nki7g: Subset of NKI dataset containing gene expression, annotations...

In survcomp: Performance Assessment and Comparison for Survival Analysis

Description

This dataset contains a subset of the gene expression, annotations and clinical data from the NKI datasets (see section details). The subset contains the seven genes introduced by Desmedt et al. 2008

Format

ExpressionSet with 7 features and 337 samples, containing:

• exprs(nki7g): Matrix containing gene expressions as measured by Agilent technology (dual-channel, oligonucleotides).

• fData(nki7g): AnnotatedDataFrame containing annotations of Agilent microarray platform.

• pData(nki7g): AnnotatedDataFrame containing Clinical information of the breast cancer patients whose tumors were hybridized.

• experimentalData(nki7g): MIAME object containing information about the dataset.

• annotation(nki7g): Name of the agilent chip.

Details

This dataset represents a subset of the study published by van't Veer et al. 2002 and van de Vijver et al. 2002. The subset contains the genes AURKA (also known as STK6, STK7, or STK15), PLAU (also known as UPA), STAT1, VEGF, CASP3, ESR1, and ERBB2, as introduced by Desmedt et al. 2008. The seven genes represent the proliferation, tumor invasion/metastasis, immune response, angiogenesis, apoptosis phenotypes, and the ER and HER2 signaling, respectively.

Source

nki:

http://www.rii.com/publications/2002/vantveer.html

References

Laura J. van't Veer, Hongyue Dai, Marc J. van de Vijver, Yudong D. He, Augustinus A.M. Hart, Mao Mao, Hans L. Peterse, Karin van der Kooy, Matthew J. Marton, Anke T. Witteveen, George J. Schreiber, Ron M. Kerkhoven, Chris Roberts, Peter S. Linsley, Rene Bernards and Stephen H. Friend (2002) "Gene expression profiling predicts clinical outcome of breast cancer", Nature, 415:530-536

M. J. van de Vijver, Y. D. He, L. van't Veer, H. Dai, A. M. Hart, D. W. Voskuil, G. J. Schreiber, J. L. Peterse, C. Roberts, M. J. Marton, M. Parrish, D. Atsma, A. Witteveen, A. Glas, L. Delahaye, T. van der Velde, H. Bartelink, S. Rodenhuis, E. T. Rutgers, S. H. Friend and R. Bernards (2002) "A Gene Expression Signature as a Predictor of Survival in Breast Cancer", New England Journal of Medicine, 347(25):1999-2009

Examples

## load Biobase package
library(Biobase)
## load the dataset
data(breastCancerData)
## show the first 5 columns of the expression data
exprs(nki7g)[ ,1:5]
## show the first 6 rows of the phenotype data
head(pData(nki7g))
## show first 20 feature names
featureNames(nki7g)
## show the experiment data summary
experimentData(nki7g)
## show the used platform
annotation(nki7g)
## show the abstract for this dataset
abstract(nki7g)

Example output

Loading required package: survival
Loading required package: prodlim
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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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")'.

           NKI_4  NKI_6  NKI_7  NKI_8  NKI_9
NM_000125 -0.007  0.074 -0.767 -0.820 -0.180
NM_004448 -0.694 -0.462 -0.397 -0.784 -0.395
NM_003600 -0.062 -0.245 -0.504  0.275 -0.247
NM_002658 -0.351 -0.331  0.043 -0.075  0.005
NM_003376 -0.178 -0.051  0.069  0.143  0.193
NM_007315  0.572 -0.387 -0.355  0.363 -0.435
NM_004346  0.040 -0.015 -0.139  0.120 -0.072
       samplename dataset series id filename size age er grade pgr her2
NKI_4       NKI_4     NKI    NKI  4       NA  2.0  41  1     3  NA   NA
NKI_6       NKI_6     NKI    NKI  6       NA  1.3  49  1     2  NA   NA
NKI_7       NKI_7     NKI    NKI  7       NA  2.0  46  0     1  NA   NA
NKI_8       NKI_8     NKI    NKI  8       NA  2.8  48  0     3  NA   NA
NKI_9       NKI_9     NKI    NKI  9       NA  1.5  48  1     3  NA   NA
NKI_11     NKI_11     NKI    NKI 11       NA  2.2  37  1     3  NA   NA
       brca.mutation e.dmfs t.dmfs node t.rfs e.rfs treatment tissue t.os e.os
NKI_4              0      0   4747    0  4747     0         0      1 4744    0
NKI_6              0      0   4075    0  4075     0         0      1 4072    0
NKI_7              0      0   3703    0  3703     0         0      1 3700    0
NKI_8              0      0   3215    0  3215     0         0      1 3213    0
NKI_9              0      0   3760    0  3760     0         0      1 3757    0
NKI_11             0      0   2120    0  2120     0         0      1 2119    0
[1] "NM_000125" "NM_004448" "NM_003600" "NM_002658" "NM_003376" "NM_007315"
[7] "NM_004346"
Experiment data
  Experimenter name: NKI 
  Laboratory: Divisions of Diagnostic Oncology, Radiotherapy and Molecular Carvinogenesis and Center for Biomedical Genetics, The Netherland Cancer Institute, Amsterdam, The Netherlands. 
  Contact information: Stephen H. Friend <[e-mail]> 
  Title: Gene expression profiling predicts clinical outcome of breast cancer. A gene-expresion signature as a predictor  of survival in breast cancer. 
  URL: http://www.rii.com/publications/2002/vantveer.html 
  PMIDs:  

  Abstract: A 61 word abstract is available. Use 'abstract' method.
[1] "rosetta"
[1] "Van de Vijver et al. 2002 and Laura J. van't Veer 2002. Series of 295 concescutive patients with primary breast carcinomas as having a gene-expression signature associated with either a poor prognosis or a good prognosis. All patients had stage I or II breast cancer and were younger than 53 years old; 151 had lymph-node-negaitve disease, and 144 had lymph-node-positive disease."

survcomp documentation built on Nov. 8, 2020, 4:54 p.m.