voom: precision weights unlock linear model analysis tools for RNA-seq read counts

Law, Charity W.; Chen, Yunshun; Shi, Wei; Smyth, Gordon K.

doi:10.1186/gb-2014-15-2-r29

Cited by 4,775 publications

(4,310 citation statements)

References 57 publications

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“…We estimated expression using STAR alignments in transcriptomic coordinates and the RSEM package 52 , and calculated differential expression using the limma package following voom transformation of the estimated counts 53,54 . Raw read counts for genes with counts per million (cpm) value >1 in at least three samples (15,729 genes) were used as inputs to tbe limma/voom pipeline and scale normalization of the RNA-seq read counts was performed using the TMM normalization method 55 .…”

Section: Methodsmentioning

confidence: 99%

The genetic basis of parental care evolution in monogamous mice

Bendesky

Kwon

Lassance

et al. 2017

Nature

210

199

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Summary Parental care is essential for the survival of mammals, yet the mechanisms underlying its evolution remain largely unknown. Here we show that two sister species of mice, Peromyscus polionotus and P. maniculatus, have large and heritable differences in parental behaviour. Using quantitative genetics, we identify 12 genomic regions that affect parental care, eight of which have sex-specific effects, suggesting that parental care can evolve independently in males and females. Furthermore, some regions affect parental care broadly, whereas others affect specific behaviours, such as nest building. Of the genes linked to differences in nest-building behaviour, vasopressin is differentially expressed in the hypothalamus of the two species, with increased levels associated with less nest building. Using pharmacology in Peromyscus and chemogenetics in Mus, we show that vasopressin inhibits nest building but not other parental behaviours. Together, our results indicate that variation in an ancient neuropeptide contributes to interspecific differences in parental care.

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Section: Methodsmentioning

confidence: 99%

The genetic basis of parental care evolution in monogamous mice

Bendesky

Kwon

Lassance

et al. 2017

Nature

210

199

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“…Counts were converted to log2 counts per million, quantile normalized and precision weighted with the voom function of the limma package. 52,53 A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. 54 A false discovery rate cut-off of 0.15 was applied for calling differentially expressed genes.…”

Section: Methodsmentioning

confidence: 99%

A point mutation in the Ncr1 signal peptide impairs the development of innate lymphoid cell subsets

et al. 2018

Self Cite

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NKp46 (CD335) is a surface receptor shared by both human and mouse natural killer (NK) cells and innate lymphoid cells (ILCs) that transduces activating signals necessary to eliminate virus-infected cells and tumors. Here, we describe a spontaneous point mutation of cysteine to arginine (C14R) in the signal peptide of the NKp46 protein in congenic Ly5.1 mice and the newly generated NCRB6C14R strain. Ly5.1C14R NK cells expressed similar levels of Ncr1 mRNA as C57BL/6, but showed impaired surface NKp46 and reduced ability to control melanoma tumors in vivo. Expression of the mutant NKp46C14R in 293T cells showed that NKp46 protein trafficking to the cell surface was compromised. Although Ly5.1C14R mice had normal number of NK cells, they showed an increased number of early maturation stage NK cells. CD49a+ILC1s were also increased but these cells lacked the expression of TRAIL. ILC3s that expressed NKp46 were not detectable and were not apparent when examined by T-bet expression. Thus, the C14R mutation reveals that NKp46 is important for NK cell and ILC differentiation, maturation and function.SignificanceInnate lymphoid cells (ILCs) play important roles in immune protection. Various subsets of ILCs express the activating receptor NKp46 which is capable of recognizing pathogen derived and tumor ligands and is necessary for immune protection. Here, we describe a spontaneous point mutation in the signal peptide of the NKp46 protein in congenic Ly5.1 mice which are widely used for tracking cells in vivo. This Ncr1 C14R mutation impairs NKp46 surface expression resulting in destabilization of Ncr1 and accumulation of NKp46 in the endoplasmic reticulum. Loss of stable NKp46 expression impaired the maturation of NKp46+ ILCs and altered the expression of TRAIL and T-bet in ILC1 and ILC3, respectively.

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“…The bioconductor package Limma was used for analysis of RNA-seq data (39,40). RNA-seq counts for 10 conditions (control þ 2 doses þ 2 timepoints for 2 cell lines) were preprocessed using the voom function (41), and linear models fit using the lmFit function. Specifically, a full model was fit (expression $ 0 þ Treatment.group þ cellline.group þ dose.group þ timepoint) and the coefficients extracted for the Treatment.group effect.…”

Section: Differential Gene Expression Analysismentioning

confidence: 99%

Dual HDAC and PI3K Inhibitor CUDC-907 Downregulates MYC and Suppresses Growth of MYC-dependent Cancers

Sun

Atoyan

Borek

et al. 2017

Molecular Cancer Therapeutics

113

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Upregulation of MYC is a common driver event in human cancers, and some tumors depend on MYC to maintain transcriptional programs that promote cell growth and proliferation. Preclinical studies have suggested that individually targeting upstream regulators of MYC, such as histone deacetylases (HDAC) and phosphoinositide 3-kinases (PI3K), can reduce MYC protein levels and suppress the growth of MYCdriven cancers. Synergy between HDAC and PI3K inhibition in inducing cancer cell death has also been reported, but the involvement of MYC regulation is unclear. In this study, we demonstrated that HDAC and PI3K inhibition synergistically downregulates MYC protein levels and induces apoptosis in "double-hit" (DH) diffuse large B-cell lymphoma (DLBCL) cells. Furthermore, CUDC-907, a small-molecule dual-acting inhibitor of both class I and II HDACs and class I PI3Ks, effectively suppresses the growth and survival of MYC-altered or MYC-dependent cancer cells, such as DH DLBCL and BRD-NUT fusion-positive NUT midline carcinoma (NMC) cells, and MYC protein downregulation is an early event induced by CUDC-907 treatment. Consistently, the antitumor activity of CUDC-907 against multiple MYC-driven cancer types was also demonstrated in animal models, including DLBCL and NMC xenograft models, Myc transgenic tumor syngeneic models, and MYC-amplified solid tumor patient-derived xenograft (PDX) models. Our findings suggest that dual function HDAC and PI3K inhibitor CUDC-907 is an effective agent targeting MYC and thus may be developed as potential therapy for MYCdependent cancers.

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voom: precision weights unlock linear model analysis tools for RNA-seq read counts

Cited by 4,775 publications

References 57 publications

The genetic basis of parental care evolution in monogamous mice

The genetic basis of parental care evolution in monogamous mice

A point mutation in the Ncr1 signal peptide impairs the development of innate lymphoid cell subsets

Dual HDAC and PI3K Inhibitor CUDC-907 Downregulates MYC and Suppresses Growth of MYC-dependent Cancers

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