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Series GSE19536 Query DataSets for GSE19536
Status Public on Dec 01, 2010
Title Molecular Characterization of Breast Cancer Subtypes Derived from Joint Analysis of High Throughput miRNA and mRNA Data
Organism Homo sapiens
Experiment type Non-coding RNA profiling by array
Expression profiling by array
Summary MicroRNAs (miRNAs) are a class of short, single-stranded widely expressed noncoding RNAs that regulate the stability or translational efficiency of target messenger RNAs. Date derived from expression profiling of 489 miRNAs in 101 human primary breast tumor samples, along with genome-wide matched mRNA profiling and extensive clinical information were investigated in this study. miRNA and mRNA expression were analyzed using correlations and enrichments analyses. The results show that particular cellular processes such as proliferation, cell adhesion, and immune response are significantly enriched among genes with strong positive or negative correlation to individual or groups of miRNAs. Functional analyses were performed to validate the influence of miRNAs on proliferation. A group of miRNAs was identified that is associated to breast cancer disease free survival. This study provides a comprehensive dataset that can be used as groundwork for further studies of the involvement of miRNA in breast cancer.
 
Overall design miRNA profiling from 101 breast cancer samples was performed. Experiments were mostly performed using duplicate hybridizations (99 samples) on different arrays and time points. Two samples were profiled only once. miRNA signal intensities for replicate probes were averaged across the platform, log2 transformed and normalized to the 75 percentile. miRNA expression status was scored as present or absent for each gene in each sample by default settings in FE v9.5. miRNAs in samples that were run in replicates were considered present if scored in one of the two arrays.
mRNA profiling from 114 breast cancer samples was performed. Replicates not included. Final processed mRNA data (quantile-normalized and averaged per Gene Symbol) is represented in the supplementary file at the foot of this record.
 
Contributor(s) Enerly E, Steinfeld I, Johnsen H, Kleivi K, Leivonen SK, Russnes HG, Rønneberg JA, Navon R, Rødland E, Aure MR, Mäkelä R, Naume B,  Perälä M, Kallioniemi O, Kristensen VN, Børresen-Dale A, Yakhini Z
Citation(s) 21364938, 26321095, 24577056
Submission date Dec 17, 2009
Last update date Feb 03, 2020
Contact name Hilde Johnsen
E-mail(s) hilde.johnsen@rr-research.no
Phone 004722934421
Fax 004722934440
Organization name Norwegian Radium Hospital
Department Genetics
Street address Montebello
City Oslo
ZIP/Postal code 0310
Country Norway
 
Platforms (2)
GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)
GPL8227 Agilent-019118 Human miRNA Microarray 2.0 G4470B (miRNA ID version)
Samples (215)
GSM487073 BreastCancer-002 (miRNA)
GSM487074 BreastCancer-003 (miRNA)
GSM487075 BreastCancer-014 (miRNA)
Relations
Affiliated with GSE19783
BioProject PRJNA122257

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
GSE19536_RAW.tar 1.4 Gb (http)(custom) TAR (of TXT)
GSE19536_final_processed_mRNAdata.txt.gz 13.8 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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