(Q30824606)

18 October 2017

Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome (English)

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18 October 2017

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William R Swindell

1

1 reference

18 October 2017

Xianying Xing

2

1 reference

18 October 2017

John J Voorhees

3

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18 October 2017

James T Elder

4

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18 October 2017

Andrew Johnston

5

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18 October 2017

Johann E Gudjonsson

6

1 reference

18 October 2017

language of work or name

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20 May 2014

1 reference

18 October 2017

Physiological Genomics

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18 October 2017

46

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18 October 2017

15

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18 October 2017

533-546

1 reference

describes a project that uses

18 October 2017

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/4121624

inferred from PubMed Central ID database lookup

cites work

Early tissue responses in psoriasis to the antitumour necrosis factor-α biologic etanercept suggest reduced interleukin-17 receptor expression and signalling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Integrative biology approach identifies cytokine targeting strategies for psoriasis

21 June 2018

1 reference

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Coupling mRNA processing with transcription in time and space.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Library preparation methods for next-generation sequencing: tone down the bias

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Dispersion estimation and its effect on test performance in RNA-seq data analysis: a simulation-based comparison of methods

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Towards the integration, annotation and association of historical microarray experiments with RNA-seq

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Modulation of epidermal transcription circuits in psoriasis: new links between inflammation and hyperproliferation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Genome-wide transcriptional effects of the anti-cancer agent camptothecin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Use of Bru-Seq and BruChase-Seq for genome-wide assessment of the synthesis and stability of RNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Dissecting the psoriasis transcriptome: inflammatory- and cytokine-driven gene expression in lesions from 163 patients

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Transcription poisoning by Topoisomerase I is controlled by gene length, splice sites, and miR-142-3p

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Creation of differentiation-specific genomic maps of human epidermis through laser capture microdissection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

IL-17A and IFN-γ synergistically induce RNase 7 expression via STAT3 in primary keratinocytes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Differential expression analysis for paired RNA-Seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Cross-study homogeneity of psoriasis gene expression in skin across a large expression range

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Noncanonical microRNAs and endogenous siRNAs in normal and psoriatic human skin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

RNA-seq and microarray complement each other in transcriptome profiling.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Expanding the psoriasis disease profile: interrogation of the skin and serum of patients with moderate-to-severe psoriasis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

RSeQC: quality control of RNA-seq experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Camera: a competitive gene set test accounting for inter-gene correlation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Heterogeneity of inflammatory and cytokine networks in chronic plaque psoriasis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Summarizing and correcting the GC content bias in high-throughput sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

A central role for RNA in the induction and biological activities of type 1 interferons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Transcriptional profiling of psoriasis using RNA-seq reveals previously unidentified differentially expressed genes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miRNAome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Method for improved Illumina sequencing library preparation using NuGEN Ovation RNA-Seq System.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Differential expression analysis for sequence count data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Impact of RNA degradation on gene expression profiling.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Biases in Illumina transcriptome sequencing caused by random hexamer priming

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Effective treatment of psoriasis with etanercept is linked to suppression of IL-17 signaling, not immediate response TNF genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

The Sequence Alignment/Map format and SAMtools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Transcript length bias in RNA-seq data confounds systems biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Statistical inferences for isoform expression in RNA-Seq

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Type I interferon: potential therapeutic target for psoriasis?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Database resources of the National Center for Biotechnology Information

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Hepatitis C virus RNA: Dinucleotide frequencies and cleavage by RNase L

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Methodological considerations for gene expression profiling of human brain.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Cytokine modulation of retinoic acid-inducible gene-I (RIG-I) expression in human epidermal keratinocytes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Effects of filtering by Present call on analysis of microarray experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Sensitivity of hepatitis C virus RNA to the antiviral enzyme ribonuclease L is determined by a subset of efficient cleavage sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Psoriatic scales: a promising source for the isolation of human skin-derived antimicrobial proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Summaries of Affymetrix GeneChip probe level data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

RNase 7, a novel innate immune defense antimicrobial protein of healthy human skin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

The relationship between mRNA stability and length in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Epidermal nucleases. III. The ribonucleases of human epidermis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121624

Enhanced expression and secretion of antimicrobial peptides in atopic dermatitis and after superficial skin injury.

21 June 2018

1 reference

https://api.crossref.org/works/10.1152%2FPHYSIOLGENOMICS.00022.2014

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

21 January 2018

1 reference

https://api.crossref.org/works/10.1152%2FPHYSIOLGENOMICS.00022.2014

The pre-mRNA splicing reaction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1152%2FPHYSIOLGENOMICS.00022.2014

Interferon action--sequence specificity of the ppp(A2'p)nA-dependent ribonuclease.

21 January 2018

1 reference

https://api.crossref.org/works/10.1152%2FPHYSIOLGENOMICS.00022.2014

MicroRNAs and potential target interactions in psoriasis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1152%2FPHYSIOLGENOMICS.00022.2014

Subcellular distribution of phosphatases, proteinases, and ribonucleases in normal human stratum corneum and psoriatic scales

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24844236

12 December 2020

inferred from PubMed ID database lookup

IFN-alpha enhances poly-IC responses in human keratinocytes by inducing expression of cytosolic innate RNA receptors: relevance for psoriasis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24844236

12 December 2020

inferred from PubMed ID database lookup

Transcriptional regulatory network for psoriasis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24844236

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1152/PHYSIOLGENOMICS.00022.2014

1 reference

18 October 2017

1 reference

18 October 2017

PubMed publication ID

24844236

1 reference