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Series GSE3494 Query DataSets for GSE3494
Status Public on Oct 21, 2005
Title An expression signature for p53 in breast cancer predicts mutation status, transcriptional effects, and patient survival
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The biological tumor samples (ie, breast tumor specimens) consisted of freshly frozen breast tumors from a population-based cohort of 315 women representing 65% of all breast cancers resected in Uppsala County, Sweden, from January 1, 1987 to December 31, 1989. Estrogen receptor status was determined by biochemical assay as part of the routine clinical procedure. An experienced pathologist determined the Elston-Ellis grades of the tumors, classifying the tumors into low, medium and high-grade tumors. The clinico-pathological characteristics accompanying each tumor include p53 status, ER status, tumor grade, lymph node status and patient age.
Keywords: Tumor sample comparisons
 
Overall design All tumor specimens were assessed on U133 A and B arrays.
 
Contributor(s) Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Liu ET, Bergh J
Citation(s) 16141321, 29136509, 28972043
Submission date Oct 21, 2005
Last update date Aug 26, 2019
Contact name Lance David Miller
E-mail(s) [email protected]
Phone 65 6478 8100
Fax 65 6478 9060
URL http://www.gis.a-star.edu.sg/internet/site/investigators.php?f=cv&user_id=7
Organization name Genome Institute of Singapore
Department Microarray and Expression Genomics
Street address 60 Bioplois Street, #02-01 Genome
City Singapore
ZIP/Postal code 138672
Country Singapore
 
Platforms (2)
GPL96 [HG-U133A] Affymetrix Human Genome U133A Array
GPL97 [HG-U133B] Affymetrix Human Genome U133B Array
Samples (502)
GSM79114 X100B08 (HG-U133A)
GSM79115 X101B88 (HG-U133A)
GSM79116 X102B06 (HG-U133A)
Relations
BioProject PRJNA93319

Clinicopathological variables of the Uppsala cohort header descriptions
INDEX (ID)
p53 seq mut status (p53+=mutant; p53-=wt)
p53 DLDA classifier result (0=wt-like, 1=mt-like)
DLDA error (1=yes, 0=no)
Elston histologic grade
ER status
PgR status
age at diagnosis
tumor size (mm)
Lymph node status
DSS TIME (Disease-Specific Survival Time in years)
DSS EVENT (Disease-Specific Survival EVENT; 1=death from breast cancer, 0=alive or censored )

Data table
INDEX (ID) p53 seq mut status (p53+=mutant; p53-=wt) p53 DLDA classifier result (0=wt-like, 1=mt-like) DLDA error (1=yes, 0=no) Elston histologic grade ER status PgR status age at diagnosis tumor size (mm) Lymph node status DSS TIME (Disease-Specific Survival Time in years) DSS EVENT (Disease-Specific Survival EVENT; 1=death from breast cancer, 0=alive or censored )
X101B88 p53+ 1 0 G3 ER- PgR- 40 12 LN- 11.833 0
X102B06 p53+ 1 0 G3 ER+ PgR+ 51 26 LN- 11.833 0
X104B91 p53+ 0 1 G3 ER+ PgR+ 80 24 LN? 3.583 0
X110B34 p53+ 1 0 G2 ER+ PgR+ 74 20 LN- 11.667 0
X111B51 p53+ 1 0 G3 ER+ PgR+ 41 33 LN- 7.167 1
X127B00 p53+ 1 0 G3 ER+ PgR+ 57 22 LN- 4.667 1
X137B88 p53+ 1 0 G2 ER- PgR- 68 6 LN- 11.5 0
X143B81 p53+ 1 0 G3 ER- PgR- 93 29 LN? 2.167 0
X144B49 p53+ 0 1 G2 ER+ PgR+ 40 21 LN- 11.5 0
X146B39 p53+ 1 0 G3 ER- PgR- 34 50 LN+ NA NA
X147B19 p53+ 1 0 G3 ER- PgR- 71 24 LN+ 5.083 0
X153B09 p53+ 1 0 G3 ER- PgR- 71 18 LN- 11.417 0
X159B47 p53+ 0 1 G2 ER+ PgR+ 57 14 LN+ 11.417 0
X164B81 p53+ 1 0 G2 ER- PgR- 62 23 LN- 11.333 0
X186B22 p53+ 0 1 G2 ER+ PgR+ 86 46 LN+ 1.417 1
X187B36 p53+ 1 0 G2 ER+ PgR+ 29 23 LN+ 0 1
X189B83 p53+ 1 0 G2 ER- PgR- 58 38 LN- NA NA
X194B60 p53+ 1 0 G3 ER+ PgR- 77 22 LN+ 3.583 0
X19C33 p53+ 1 0 G1 ER+ PgR+ 61 31 LN+ 4.167 1
X208C06 p53+ 1 0 G2 ER+ PgR+ 67 22 LN? 0.083 0

Total number of rows: 251

Table truncated, full table size 11 Kbytes.




GEO Sample Accession Numbers and associated Patient IDs header descriptions
GEO Sample Accession #
Patient ID
Affy platform

Data table
GEO Sample Accession # Patient ID Affy platform
GSM79114 X100B08 HG-U133A
GSM79115 X101B88 HG-U133A
GSM79116 X102B06 HG-U133A
GSM79117 X103B41 HG-U133A
GSM79118 X104B91 HG-U133A
GSM79119 X105B13 HG-U133A
GSM79120 X106B55 HG-U133A
GSM79121 X10B88 HG-U133A
GSM79122 X110B34 HG-U133A
GSM79123 X111B51 HG-U133A
GSM79124 X112B55 HG-U133A
GSM79125 X113B11 HG-U133A
GSM79126 X114B68 HG-U133A
GSM79127 X11B47 HG-U133A
GSM79128 X120B73 HG-U133A
GSM79129 X122B81 HG-U133A
GSM79130 X124B25 HG-U133A
GSM79131 X127B00 HG-U133A
GSM79132 X128B48 HG-U133A
GSM79133 X130B92 HG-U133A

Total number of rows: 502

Table truncated, full table size 13 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE3494_RAW.tar 1.7 Gb (http)(custom) TAR (of CEL)

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