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Fig. 2 | BMC Bioinformatics

Fig. 2

From: PhenoExam: gene set analyses through integration of different phenotype databases

Fig. 2

PhenoExamWeb shiny app possible workflows. a Phenotype Enrichment Analysis: requires one gene symbol file as input file, which gene symbol nomenclature (Organism nomenclature: Human or Mouse) we use, the phenotype/disease annotation databases to be considered and the top number of terms shown in the graph. The results generate an interactive table and graph which include phenotypes, genes implicated with each term and P values as output. b The Phenotype Comparator requires two gene sets as input together with the gene symbol nomenclature (Human or Mouse) used, the annotation databases of interest for the analysis and the number of random tests to obtain empirical P values, the relevant P value threshold and whether our analysis is a conditional case (i.e., if one gene set was generated after a prediction analysis from the other and they are totally different gene sets). Finally, we obtain the summary of the analysis with the similarities phenotype scores, the differential phenotypes, interactive tables and graphs with phenotypes, genes and P values as output for detailed inspection and result presentation. We acknowledge all the sources for their contributions and we are grateful to those who permitted us to use their logos in this figure

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