Updating RNA-Seq analyses after re-annotation

Roberts, Anjeanette; Schaeffer, Lorian; Pachter, Lior

doi:10.1093/bioinformatics/btt197

Cited by 24 publications

(13 citation statements)

References 18 publications

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“…In the case of genome sequencing or mRNA-seq, longer reads or paired-end 47 approaches can help to resolve such ambiguities, but the inherently short size of ribosome footprints precludes these experimental approaches. Computational methods developed for mRNA-seq data to assign multiply mapping reads probabilistically based on overall read distributions 48 can, however, be applied to ribosome profiling data to mitigate this limitation.…”

Section: What Are the Caveats And Weaknesses Of The Method?mentioning

confidence: 99%

Ribosome profiling reveals the what, when, where and how of protein synthesis

Brar

Weissman

2015

Nat Rev Mol Cell Biol

410

340

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Section: What Are the Caveats And Weaknesses Of The Method?mentioning

confidence: 99%

Ribosome profiling reveals the what, when, where and how of protein synthesis

Brar

Weissman

2015

Nat Rev Mol Cell Biol

410

340

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“…Quality control of trimmed Fastq files was achieved with FastQC v0.11.2 software (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Transcript quantitation was accomplished with eXpress v1.5.1 (51, 52) streaming pass filter reads aligned to Ensembl v78 transcriptome annotation using Bowtie2 v2.2.6 (53) as previously described (54). BAM files were generated by aligning to the GRCm38.p3/Ensembl v78 assembly and annotation with TopHat2 v2.1.0 (55) as previously noted (54).…”

Section: Methodsmentioning

confidence: 99%

Synergistically acting agonists and antagonists of G protein–coupled receptors prevent photoreceptor cell degeneration

Palczewska

Masuho

et al. 2016

Sci. Signal.

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Photoreceptor cell degeneration leads to visual impairment and blindness in several types of retinal disease. However, the discovery of safe and effective therapeutic strategies conferring photoreceptor cell protection remains challenging. Targeting distinct cellular pathways with low doses of different drugs that produce a functionally synergistic effect could provide a strategy for preventing or treating retinal dystrophies. We took a systems pharmacology approach to identify potential combination therapies using a mouse model of light-induced retinal degeneration. We showed that a combination of U.S. Food and Drug Administration–approved drugs that act on different G protein (guanine nucleotide–binding protein)–coupled receptors (GPCRs) exhibited synergistic activity that protected retinas from light-induced degeneration even when each drug was administered at a low dose. In functional assays, the combined effects of these drugs were stimulation of Gi/o signaling by activating the dopamine receptors D2R and D4R, as well as inhibition of Gs and Gq signaling by antagonizing D1R and the α1A-adrenergic receptor ADRA1A, respectively. Moreover, transcriptome analyses demonstrated that such combined GPCR-targeted treatments preserved patterns of retinal gene expression that were more similar to those of the normal retina than did higher-dose monotherapy. Our study thus supports a systems pharmacology approach to identify treatments for retinopathies, an approach that could extend to other complex disorders.

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Section: Discussionmentioning

confidence: 99%

“…Simultaneously, experimental methods, their limits, and associated errors and biases will require more rigorous analyses in order to contribute towards a more accurate description of the precision associated with the actual observations (e.g. for sequencing errors see (R oberts et al 2013; R obert and W atson 2015), for n-fold gene expression see (C anales et al 2006; C anales 2016), for PCR see (B ustin 2002; B ustin and N olan 2004; V an G uilder et al 2008), for tests of a parameter estimation method, e.g. see (D aigle et al 2012); many more analyses for other methods are needed).…”

Section: Discussionmentioning

confidence: 99%

FlyClockbase: Importance of Biological Model Curation for Analyzing Variability in the Circadian Clock of Drosophila melanogaster by Integrating Time Series from 25 Years of Research

Scheuer

Hanlon

Dresel

et al. 2017

Preprint

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General Article SummarySubstantial biological model curation was essential for identifying differences in peak 23 time variance of the clock-proteins 'PERIOD' and 'TIMELESS', which probably stem 24 from differences in phosphorylation-network complexity. 25 We repeatedly encountered systemic limitations of contemporary data analysis 26 strategies in our work on circadian clocks. Thus, we used it as an opportunity for 27 composing a panoramic view of the broader challenges in biological model curation, 28 which are likely to increase as biologists aim to integrate all existing expertise in order to 29 address diverse grand challenges. We developed and tested a trans-disciplinary 30 research workflow, which enables biologists and compiler-architects to define biology-31 friendly compilers for efficiently constructing and maintaining Versioned Biological 32 Information Resources (VBIRs). We report insights gleaned from our practical clock 33 research that are essential for defining a VBIRs infrastructure, which improves the 34 efficiency of biological model curation to the point where it can be democratized. . CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It ...

show abstract

Updating RNA-Seq analyses after re-annotation

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 24 publications

References 18 publications

Ribosome profiling reveals the what, when, where and how of protein synthesis

Ribosome profiling reveals the what, when, where and how of protein synthesis

Synergistically acting agonists and antagonists of G protein–coupled receptors prevent photoreceptor cell degeneration

FlyClockbase: Importance of Biological Model Curation for Analyzing Variability in the Circadian Clock of Drosophila melanogaster by Integrating Time Series from 25 Years of Research

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