Open Access Highly Accessed Research article

Human colon cancer profiles show differential microRNA expression depending on mismatch repair status and are characteristic of undifferentiated proliferative states

Aaron L Sarver1*, Amy J French2, Pedro M Borralho3, Venugopal Thayanithy4, Ann L Oberg5, Kevin AT Silverstein1, Bruce W Morlan5, Shaun M Riska5, Lisa A Boardman6, Julie M Cunningham2, Subbaya Subramanian4, Liang Wang2, Tom C Smyrk2, Cecilia MP Rodrigues3, Stephen N Thibodeau2 and Clifford J Steer78

Author Affiliations

1 Biostatistics and Informatics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA

2 Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA

3 Research Institute for Medicines and Pharmaceutical Sciences, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal

4 Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA

5 Department of Health Sciences Research, Division of Biomedical Informatics and Statistics, Mayo Clinic, Rochester, Minnesota, USA

6 Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA

7 Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA

8 Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA

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BMC Cancer 2009, 9:401  doi:10.1186/1471-2407-9-401

Published: 18 November 2009

Additional files

Additional file 1:

qRT-PCR primer sequences. Sequences used for qRT-PCR of miRNA levels.

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Additional file 2:

Tissue clinical data. Additional clinical data shown in Table 1 broken down by tumor id.

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Additional file 3:

miRNA profiles in Colon Cancer and normal tissues. All data, both raw and normalized. A)Raw Log base 2 transformed miRNA data B)Quantile normalized log base 2 miRNA data C) Averaged log base 2 quantile normalized miRNA data D) Averaged, quantile normalized miRNA data E)quantile normalized averaged data normalized by average of normal colon tissue.

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Additional file 4:

SVM confusion matrices. Confusion matrices for A) normal vs tumor comparison using all miRNA B) dMMR vs pMMR tumor comparison.

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Additional file 5:

Complete statistical data. A linear mixed effects model was used to determine statistically significant miRNAs for A) normal tissue compared with colon cancer tissue and B) dMMR tumor tissue compared with pMMR tumor tissue.

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Additional file 6:

Illumina platform analyses. Illumina platform performance analysis for previously reported miRNAs altered in CC. Heat map describing fold change from normal tissue for known high concentration miRNAs (let-7a), a negative control element (neg.con.), miRNAs reported involved in colon tumorigenesis (miR-21 and miR-143) and miRNAs we observed to be altered in tumor specimens (miR-31, miR-135b, miR-30a-3p). The log base 2 raw fluorescent intensity is shown for each miRNA. The highest value found on the array was less than 16 on the log base 2 scale.

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Additional file 7:

Probes with high average expression and low variance. Probes with high average expression and low variance.

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Additional file 8:

Unsupervised hierarchical clustering of cell line miRNA profiles obtained from Illumina platform and cDNA arrays. Following removal of high expressing low variability Illumina probes and low expressing cDNA probes the remaining miRNA cluster together by cell line of sample origin.

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