Interpretation of differential gene expression results of RNA-seq data: review and integration

McDermaid, Adam; Monier, Brandon; Zhao, Jing; Liu, Bingqiang; Ma, Qin

doi:10.1093/bib/bby067

Cited by 200 publications

(125 citation statements)

References 48 publications

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“…RNA sequencing has become an important technique to understand genomic functions ( Hrdlickova et al , 2017 ). The most common application of RNA-seq is for the identification of differentially regulated genes under two or more conditions ( McDermaid et al , 2018 ). In this study, RNA-seq was applied to identify differentially regulated genes in C .…”

Section: Resultsmentioning

confidence: 99%

Transcriptome Analyses of Candida albicans Biofilms, Exposed to Arachidonic Acid and Fluconazole, Indicates Potential Drug Targets

Kuloyo¹,

Fourie²,

Cason³

et al. 2020

G3 Genes|Genomes|Genetics

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Candida albicans is an opportunistic yeast pathogen within the human microbiota with significant medical importance because of its pathogenic potential. The yeast produces highly resistant biofilms, which are crucial for maintaining infections. Though antifungals are available, their effectiveness is dwindling due to resistance. Alternate options that comprise the combination of existing azoles and polyunsaturated fatty acids, such as arachidonic acid (AA), have been shown to increase azoles susceptibility of C. albicans biofilms; however, the mechanisms are still unknown. Therefore, transcriptome analysis was conducted on biofilms exposed to sub-inhibitory concentrations of AA alone, fluconazole alone, and AA combined with fluconazole to understand the possible mechanism involved with the phenomenon. Protein ANalysis THrough Evolutionary Relationships (PANTHER) analysis from the differentially expressed genes revealed that the combination of AA and fluconazole influence biological processes associated with essential processes including methionine synthesis processes and those involved in ATP generation, such as AMP biosynthesis, fumarate metabolism and fatty acid oxidation. These observation suggests that the interference of AA with these processes may be possible mechanisms to induce increased antifungal susceptibility

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Section: Resultsmentioning

confidence: 99%

Transcriptome Analyses of Candida albicans Biofilms, Exposed to Arachidonic Acid and Fluconazole, Indicates Potential Drug Targets

Kuloyo¹,

Fourie²,

Cason³

et al. 2020

G3 Genes|Genomes|Genetics

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show abstract

“…Analysis of differential gene transcription and normalization of read counts and PCA were performed with R package DESeq2 (v.1.22.2) ( Love et al, 2014 ). Four-way plots were generated with R package vidger (v.1.2.1) ( McDermaid et al, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Umbilical cord blood-derived ILC1-like cells constitute a novel precursor for mature KIR+NKG2A- NK cells

Bennstein

Weinhold

Manser

et al. 2020

eLife

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Despite their identification several years ago, molecular identity and developmental relation between human ILC1 and NK cells, comprising group 1 ILCs, is still elusive. To unravel their connection, thorough transcriptional, epigenetic, and functional characterization was performed from umbilical cord blood (CB). Unexpectedly, ILC1-like cells lacked Tbet expression and failed to produce IFNγ. Moreover, in contrast to previously described ILC1 subsets they could be efficiently differentiated into NK cells. These were characterized by highly diversified KIR repertoires including late stage NKG2A-KIR+ effector cells that are commonly not generated from previously known NK cell progenitor sources. This property was dependent on stroma cell-derived Notch ligands. The frequency of the novel ILC1-like NK cell progenitor (NKP) significantly declined in CB from early to late gestational age. The study supports a model in which circulating fetal ILC1-like NKPs travel to secondary lymphoid tissues to initiate the formation of diversified NK cell repertoires after birth.

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“…To identify DEGs in the SREBP-1c KO mice in comparison to in the WT mice, the EdgeR package was chosen since, up to 2018, it has been the most widely used by researchers [16] and has demonstrated better performance in identifying true positives [17] compared to Cuffdiff2 and DESeq. The ExactTest function in the EdgeR package was used to analyze DEGs [18].…”

Section: Identification Of Degs In the Hippocampus Of Srebp-1c Ko Micmentioning

confidence: 99%

Transcriptome Profiling Reveals Novel Candidate Genes Related to Hippocampal Dysfunction in SREBP-1c Knockout Mice

Ang

Kim

Lee

et al. 2020

IJMS

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Lipid homeostasis is an important component of brain function, and its disturbance causes several neurological disorders, such as Huntington’s, Alzheimer’s, and Parkinson’s diseases as well as mood disorders. Sterol regulatory element-binding protein-1c (SREBP-1c) is a key modulatory molecule involved in lipid homeostasis in the central nervous system. However, little is known about the biological effects of SREBP-1c in the brain. Our previous study uncovered that mice deficient in SREBP-1c exhibit schizophrenia-like behaviors. To investigate whether there are novel molecular mechanisms involved in the neurological aberrations caused by SREBP-1c deficiency, we analyzed the transcriptomes of the hippocampus of SREBP-1c knockout (KO) mice and wild-type mice. We found seven differentially expressed genes (three up-regulated and four down-regulated genes) in the hippocampus of SREBP-1c KO mice. For further verification, we selected the three most significantly changed genes: glucagon-like peptide 2 receptors (GLP2R) involved in hippocampal neurogenesis and neuroplasticity as well as in cognitive impairments; necdin (NDN) which is related to neuronal death and neurodevelopmental disorders; and Erb-B2 receptor tyrosine kinase 4 (ERBB4) which is a receptor for schizophrenia-linked protein, neuregulin-1. The protein levels of GLP2R and NDN were considerably decreased, but the level of ERBB4 was significantly increased in the hippocampus of SREBP-1c KO mice. However, further confirmation is warranted to establish the translatability of these findings from this rodent model into human patients. We suggest that these data provide novel molecular evidence for the modulatory role of SREBP-1c in the mouse hippocampus.

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Interpretation of differential gene expression results of RNA-seq data: review and integration

Cited by 200 publications

References 48 publications

Transcriptome Analyses of Candida albicans Biofilms, Exposed to Arachidonic Acid and Fluconazole, Indicates Potential Drug Targets

Transcriptome Analyses of Candida albicans Biofilms, Exposed to Arachidonic Acid and Fluconazole, Indicates Potential Drug Targets

Umbilical cord blood-derived ILC1-like cells constitute a novel precursor for mature KIR+NKG2A- NK cells

Transcriptome Profiling Reveals Novel Candidate Genes Related to Hippocampal Dysfunction in SREBP-1c Knockout Mice

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