sig.gene70: Signature used to compute the 70 genes prognosis profile...

In genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

Description

List of 70 agilent probe ids representing 56 unique genes included in the GENE70 signature. The EntrezGene.ID allows for mapping and the "average.good.prognosis.profile" values allows for signature computation.

Usage

data(sig.gene70)

Format

sig.gene70 is a matrix with 9 columns containing the annotations and information related to the signature itself.

Source

http://www.nature.com/nature/journal/v415/n6871/full/415530a.html

References

L. J. van't Veer and H. Dai and M. J. van de Vijver and Y. D. He and A. A. Hart and M. Mao and H. L. Peterse and K. van der Kooy and M. J. Marton and A. T. Witteveen and G. J. Schreiber and R. M. Kerkhiven and C. Roberts and P. S. Linsley and R. Bernards and S. H. Friend (2002) "Gene Expression Profiling Predicts Clinical Outcome of Breast Cancer", Nature, 415:530–536.

Examples

data(sig.gene70)
head(sig.gene70)

Example output

Loading required package: survcomp
Loading required package: survival
Loading required package: prodlim
Loading required package: mclust
Package 'mclust' version 5.3
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: limma
Loading required package: biomaRt
Loading required package: iC10
Loading required package: pamr
Loading required package: cluster
Loading required package: iC10TrainingData
Loading required package: AIMS
Loading required package: e1071
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 object is masked from 'package:limma':

    plotMA

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
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    'citation("Biobase")', and for packages 'citation("pkgname")'.

                        probe correlation average.good.prognosis.profile
NM_003748           NM_003748   -0.420671                     0.12350000
NM_003862           NM_003862   -0.410964                     0.05159091
Contig32125_RC Contig32125_RC   -0.409054                     0.05409091
U82987                 U82987   -0.407002                     0.06150000
AB037863             AB037863   -0.402335                     0.06334091
NM_020974           NM_020974   -0.399987                    -0.06231818
               EntrezGene.ID NCBI.gene.symbol HUGO.gene.symbol      Cytoband
NM_003748               8659          ALDH4A1          ALDH4A1          1p36
NM_003862               8817            FGF18            FGF18          5q34
Contig32125_RC            NA             <NA>             <NA>          <NA>
U82987                 27113             BBC3             BBC3 19q13.3-q13.4
AB037863                  NA             <NA>             <NA>          <NA>
NM_020974              57758           SCUBE2           SCUBE2       11p15.3
                                         Alternative.symbols
NM_003748                     ALDH4|P5CD|P5CDh|P5CDhL|P5CDhS
NM_003862                                       FGF-18|ZFGF5
Contig32125_RC                                          <NA>
U82987                                   JFY1|PUMA|PUMA/JFY1
AB037863                                                <NA>
NM_020974      CEGP1|Cegb1|Cegf1|FLJ16792|FLJ35234|MGC133057
                                              Description
NM_003748      aldehyde dehydrogenase 4 family, member A1
NM_003862                     fibroblast growth factor 18
Contig32125_RC                                       <NA>
U82987                           BCL2 binding component 3
AB037863                                             <NA>
NM_020974          signal peptide, CUB domain, EGF-like 2
Warning message:
system call failed: Cannot allocate memory 

genefu documentation built on Jan. 28, 2021, 2:01 a.m.