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Series GSE55918 Query DataSets for GSE55918
Status Public on Dec 21, 2014
Title Defining glioma subtypes based on robust transcriptional patterns from 16 prior studies
Organism Homo sapiens
Experiment type Expression profiling by array
Third-party reanalysis
Summary The purpose of our study was to define robust glioma subtypes by applying rigorous preprocessing and validation steps to 1,952 microarray samples aggregated from public data repositories for 16 prior studies. We evaluated each sample for quality-control issues, normalized high-quality samples using the Single-Channel Array Normalization (SCAN) algorithm (PMID: 22959562), corrected for probe-composition biases and inter-platform variability, and adjusted for intra- and inter-study batch effects. The deposited data in GEO include the 1,841 microarray samples that passed quality control tests, and underwent normalization and batch effect adjustment.

Where available, we retrieved treatment, histological and clinical data, such as tumor grade, histopathology, age-at-diagnosis, and survival time after diagnosis for these samples. Using a training/testing validation design, we identified six transcriptional subtypes in the training set, and evaluated clinically observable characteristics in the test set. Three of our clusters contained a heterogeneous mix of histopathological subtypes and tumor grades. We evaluated age, survival, and treatment patterns across our test samples and observed highly significant differences among the clusters. We also observed the potential to use gene expression patterns to further understanding of the biological mechanisms that drive gliomagenesis for each subtype. Our findings provide clinical and biological insights that may not be apparent with alternative approaches or smaller data sets, and our approach serves as an example for gene-expression meta-analyses that can be applied to other complex diseases.

 
Overall design Total 1,841 microarray samples aggregated from public data repositories from 16 prior studies were used to define six robust glioma subtypes by applying rigorous preprocessing and validation steps.

We collected raw microarray data from publicly available repositories for histologically defined glioma patients. We downloaded 11 of the data sets from general-purpose databases—either NCBI GEO (http://ncbi.nlm.nih.gov/geo) or ArrayExpress (http://www.ebi.ac.uk/arrayexpress) —and 5 of the data sets from disease-focused databases. We focused on data sets that used the Human Genome U133A and U133 Plus 2.0 Affymetrix platforms because they constitute the majority of available microarray samples that have been used to profile glioma patients, and these two Affymetrix platforms have many overlapping probes.

Step 1: We performed quality control tests, SCAN normalization and batch effect adjustment. We excluded low-quality samples.

Step 2: We separated data sets into training and testing sets according to clinical data availability. Unsupervised clustering analysis and internal validation was performed on the training data to determine an optimal cluster size.

Step 3: Cluster Assignment for the test data set was performed and clinical characteristics across transcriptional clusters were examined.

Results are reported as normalized log2 signal intensity which was mapped to human 12,078 Entrez Gene IDs from the Human Genome U133A and U133 Plus 2.0 Affymetrix platforms probe-set IDs (File: GSE55918_Matrix_GliomaClusteringAnalysis.txt).

 
Contributor(s) Lee S, Piccolo S, Allen-Brady K
Citation(s) 25142794
BioProject PRJNA242416
Submission date Mar 14, 2014
Last update date Dec 21, 2014
Contact name Sanghoon Lee
E-mail(s) felix.dtc@gmail.com
Organization name University of Utah
Department Biochemistry
Lab Biochemistry
Street address 15 North Medical Drive East
City Salt Lake City
State/province Utah
ZIP/Postal code 84112
Country USA
 
Relations
Affiliated with GSE1993
Affiliated with GSE4271
Affiliated with GSE4412
Affiliated with GSE7696
Affiliated with GSE8692
Affiliated with GSE16011
Affiliated with GSE19728
Affiliated with GSE21354
Affiliated with GSE24072
Affiliated with GSE45921

Data table header descriptions
Sample name
raw data file
source name
organism
data set name
Array platform
Array download source
characteristics: Study design
characteristics: Clustering
characteristics: Tumor grade diagnosis
characteristics: Histological dianosis
characteristics: Age-at-diag1sis (years)
characteristics: Survival time (months)
characteristics: Censored
characteristics: Treatment type
characteristics: Chemotherapy drug name

