3034814 0.2987684
PIK3AP1 0.4550403 0.4483257 0.4670998 0.4435228 0.42557491 0.4235888 0.4229616
CD19    0.2631298 0.3373790 0.2965144 0.2766676 0.08943578 0.1068839 0.1894865
          T2_24_B   T2_32_B   T2_40_B   T2_48_B
CBLB    0.4849842 0.3796414 0.4288892 0.4555836
PIK3AP1 0.4184705 0.4778378 0.4220795 0.5179748
CD19    0.1606898 0.3021157 0.3965885 0.2999353

splineTimeR documentation built on Nov. 8, 2020, 6:52 p.m.