Biomarker Benchmark - GSE21510

Version 6 2016-03-17, 22:19

Version 5 2016-03-17, 21:23

Version 4 2016-03-17, 21:19

Version 3 2016-02-23, 23:34

Version 2 2016-02-04, 22:16

Version 1 2016-02-02, 22:07

dataset

posted on 2016-03-17, 22:19 authored by Anna GuyerAnna Guyer, Stephen PiccoloStephen Piccolo

[NOTICE: This data set has been deprecated. Please see our new version of the data (and additional data sets) here: https://osf.io/mhk93 ]

"Purpose: This study aimed to identify a novel biomarker or a target of treatment for colorectal cancer (CRC).

Experimental Design: The expression profiles of cancer cells in 104 patients with CRC were examined using laser microdissection and oligonucleotide microarray analysis. Overexpression in CRC cells especially in patients with distant metastasis was a prerequisite to select candidate genes. The mRNA expression of candidate gene was investigated by quantitative reversetranscription polymerase chain reaction (RT-PCR) in 77 patients as a validation study. We analyzed the protein expression and localization of the candidate gene by immunohistochemical study, and investigated the relationship between the expression and the clinicopathological feature in 274 CRC patients.
Results: We identified 6 genes as candidates related to distant metastasis in CRC patients by microarray analysis. Among these genes, Osteoprotegerin (OPG) is known to have an association with aggressiveness in several cancers through inhibiting apoptosis by neutralizing the function of tumor necrosis factor related apoptosis inducing ligand (TRAIL). The mRNA expression of OPG in cancer tissues was significantly higher in patients with distant metastasis than those without metastasis. The overexpression of OPG protein was significantly associated with worse overall survival and relapse free survival (RFS). Moreover, the overexpression of OPG protein was an independent risk factor for recurrence of CRC.
Conclusion: The overexpression of OPG would be a predictive biomarker of recurrence and a target of the treatment for CRC."

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21510

We have included gene-expression data, the outcome (class) being predicted, and any clinical covariates. When gene-expression data were processed in multiple batches, we have provided batch information. Each data set is organized into a file set, where each contains all pertinent files for an individual dataset. The gene expression files have been normalized using both the SCAN and UPC methods using the SCAN.UPC package in Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). We summarized the data at the gene level using the BrainArray resource (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/ensg.asp). We used Ensembl identifiers. The class, clinical, and batch data were hand curated to ensure consistency ("tidy data" formatting). In addition, the data files have been formatted to be imported easily into the ML-Flex machine learning package (http://mlflex.sourceforge.net/).