ggsignif: R Package for Displaying Significance Brackets for 'ggplot2'

Ahlmann-Eltze, Constantin; Patil, Indrajeet

doi:10.31234/osf.io/7awm6

Cited by 227 publications

(167 citation statements)

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“…We constructed and ran bioinformatics pipelines using snakemake (v.5.17.0 [110]) within a python conda environment (v3.6). We analyzed and visualized data in R (v3.6.2 [91]) using the following major packages: tidyverse (v1.3.0 [111]), viridis (v0.5.1 [112]), bedr (v1.0.7 [104]), boot (v.1.3 25 [113, 114]), gridExtra (v2.3 [115]), ggupset (v0.3.0 [116]) and tidygraph (1.2.0 [117]). All scripts can be found on our gitHub repository, https://github.com/ecalfee/hilo, which also includes a full list of software and versions (see envs/environment.yaml).…”

Section: Methodsmentioning

confidence: 99%

Selective sorting of ancestral introgression in maize and teosinte along an elevational cline

Calfee¹,

Gates²,

Lorant

et al. 2021

Preprint

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While often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize (Zea mays ssp. mays), and its wild teosinte relative. Introgression from ecologically diverse teosinte may have facilitated maize's global range expansion, in particular to challenging high elevation regions (> 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of Zea mays ssp. mexicana, a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed >1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low Fst between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana, especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized Inv4m and a new 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. The bulk of our ancestry selection outliers show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize landrace populations.

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Section: Methodsmentioning

confidence: 99%

Selective sorting of ancestral introgression in maize and teosinte along an elevational cline

Calfee¹,

Gates²,

Lorant

et al. 2021

Preprint

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“…Expression boxplots of each group specific transcription factor were drawn by "ggplot2" package function "ggplot" (Wickham, 2016). To add the significance scores, "ggsignif" package was used by using basic Student's t test for statistical analysis (Ahlmann-Eltze, 2021).…”

Section: Processing Of Nmibc and Mibc Patient Gene Expression Datamentioning

confidence: 99%

FLI1 and FRA1 transcription factors drive the transcriptional regulatory networks characterizing muscle invasive bladder cancer

Sozeri

Yilmaz

Kisim

et al. 2021

Preprint

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SUMMARYBladder cancer is mostly present in the form of urothelium carcinoma, causing over 150.000 deaths each year. Its histopathological classification as muscle invasive (MIBC) and non-muscle invasive (NMIBC) is the most prominent aspect, affecting the prognosis and progression of this disease. In this study, we defined the active regulatory landscape of MIBC and NMIBC cell lines using H3K27ac-seq and used an integrative data approach to combine our findings with existing data. Our analysis revealed FRA1 and FLI1 as the two critical transcription factors differentially regulating MIBC regulatory landscape. Importantly, we show that FRA1 and FLI1 regulate the genes involved in epithelial cell migration and cell junction organization. Knock-down of FRA1 and FLI1 in MIBC revealed the downregulation of several EMT-related genes such as MAP4K4 and FLOT1. Further, ChIP-SICAP performed for FRA1 and FLI1 enabled us to infer chromatin binding partners of these two transcription factors and link this information with their target genes, providing a comprehensive regulatory circuit for the genes implicated in invasive ability of the bladder cancer cells. Finally, for the first time we show that knock-down of FRA1 and FRA1-FLI1 double knock-down results in significant reduction of invasion capacity of MIBC cells towards muscle microenvironment using IC-CHIP assays. Our results collectively highlight the role of these two transcription factors in invasive characteristics of bladder cancer in selection and design of targeted options for treatment of MIBC.

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“…Paired t-tests and Wilcox tests (R [45] package ggsignif [46]) were used to assess the statistical significance of differences in the relative number of pits on the distal most 20% of the beak between the different types of soft tissue arrangements found in the extant bird species sampled.…”

Section: (F ) Statistical Analyses and Plotting Of Figuresmentioning

confidence: 99%

Cretaceous origins of the vibrotactile bill-tip organ in birds

2020

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Some probe-foraging birds locate their buried prey by detecting mechanical vibrations in the substrate using a specialized tactile bill-tip organ comprising mechanoreceptors embedded in densely clustered pits in the bone at the tip of their beak. This remarkable sensory modality is known as ‘remote touch’, and the associated bill-tip organ is found in probe-foraging taxa belonging to both the palaeognathous (in kiwi) and neognathous (in ibises and shorebirds) clades of modern birds. Intriguingly, a structurally similar bill-tip organ is also present in the beaks of extant, non-probing palaeognathous birds (e.g. emu and ostriches) that do not use remote touch. By comparison with our comprehensive sample representing all orders of extant modern birds (Neornithes), we provide evidence that the lithornithids (the most basal known palaeognathous birds which evolved in the Cretaceous period) had the ability to use remote touch. This finding suggests that the occurrence of the vestigial bony bill-tip organ in all modern non-probing palaeognathous birds represents a plesiomorphic condition. Furthermore, our results show that remote-touch probe foraging evolved very early among the Neornithes and it may even have predated the palaeognathous–neognathous divergence. We postulate that the tactile bony bill-tip organ in Neornithes may have originated from other snout tactile specializations of their non-avian theropod ancestors.

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ggsignif: R Package for Displaying Significance Brackets for 'ggplot2'

Cited by 227 publications

References 0 publications

Selective sorting of ancestral introgression in maize and teosinte along an elevational cline

Selective sorting of ancestral introgression in maize and teosinte along an elevational cline

FLI1 and FRA1 transcription factors drive the transcriptional regulatory networks characterizing muscle invasive bladder cancer

Cretaceous origins of the vibrotactile bill-tip organ in birds

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