An Operational Definition of a Statistically Meaningful Trend

Bryhn, Andreas C.; Dimberg, Peter H.

doi:10.1371/journal.pone.0019241

Cited by 53 publications

(34 citation statements)

References 9 publications

(16 reference statements)

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“…The large reduction in significant changes in an incorrectly ordered time series indicates that the findings in the correctly ordered set are of high confidence and likely have a false-positive rate of around 3% to 5%. This false-positive rate is also consistent with the 5% error rate that has been predicted when selecting an r 2 of 0.65 for significant trends in a regression analysis (Bryhn and Dimberg, 2011).…”

Section: Seed Embryo and Endosperm Undergo Hundreds Of Developmentasupporting

confidence: 83%

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

et al. 2015

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Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage-or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.After transcription, the majority of eukaryotic premRNA is subjected to a series of posttranscriptional modifications, including the removal of introns to form a mature mRNA (Stamm et al., 2005). Although some introns are removed constitutively, many can be processed in a variety of alternative ways, including exon skipping, intron retention, alternative acceptor, alternative donor, and alternative position (change in both acceptor and donor positions; Lorkovic et al., 2000). These alternative splicing events form a crucial regulatory level and have the ability to alter an mRNA's stability, localization, and protein products. Alternative splicing events are controlled by a variety of cis-elements, including the presence of consensus splice sequences at the intron-exon border and intronic and exonic splicing enhancer sequences (Pertea et al., 2007). Trans-acting factors also exert a strong effect on splicing and are mostly composed of Ser/Arg-rich proteins, which typically promote intron removal, and heterogenous nuclear ribonucleoproteins, which typically inhibit it (Erkelenz et al., 2013). A host of other indirect factors can affect splicing, including transcription rate, methylation status, and any cellular conditions that alter RNA secondary structure (Kornblihtt et al

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Section: Seed Embryo and Endosperm Undergo Hundreds Of Developmentasupporting

confidence: 83%

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

et al. 2015

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“…The method of linear contrasts was used to compare the mean expression of SOX9 in the control with that in the father, the three XY siblings (III1, III3, III5) treated as a group, the two unaffected siblings (III2, III4) treated as a group, and the mother(13, 14). Adjustment was made for the fact that there were replicated observations for each subject.…”

Section: Methodsmentioning

confidence: 99%

Familial 46,XY sex reversal without campomelic dysplasia caused by a deletion upstream of the SOX9 gene

Bhagavath

Layman

Ullmann

et al. 2014

Molecular and Cellular Endocrinology

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Background-46,XY sex reversal is a rare disorder and familial cases are even more rare. The purpose of the present study was to determine the molecular basis for a family with three affected siblings who had 46,XY sex reversal.Methods-DNA was extracted from three females with 46,XY sex reversal, two normal sisters, and both unaffected parents. All protein coding exons of the SRY and NR5A1 genes were subjected to PCR-based DNA sequencing. In addition, array comparative genomic hybridization was performed on DNA from all seven family members. A deletion was confirmed using quantitative polymerase chain reaction. Expression of SOX9 gene was quantified using reverse transcriptase polymerase chain reaction.© 2014 Elsevier Ireland Ltd. All rights reserved.Correspondence to: Bala Bhagavath. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptResults-A 349kb heterozygous deletion located 353kb upstream of the SOX9 gene on the long arm of chromosome 17 was discovered in the father and three affected siblings, but not in the mother. The expression of SOX9 was significantly decreased in the affected siblings. Two of three affected sisters had gonadoblastomas.Conclusion-This is the first report of 46,XY sex reversal in three siblings who have a paternally inherited deletion upstream of SOX9 associated with reduced SOX9 mRNA expression.

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“…This study uses statistical tests to compare the observed GST anomaly data record with model-simulated records and detect evidence of warming hiatus periods. Two different statistical methods are used to identify hiatus periods: (1) a type of statistical significance test for data trends-called a "statistical meaningfulness" test [13]-is performed to find periods in model data records with no statistically meaningful GST warming or cooling and (2) large, rapid changes in the GST rate are identified in the model data records which are consistent with variations observed in the recent hiatus.…”

Section: Methodsmentioning

confidence: 99%

Detecting Warming Hiatus Periods in CMIP5 Climate Model Projections

Baker

2016

International Journal of Atmospheric Sciences

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The observed slow-down in the global-mean surface temperature (GST) warming from 1998 to 2012 has been called a “warming hiatus.” Certain climate models, operating under experiments which simulate warming by increasing radiative forcing, have been shown to reproduce periods which resemble the observed hiatus. The present study provides a comprehensive analysis of 38 CMIP5 climate models to provide further evidence that models produce warming hiatus periods during warming experiments. GST rates are simulated in each model for the 21st century using two experiments: a moderate warming scenario (RCP4.5) and high-end scenario (RCP8.5). Warming hiatus periods are identified in model simulations by detecting (1) ≥15-year periods lacking a statistically meaningful trend and (2) rapid changes in the GST rate which resemble the observed 1998–2012 hiatus. Under the RCP4.5 experiment, all tested models produce warming hiatus periods. However, once radiative forcing exceeds 5 W/m2—about 2°C GST increase—as simulated in the RCP8.5 experiment after 2050, nearly all models produce only positive warming trends. All models show evidence of rapid changes in the GST rate resembling the observed hiatus, showing that the climate variations associated with warming hiatus periods are still evident in the models, even under accelerated warming conditions.

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An Operational Definition of a Statistically Meaningful Trend

Cited by 53 publications

References 9 publications

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

Familial 46,XY sex reversal without campomelic dysplasia caused by a deletion upstream of the SOX9 gene

Detecting Warming Hiatus Periods in CMIP5 Climate Model Projections

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