Fig 1.
A metagene analysis requires 3 types of inputs: 1) a list of genomic regions (BED or GRanges formats), 2) alignment files (BAM format) and 3) a design sheet (data frame format) explaining the relations between samples. The alignment files are processed to extract the coverages of every genomic regions. Afterward, the background is removed from the coverages and the signal is normalized (reads per millions aligned or RPM) to allow comparison between samples. The main output is the metagene plot. The other outputs are the curve values and confidence intervals (CI) used to produce the plot and an interactive heatmap with Imetagene. The results are compatible with similaRpeak for profile characterization.
Fig 2.
Impact of noise removal and description of the pseudometrics.
Metagene plots of the BCL11A transcription factor (A) with noise removal using the NCIS algorithm and (B) without noise removal. The x-axis is centered on enhancers and promoters ±1000bp. The y-axis represents the mean occupancy normalized in reads per million (RPM). Each line represents the mean occupancy of the BCL11A replicates. Groups of transcriptional activity of enhancers or promoters are identified by different colors (red = no CAGE signal; green = low CAGE signal; blue = moderate CAGE signal; purple = high CAGE signal; see S1 Text). Ribbons represent the 95% confidence interval of the mean calculated using 1000 bootstraps. (C) Description of some of the pseudometrics implemented in the similaRpeak packages.
Fig 3.
Metagene profiles in enhancer and promoter regions.
(A) POLR2A, the largest subunit of Pol II. (B) TAF1, a general transcription factor. (C) ELF1, a transcription factor. The x-axis is centered on enhancers and promoters ±1000bp. The y-axis represents the mean occupancy normalized in reads per million (RPM). Each line represents the mean occupancy of the factor replicates. Groups of transcriptional activity of enhancers or promoters are identified by different colors (red = no CAGE signal; green = low CAGE signal; blue = moderate CAGE signal; purple = high CAGE signal). The ribbons represent the 95% confidence interval of the mean calculated using 1000 bootstraps.