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Fig. 3 | BMC Bioinformatics

Fig. 3

From: A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data

Fig. 3

Results from IPF scRNA-seq Data Analysis. A Number of cell-type specific DEGs identified using original test statistics alone, and two MRF models with the BioGrid and IntAct database for four types of test statistic inputs: two-sample t-test, the Wilcoxon rank sum test, and MAST. For instance, the upper-left figure in A shows the number of cell-type specific DEGs inferred using two-sample t-test alone (w/o MRF), and the DE results from two MRF models that incorporated t-test statistics as observed DE evidence and two gene network structures (MRF w/ BioGrid and MRF w/ IntAct, respectively). B The UpSet plot shows the overlap of DEGs identified by the original models and our proposed MRF models utilizing the BioGrid and IntAct gene networks. C The top canonical pathways from Ingenuity Pathways Analysis. The p-value cutoff was set at 0.005 and gene ratio cutoff was set at 0.25 in order to better visualize top enriched pathways

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