sig.ggi: Gene expression Grade Index (GGI) as published in Sotiriou et...

Description Usage Format Source References Examples


List of 128 affymetrix hgu133a probesets representing 97 unique genes included in the GGI signature. The "EntrezGene.ID" column allows for mapping and "grade" defines the up-regulation of the expressions either in histological grade 1 or 3.




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



Sotiriou C, Wirapati P, Loi S, Harris A, Bergh J, Smeds J, Farmer P, Praz V, Haibe-Kains B, Lallemand F, Buyse M, Piccart MJ and Delorenzi M (2006) "Gene expression profiling in breast cancer: Understanding the molecular basis of histologic grade to improve prognosis", Journal of National Cancer Institute, 98:262–272



Example output

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

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    clusterExport, clusterMap, parApply, parCapply, parLapply,
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The following object is masked from 'package:limma':


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

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    order, paste, pmax,, pmin,, rank, rbind,
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    union, unique, unsplit, which, which.max, which.min

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                  probe grade    Gb.acc EntrezGene.ID NCBI.gene.symbol
201088_at     201088_at     3 NM_002266          3838            KPNA2
201090_x_at 201090_x_at     3 NM_006082            NA             <NA>
201195_s_at 201195_s_at     3  AB018009          8140           SLC7A5
201475_x_at 201475_x_at     3 NM_004990          4141             MARS
201524_x_at 201524_x_at     3 NM_003348          7334            UBE2N
201584_s_at 201584_s_at     3 NM_005804         10212            DDX39
            HUGO.gene.symbol      Cytoband
201088_at              KPNA2 17q23.1-q23.3
201090_x_at             <NA>          <NA>
201195_s_at           SLC7A5       16q24.3
201475_x_at             MARS       12q13.2
201524_x_at            UBE2N         12q22
201584_s_at            DDX39      19p13.12
201088_at                  IPOA1|QIP2|RCH1|SRP1alpha
201090_x_at                                     <NA>
201195_s_at 4F2LC|CD98|D16S469E|E16|LAT1|MPE16|hLAT1
201475_x_at                     FLJ35667|METRS|MTRNS
201524_x_at         MGC131857|MGC8489|UBC13|UbcH-ben
201584_s_at   BAT1|BAT1L|DDXL|MGC18203|MGC8417|URH49
201088_at                             karyopherin alpha 2 (RAG cohort 1, importin alpha 1)
201090_x_at                                                                           <NA>
201195_s_at solute carrier family 7 (cationic amino acid transporter, y+ system), member 5
201475_x_at                                                     methionine-tRNA synthetase
201524_x_at                        ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast)
201584_s_at                                      DEAD (Asp-Glu-Ala-Asp) box polypeptide 39

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