BootstRatio: A web-based statistical analysis of fold-change in qPCR and RT-qPCR data using resampling methods

Clèries, Ramón; Gálvez, Jordi; Espino, Meritxell; Ribes, Josepa; Nunes, Virginia; Heredia, Miguel López de

doi:10.1016/j.compbiomed.2011.12.012

Cited by 57 publications

(43 citation statements)

References 17 publications

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“…Data presentation and statistical analysis was performed using the GraphPad Prism v5.03 software package or the Bootstratio algorithm (Cleries et al, 2012). …”

Section: Methodsmentioning

confidence: 99%

Harnessing Bacterial Signals for Suppression of Biofilm Formation in the Nosocomial Fungal Pathogen Aspergillus fumigatus

et al. 2016

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Faced with the continued emergence of antibiotic resistance to all known classes of antibiotics, a paradigm shift in approaches toward antifungal therapeutics is required. Well characterized in a broad spectrum of bacterial and fungal pathogens, biofilms are a key factor in limiting the effectiveness of conventional antibiotics. Therefore, therapeutics such as small molecules that prevent or disrupt biofilm formation would render pathogens susceptible to clearance by existing drugs. This is the first report describing the effect of the Pseudomonas aeruginosa alkylhydroxyquinolone interkingdom signal molecules 2-heptyl-3-hydroxy-4-quinolone and 2-heptyl-4-quinolone on biofilm formation in the important fungal pathogen Aspergillus fumigatus. Decoration of the anthranilate ring on the quinolone framework resulted in significant changes in the capacity of these chemical messages to suppress biofilm formation. Addition of methoxy or methyl groups at the C5–C7 positions led to retention of anti-biofilm activity, in some cases dependent on the alkyl chain length at position C2. In contrast, halogenation at either the C3 or C6 positions led to loss of activity, with one notable exception. Microscopic staining provided key insights into the structural impact of the parent and modified molecules, identifying lead compounds for further development.

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“…Data presentation and statistical analysis was performed using the GraphPad Prism v5.03 software package or the Bootstratio algorithm (Cleries et al, 2012). …”

Section: Methodsmentioning

confidence: 99%

Harnessing Bacterial Signals for Suppression of Biofilm Formation in the Nosocomial Fungal Pathogen Aspergillus fumigatus

et al. 2016

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“…For histone modifications, the abundance of each PCR amplicon was normalized to primer set 6 (Table S5), and then the ratio of modified histone to total histone was calculated. The SE of the ratio was obtained using BootstRatio (56).…”

Section: Methodsmentioning

confidence: 99%

Regional centromeres in the yeast Candida lusitaniae lack pericentromeric heterochromatin

Kapoor

Zhu

Froyd

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Point centromeres are specified by a short consensus sequence that seeds kinetochore formation, whereas regional centromeres lack a conserved sequence and instead are epigenetically inherited. Regional centromeres are generally flanked by heterochromatin that ensures high levels of cohesin and promotes faithful chromosome segregation. However, it is not known whether regional centromeres require pericentromeric heterochromatin. In the yeast Candida lusitaniae, we identified a distinct type of regional centromere that lacks pericentromeric heterochromatin. Centromere locations were determined by ChIP-sequencing of two key centromere proteins, Cse4 and Mif2, and are consistent with bioinformatic predictions. The centromeric DNA sequence was unique for each chromosome and spanned 4-4.5 kbp, consistent with regional epigenetically inherited centromeres. However, unlike other regional centromeres, there was no evidence of pericentromeric heterochromatin in C. lusitaniae. In particular, flanking genes were expressed at a similar level to the rest of the genome, and a URA3 reporter inserted adjacent to a centromere was not repressed. In addition, regions flanking the centromeric core were not associated with hypoacetylated histones or a sirtuin deacetylase that generates heterochromatin in other yeast. Interestingly, the centromeric chromatin had a distinct pattern of histone modifications, being enriched for methylated H3K79 and H3R2 but lacking methylation of H3K4, which is found at other regional centromeres. Thus, not all regional centromeres require flanking heterochromatin.centromere | heterochromatin | Candida | CSE4 | Sir2

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“…TaqMan® probes and the TaqMan Gene Expression Assay (Life Technologies) were purchased for SLFN5 (Hs00288058_m1) and 18S RNA (Hs 99999901_s1) and normalized to beta actin (#Hs01060665_g1). Normalized values for IFNα-treated samples (N=9) were compared to untreated controls (N=9) using Bootsratio statistical software [9]. …”

Section: Methodsmentioning

confidence: 99%

SCHLAFEN 5 expression correlates with intestinal metaplasia that progresses to gastric cancer

et al. 2016

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Background Intestinal metaplasia (IM) is a gastric cancer precursor lesion (GCPL), with the highest risk to progress to gastric cancer (GC). Clinical guidelines recommend gastroscopy every 3 years for extensive IM. Unfortunately, studies on protein biomarkers indicating a transition from IM to GC are lacking. We have recently found that the IFNα-responsive gene Schlafen 4 (Slfn4) present in immune cells correlates with metaplastic changes in Helicobacter-infected mice. Therefore we tested the hypothesis that a human homolog of Slfn4, which is Schlafen 5 (SLFN5) correlates with progression of GCPL to GC. Methods Jurkat T-lymphoid and HL-60 myeloid cell lines were treated with IFNα and SLFN5 mRNA was quantified by qPCR. SLFN5 protein expression in the inflamed gastric mucosa was co-localized to specific immune cell types by immunohistochemistry using CD20, CD2 and MAC2 antibodies. SLFN5 expression was also determined by immunohistochemistry in FFPE samples from individuals with non-atrophic, atrophic gastritis, complete and incomplete IM as well as GC. Results We demonstrated that IFNα treatment of Jurkat and HL-60 cells induced SLFN5 mRNA. SLFN5 protein was expressed mainly by T lymphocytes in inflamed gastric mucosa. The highest level of SLFN5 expression was observed in subjects with IM that progressed to GC. ROC curves demonstrated that combining SLFN5 expression with the histological diagnosis of IM significantly increased the probability of identifying patients that might progress to GC. Conclusion Elevated SLFN5 protein expression in subjects with IM correlated with progression to gastric cancer.

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BootstRatio: A web-based statistical analysis of fold-change in qPCR and RT-qPCR data using resampling methods

Cited by 57 publications

References 17 publications

Harnessing Bacterial Signals for Suppression of Biofilm Formation in the Nosocomial Fungal Pathogen Aspergillus fumigatus

Harnessing Bacterial Signals for Suppression of Biofilm Formation in the Nosocomial Fungal Pathogen Aspergillus fumigatus

Regional centromeres in the yeast Candida lusitaniae lack pericentromeric heterochromatin

SCHLAFEN 5 expression correlates with intestinal metaplasia that progresses to gastric cancer

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