Data table
Sample name raw data file source name organism data set name Array platform Array download source characteristics: Study design characteristics: Clustering characteristics: Tumor grade diagnosis characteristics: Histological dianosis characteristics: Age-at-diag1sis (years) characteristics: Survival time (months) characteristics: Censored characteristics: Treatment type characteristics: Chemotherapy drug name
E-MEXP-567-raw-cel-890390805.CEL E-MEXP-567-raw-cel-890390805.CEL "brain tissue, glioma" Homo sapiens E-MEXP-567 Affymetrix HG U133A_2 ArrayExpress Training data K6 G4 Glioblastoma Null Null 1 Null Null
E-MEXP-567-raw-cel-890390826.CEL E-MEXP-567-raw-cel-890390826.CEL "brain tissue, glioma" Homo sapiens E-MEXP-567 Affymetrix HG U133A_2 ArrayExpress Training data K6 G2 Astrocytoma Null Null 1 Null Null
E-MEXP-567-raw-cel-890390847.CEL E-MEXP-567-raw-cel-890390847.CEL "brain tissue, glioma" Homo sapiens E-MEXP-567 Affymetrix HG U133A_2 ArrayExpress Training data K4 G4 Glioblastoma Null Null 1 Null Null
E-MEXP-567-raw-cel-890390868.CEL E-MEXP-567-raw-cel-890390868.CEL "brain tissue, glioma" Homo sapiens E-MEXP-567 Affymetrix HG U133A_2 ArrayExpress Training data K4 G2 Astrocytoma Null Null 1 Null Null
E-MEXP-567-raw-cel-890390889.CEL E-MEXP-567-raw-cel-890390889.CEL "brain tissue, glioma" Homo sapiens E-MEXP-567 Affymetrix HG U133A_2 ArrayExpress Training data K2 G2 Astrocytoma Null Null 1 Null Null
E-MEXP-567-raw-cel-890390910.CEL E-MEXP-567-raw-cel-890390910.CEL "brain tissue, glioma" Homo sapiens E-MEXP-567 Affymetrix HG U133A_2 ArrayExpress Training data K2 G4 Glioblastoma Null Null 1 Null Null
E-MEXP-567-raw-cel-890390931.CEL E-MEXP-567-raw-cel-890390931.CEL "brain tissue, glioma" Homo sapiens E-MEXP-567 Affymetrix HG U133A_2 ArrayExpress Training data K6 G2 Astrocytoma Null Null 1 Null Null
E-MEXP-567-raw-cel-890390952.CEL E-MEXP-567-raw-cel-890390952.CEL "brain tissue, glioma" Homo sapiens E-MEXP-567 Affymetrix HG U133A_2 ArrayExpress Training data K3 G2 Astrocytoma Null Null 1 Null Null
E-MEXP-567-raw-cel-890390973.CEL E-MEXP-567-raw-cel-890390973.CEL "brain tissue, glioma" Homo sapiens E-MEXP-567 Affymetrix HG U133A_2 ArrayExpress Training data K1 G2 Astrocytoma Null Null 1 Null Null
E-MEXP-567-raw-cel-890390994.CEL E-MEXP-567-raw-cel-890390994.CEL "brain tissue, glioma" Homo sapiens E-MEXP-567 Affymetrix HG U133A_2 ArrayExpress Training data K1 G4 Glioblastoma Null Null 1 Null Null
E-MEXP-567-raw-cel-890391015.CEL E-MEXP-567-raw-cel-890391015.CEL "brain tissue, glioma" Homo sapiens E-MEXP-567 Affymetrix HG U133A_2 ArrayExpress Training data K1 G4 Glioblastoma Null Null 1 Null Null
E-MEXP-567-raw-cel-890391036.CEL E-MEXP-567-raw-cel-890391036.CEL "brain tissue, glioma" Homo sapiens E-MEXP-567 Affymetrix HG U133A_2 ArrayExpress Training data K3 G2 Astrocytoma Null Null 1 Null Null
E-MEXP-567-raw-cel-890391057.CEL E-MEXP-567-raw-cel-890391057.CEL "brain tissue, glioma" Homo sapiens E-MEXP-567 Affymetrix HG U133A_2 ArrayExpress Training data K4 G4 Glioblastoma Null Null 1 Null Null
GSM99432.CEL GSM99432.CEL "brain tissue, glioma" Homo sapiens GSE4412 Affymetrix HG U133A GEO Training data K1 G4 Glioblastoma 49 6.16 1 Null Null
GSM99434.CEL GSM99434.CEL "brain tissue, glioma" Homo sapiens GSE4412 Affymetrix HG U133A GEO Training data K1 G4 Glioblastoma 18 3.21 1 Null Null
GSM99436.CEL GSM99436.CEL "brain tissue, glioma" Homo sapiens GSE4412 Affymetrix HG U133A GEO Training data K3 G4 Glioblastoma 64 11.67 1 Null Null
GSM99438.CEL GSM99438.CEL "brain tissue, glioma" Homo sapiens GSE4412 Affymetrix HG U133A GEO Training data K3 G4 Glioblastoma 58 5.97 1 Null Null
GSM99440.CEL GSM99440.CEL "brain tissue, glioma" Homo sapiens GSE4412 Affymetrix HG U133A GEO Training data K5 G4 Glioblastoma 48 31.51 0 Null Null
GSM99442.CEL GSM99442.CEL "brain tissue, glioma" Homo sapiens GSE4412 Affymetrix HG U133A GEO Training data K3 G4 Glioblastoma 56 10.66 1 Null Null
GSM99444.CEL GSM99444.CEL "brain tissue, glioma" Homo sapiens GSE4412 Affymetrix HG U133A GEO Training data K3 G4 Glioblastoma 78 12.98 0 Null Null

Total number of rows: 1841

Table truncated, full table size 374 Kbytes.




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

Supplementary file Size Download File type/resource
GSE55918_Matrix_GliomaClusteringAnalysis.txt.gz 51.0 Mb (ftp)(http) TXT
Processed data are available on Series record
Raw data not provided for this record

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