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Output format
The output from MetaRanker consists of the following parts:
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A table showing the 20 highest ranking genes. Here you will find
the overall score of the gene, the gene's permutation-based p-value, and other gene-specific information, such as the gene's normalized score from each layer used in the analysis (in ascending order; 1 means that the gene was not part of the original input or formation of that particular layer).
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A downloadable file containing the results of all genes.
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A overview figure of the 20 highest ranking genes (Figure 3a, Pers and Hansen et al. Genetic Epidemiology 2011).
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A downloadable file containing a pdf-version of the overview figure.
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Downloadable Cytoscape files that can be used for construction of the seed
gene network (Figure 3b, Pers and Hansen et al. Genetic Epidemiology 2011).
The file with the .sif extension contains the network, the .csv
file contains gene specific information used for assigning
attribute to the nodes in the network, and the .eda file that
contains confidence levels for the protein-protein interactions.
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Details on the genome-wide association evidence layer: Number of SNPs that were mapped, number of SNPs that were discarded due to missing or wrongly specified p-values, number of SNPs that were discarded because they were not mapped to genes, and the total number of genes scored in that layer.
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Details on the candidate gene interaction evidence layer: Number of input seed genes specified by the user that could mapped to the protein-protein interaction meta database used in this work (previously reported in Lage et al. Nature Biotechnology 2007), and the total number of genes scored in that layer.
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Details on the differential gene expression evidence layer: The number of user-specified genes and the total number of genes scored in that layer.
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Details on the linkage interval evidence layer: The total number of genes in each distinct user-specified linkage interval, and the total number of genes scored in that layer.
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Details on the phenotype similarity evidence layer: The phenotypes that were most similar to the phenotype specified by the user, and the total number of genes assigned a phenotype similarity score.
Please note, that the layer details only are reported if the specific layer was chosen by the user prior to the analysis.
Example of output
Top 20 genes
Download MetaRanker results.
Download dot-figure.
Download Cytoscape files for seed-network construction:
Cytoscape CSV file
Cytoscape EDA file
Cytoscape SIF file
Genome-wide association layer
Number of mapped SNPs: 11361887
Number of discarded SNPs due to undefined p-value: 0
Number of discarded SNPs because they were not within or close to genes: 0
Number of scored genes: 17457
Candidate gene interaction layer
Number of input susceptibility genes in InWeb database: 32 of 35
Number of genes scored: 516
Linkage layer
Chromosome Band Number of genes
16 p12.1 104
16 p12.2 104
16 p12.3 104
18 p11.1 84
18 p11.21 84
18 p11.22 84
18 p11.23 84
18 p11.31 84
18 p11.32 84
2 q24.1 54
2 q24.2 54
2 q24.3 54
21 q22.13 14
22 q12.1 136
22 q12.2 136
22 q12.3 136
6 q23.1 90
6 q23.2 90
6 q23.3 90
6 q24.1 90
6 q24.2 90
6 q24.3 90
X q28 130
Number of genes scored: 612
Phenotype similarity layer
Disease term and most similar diseases:
bipolar disorder
schizophrenia
mood disorders
involutional depression
mental disorders
psychotic disorders
neurodegenerative diseases
schizoaffective disorder
parkinson disease
child attention deficit disorder
Number of genes scored: 3784
Differential expression layer
Number of genes scored: 12916
GETTING HELP
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