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PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes

Andreas Ruepp1*, Andreas Kowarsch1, Daniel Schmidl12, Felix Buggenthin1, Barbara Brauner1, Irmtraud Dunger1, Gisela Fobo1, Goar Frishman1, Corinna Montrone1 and Fabian J Theis12*

Author Affiliations

1 Institute for Bioinformatics and Systems Biology (MIPS), Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany

2 Department of Mathematics, University of Technology Munich, Boltzmannstraße 3, D-85747 Garching, Germany

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Genome Biology 2010, 11:R6  doi:10.1186/gb-2010-11-1-r6

Published: 20 January 2010

Additional files

Additional file 1:

The PhenomiR dataset.

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Additional file 2:

T, number of diseases for which each cluster showing a homogeneous expression pattern; F, number of diseases for which each cluster shows no homogeneous expression pattern; Homogeneous-fraction, number of diseases for which each cluster shows a homogeneous expression pattern for each miRNA cluster as defined; P-value, estimate by randomly linking miRNA-expression patterns 10,000 times within each disease.

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Additional file 3:

For each disease the log-odds (LOD) score is plotted. We found that polycistronic loci are on average 3.5 times (LOD = 1.83) more disease-associated than expected. For abbreviations of disease names see Additional file 13.

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Additional file 4:

For each disease the log-odds (LOD) score is plotted. The LOD score for disease d is given by: LODd = log2 ((yd/(xd + yd))/(yoverall/(xoverall + yoverall))) (see Materials and methods for a detailed description). We found that differentially expressed single miRNA loci are not enriched in diseases. Red points depict disorders with few deregulated single miRNA loci and black points indicate diseases without enrichment compared to random. For abbreviations of disease names see Additional file 13.

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Additional file 5:

(a) miRNA cluster enrichment for cancer diseases. (b) miRNA cluster enrichment for non-cancer diseases. For each disease the log odds (LOD) score is plotted. Green points depict enriched diseases. Black points indicate diseases without enrichment compared to random and red points depict disorders with few deregulated cluster members.

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Additional file 6:

T, number of diseases for which each cluster shows a homogeneous expression pattern; F, number of diseases for which each cluster shows no homogeneous expression pattern; Homogeneous-fraction, number of diseases for which each cluster shows a homogeneous expression pattern for each miRNA cluster as defined; P-value, estimate by randomly linking miRNA-expression patterns 10,000 times within each disease.

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Additional file 7:

T, number of diseases for which each cluster shows a homogeneous expression pattern; F, number of diseases for which each cluster shows no homogeneous expression pattern; Homogeneous-fraction, number of diseases for which each cluster shows a homogeneous expression pattern for each miRNA cluster as defined; P-value, estimate by randomly linking miRNA-expression patterns 10,000 times within each disease.

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Additional file 8:

For each disease the log odds (LOD) score is plotted. Order is based on LOD scores for polycistronic miRNA loci using a 5-kb distance threshold according to chromosomal locations. For abbreviations of disease names see Additional file 13.

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Additional file 9:

The dashed line shows the background frequency, which is given by the number of the 62 human polycistronic miRNA loci, and the sum of polycistronic loci and the 455 human miRNAs that are not contained in any cluster as obtained from mirBase (release 12.0) using a 5-kb distance threshold according to chromosomal locations. For abbreviations of disease names see Additional file 13.

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Additional file 10:

The dashed line shows the background frequency, which is given by the number of the 65 human polycistronic miRNA loci, and the sum of polycistronic loci and the 452 human miRNAs that are not contained in any cluster as obtained from miRBase (release 12.0) using a 10-kb distance threshold according to chromosomal locations. For abbreviations of disease names see Additional file 13.

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Additional file 11:

The dashed line shows the background frequency, which is given by the number of the 72 human polycistronic miRNA loci, and the sum of polycistronic loci and the 445 human miRNAs that are not contained in any cluster as obtained from mirBase (release 12.0) using a 50-kb distance threshold according to chromosomal locations. For abbreviations of disease names see Additional file 13.

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Additional file 12:

For each disease the log odds (LOD) score is plotted. Order is based on LOD scores for miRNA clusters using a 5-kb threshold.

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Additional file 13:

Diseases used in this analysis and corresponding short names.

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