Open Access Research article

miRConnect 2.0: identification of oncogenic, antagonistic miRNA families in three human cancers

Youjia Hua1, Niels Larsen2, Shanker Kalyana-Sundaram3, Jørgen Kjems2, Arul M Chinnaiyan3 and Marcus E Peter1*

Author Affiliations

1 Feinberg School of Medicine, Division Hematology/Oncology, Northwestern University, Chicago, 60611, USA

2 Department of Molecular Biology, Aarhus University, Århus, Denmark

3 Michigan Center for Translational Pathology, Ann Arbor, MI, 48109, USA

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BMC Genomics 2013, 14:179  doi:10.1186/1471-2164-14-179

Published: 15 March 2013

Additional files

Additional file 1: Table S1:

Oncogenic signatures used in the study.

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Additional file 2: Table S2:

Correlation of positively correlating miRNA clusters of the NCI60 Q data with 3 EMT signatures.

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Additional file 3: Table S3:

Correlation of negatively correlating miRNA clusters of the NCI60 Q data with 3 EMT signatures.

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Additional file 4: Table S4:

The TCGA data sets used in the study.

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Additional file 5: Figure S1:

Venn Diagrams of overlapping miRNAs or mRNAs deregulated >1.5 fold in OvCa, GBM and KIRC. Figure S2. Scheme illustrating the flow of the analysis. Figure S3. The genomic clusters and seed families of the miR-17, miR-221/222 and miR-200 families. Figure S4. Functional clusters of deregulated cancer relevant miRNAs in three primary cancers according to positively correlated genes based on the sPCC method.

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Additional file 6: Table S5:

miRNA clusters in all data sets based on positively and negatively correlating genes.

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Additional file 7: Table S6:

Correlation of positively correlating miRNA clusters of the OvCa data with 3 EMT signatures.

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Additional file 8: Table S7:

Correlation of positively correlating miRNA clusters of the OvCa data with 158 oncogenic signatures.

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Additional file 9: Table S8:

miRNAs that are found in the the agonistic miRNA groups in different cancers.

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Additional file 10: Table S9:

sPCC analysis of agonistic and antagonistic miRNAs as shown in Figure 5A-OvCa.

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Additional file 11: Table S10:

Lists of genes that positively correlale with the agonists and antagonists in three cancers.

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Additional file 12: Table S11-1:

Functional networks covered by genes correlating with the agonists. Table S11-2. Functional networks covered by genes correlating with the antagonists.

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Additional file 13: Table S12:

Correlations between individual agonistic and antagonistic miRNAs in OvCa.

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Additional file 14: Table S13:

Overlap of deregulated miRNAs and mRNAs in the three cancers.

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Additional file 15: Table S14:

Analysis of patient data.

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