Dataset Information

Analysis of differentially expressed genes in colorectal adenocarcinoma with versus without metastasis by three-dimensional oligonucleotide microarray.

ABSTRACT:

Background

Our objective was to examine how the gene expression profile of tumor tissue correlates with lymph node metastasis in patients with advanced colorectal adenocarcinoma (CRAC).

Methods

We studied 36 patients (20 men and 16 women, 22-90 years of age) treated for CRAC (classifications of T2, T3, or T4; histological grade of G1 or G2). Amplified tumor mRNA samples were exposed to 20,000 human sequence probes and digitized images of the hybridized samples were analyzed.

Results

On average, 2389 probes were detected above the background, with an average correlation R value of 0.19 between data from different patient groups (with or without lymph node invasion, colon or rectal, with or without angio-lymphatic invasion, with or without recurrence). Lymph node metastasis had a statistically significant signature according to Significance Analysis of Microarrays (SAM) and parametric t-tests, with a false discovery rate (FDR)=0.1% and p=0.001, respectively. Cross-correlation of these two tests identified 102 transcripts as being potentially related to node metastases, with fold changes in the range of 2.182-12.960.

Conclusion

We identified 102 differentially expressed genes related to the presence of lymph node metastases in patients with advanced colorectal cancer.

SUBMITTER: Moura Franco RM

PROVIDER: S-EPMC3885480 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Publications

Analysis of differentially expressed genes in colorectal adenocarcinoma with versus without metastasis by three-dimensional oligonucleotide microarray.

Moura Franco Rita M A M RM Linhares Marcelo M MM Lustosa Suzana S SS Silva Ismael D G C ID Souza Naiara C N NC Matos Delcio D

International journal of clinical and experimental pathology 20131215 1

<h4>Background</h4>Our objective was to examine how the gene expression profile of tumor tissue correlates with lymph node metastasis in patients with advanced colorectal adenocarcinoma (CRAC).<h4>Methods</h4>We studied 36 patients (20 men and 16 women, 22-90 years of age) treated for CRAC (classifications of T2, T3, or T4; histological grade of G1 or G2). Amplified tumor mRNA samples were exposed to 20,000 human sequence probes and digitized images of the hybridized samples were analyzed.<h4>Re ...[more]

PMID: 24427346

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Project description:BackgroundMicroarray experiments are often performed with a small number of biological replicates, resulting in low statistical power for detecting differentially expressed genes and concomitant high false positive rates. While increasing sample size can increase statistical power and decrease error rates, with too many samples, valuable resources are not used efficiently. The issue of how many replicates are required in a typical experimental system needs to be addressed. Of particular interest is the difference in required sample sizes for similar experiments in inbred vs. outbred populations (e.g. mouse and rat vs. human).ResultsWe hypothesize that if all other factors (assay protocol, microarray platform, data pre-processing) were equal, fewer individuals would be needed for the same statistical power using inbred animals as opposed to unrelated human subjects, as genetic effects on gene expression will be removed in the inbred populations. We apply the same normalization algorithm and estimate the variance of gene expression for a variety of cDNA data sets (humans, inbred mice and rats) comparing two conditions. Using one sample, paired sample or two independent sample t-tests, we calculate the sample sizes required to detect a 1.5-, 2-, and 4-fold changes in expression level as a function of false positive rate, power and percentage of genes that have a standard deviation below a given percentile.ConclusionsFactors that affect power and sample size calculations include variability of the population, the desired detectable differences, the power to detect the differences, and an acceptable error rate. In addition, experimental design, technical variability and data pre-processing play a role in the power of the statistical tests in microarrays. We show that the number of samples required for detecting a 2-fold change with 90% probability and a p-value of 0.01 in humans is much larger than the number of samples commonly used in present day studies, and that far fewer individuals are needed for the same statistical power when using inbred animals rather than unrelated human subjects.

Dataset Information

Analysis of differentially expressed genes in colorectal adenocarcinoma with versus without metastasis by three-dimensional oligonucleotide microarray.

Background

Methods

Results

Conclusion

Publications

Analysis of differentially expressed genes in colorectal adenocarcinoma with versus without metastasis by three-dimensional oligonucleotide microarray.

Similar Datasets

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