cgps: Part of the large pharmacogenomic dataset published by...

Description Usage Format Details Source References Examples

Description

This dataset contains gene expression of 200 cancer cell lines for which sensitivity (IC50) to Camptothecin was measured (release 2).

Usage

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data(cgps)

Format

The cgps dataset is composed of three objects

cgps.annot

Dataframe containing gene annotations

cgps.ge

Matrix containing expressions of 1000 genes; cell lines in rows, genes in columns

cgps.ic50

Drug sensitivity measurements (IC50) for Camptothecin

Details

Camptothecin is a drug mainly used in colorectal cancer.

Source

http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-783

http://www.nature.com/nature/journal/v483/n7391/extref/nature11005-s2.zip

References

Garnett MJ et al. "Systematic identification of genomic markers of drug sensitivity in cancer cells", Nature, 483:570-575, 2012.

Examples

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set.thread.count(2)
data(cgps)

message("Gene expression data:")
print(cgps.ge[1:3, 1:3])

message("Gene annotations:")
print(head(cgps.annot))

message("Drug sensitivity (IC50) values:")
print(head(cgps.ic50))

Example output

Loading required package: survival
Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

[1] 2
Gene expression data:
      geneid_3310 geneid_2978 geneid_6352
22RV1    4.714871    3.852822    4.367895
5637     4.349628    3.762097    4.400742
639_V    4.389094    3.744586    4.249098
Gene annotations:
                   probe entrezgene ensembl_gene_id hgnc_symbol   unigene
geneid_3310       117_at       3310 ENSG00000173110       HSPA6 Hs.654614
geneid_2978    1255_g_at       2978 ENSG00000048545      GUCA1A      <NA>
geneid_6352    1405_i_at       6352 ENSG00000161570        CCL5      <NA>
geneid_2621    1598_g_at       2621 ENSG00000183087        GAS6      <NA>
geneid_5337       177_at       5337 ENSG00000075651        PLD1 Hs.600897
geneid_10594 200000_s_at      10594 ENSG00000174231       PRPF8 Hs.181368
                                                                                          description
geneid_3310                        heat shock 70kDa protein 6 (HSP70B') [Source:HGNC Symbol;Acc:5239]
geneid_2978                     guanylate cyclase activator 1A (retina) [Source:HGNC Symbol;Acc:4678]
geneid_6352                             chemokine (C-C motif) ligand 5 [Source:HGNC Symbol;Acc:10632]
geneid_2621                                    growth arrest-specific 6 [Source:HGNC Symbol;Acc:4168]
geneid_5337              phospholipase D1, phosphatidylcholine-specific [Source:HGNC Symbol;Acc:9067]
geneid_10594 PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:17340]
             chromosome_name start_position end_position strand   band
geneid_3310                1      161494036    161496681      1  q23.3
geneid_2978                6       42123144     42147794      1  p21.1
geneid_6352               17       34198495     34207797     -1    q12
geneid_2621               13      114523524    114567046     -1    q34
geneid_5337                3      171318195    171528740     -1 q26.31
geneid_10594              17        1553923      1588176     -1  p13.3
             EntrezGene.ID jetset.nProbes jetset.EntrezID jetset.process
geneid_3310           3310             16            3310          548.0
geneid_2978           2978             16            2978          192.5
geneid_6352           6352             14            6352          252.5
geneid_2621           2621             16            2621          232.5
geneid_5337           5337             16            5337         2688.0
geneid_10594         10594             11           10594          311.0
             jetset.specificity jetset.coverage jetset.robust jetset.overall
geneid_3310           0.1250000               1    0.40087914    0.050109893
geneid_2978           0.8125000               1    0.72534999    0.589346869
geneid_6352           1.0000000               1    0.65626906    0.656269062
geneid_2621           0.6875000               1    0.67853225    0.466490919
geneid_5337           0.6875000               1    0.01129113    0.007762654
geneid_10594          0.9090909               1    0.59525478    0.541140712
             jetset.symbol best
geneid_3310          HSPA6 TRUE
geneid_2978         GUCA1A TRUE
geneid_6352           CCL5 TRUE
geneid_2621           GAS6 TRUE
geneid_5337           PLD1 TRUE
geneid_10594         PRPF8 TRUE
Drug sensitivity (IC50) values:
   22RV1     5637    639_V    647_V      697    769_P 
8.025115 8.383408 9.212911 9.050050 8.688717 7.605587 

mRMRe documentation built on Nov. 17, 2017, 6:33 a.m.