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Fig. 4 | BMC Bioinformatics

Fig. 4

From: MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts

Fig. 4

Graphs of small-non coding main biotypes in human libraries. Each vertex is an annotated features with size proportional to its number of aligned reads and color representing its gene symbol in relation to the Hugo Gene Nomenclature Committee (HGNC) (annotations not following HGNC are colored in gray and often correspond to computationally predicted annotations). Each edge connects two features with shared multi-mappers with thickness proportional to the fraction of shared multi-mappers over the total alignments. Shared grey areas delineate MG communities. a snRNA graph. Vertices are colored by first number after “RNU” pattern in transcript symbol. b snoRNA graph. Vertices are colored by first number after “SNORNA” pattern in transcript symbol. c microRNA graph. Vertices are colored by “3p” (orange) and “5p” (blue) patterns in transcript symbol. d piRNA graph. Vertices are colored by first number after “PIRNA” pattern. e miscRNA graph. Vertices are colored separately by YNY1, YNY3, YNY4, RN7SK, RN7SL, VT patterns in transcript symbol. f tRNA graph. Vertices are colored by amino-acid 3-letters reference pattern in transcript symbol. g–h Matrices comparing the similarity between MG communities obtained from different input data or algorithm runs using the the Normalized Mutual Information (NMI) index. Last column in each panel shows comparison with a random permutation of the cluster labels. i Linear regression fit (black dashed line) and its 95% confidence level interval (gray area) modelling the relationship between RT-qPCR and NGS fold change estimation of Human Brain and K562 expression for 20 small-RNA markers of different biotypes. Linear regression fit (black dashed line) and its 95% confidence level interval (gray area) modelling the relationship between RT-qPCR and NGS fold change estimation of human brain and K562 expression for 20 small-RNA markers of different biotypes. (HBR: Human Brain)

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