Literature DB >> 33051456

Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients.

Antonio Federico1,2, Veera Hautanen1,2, Nils Christian3, Andreas Kremer3, Angela Serra1,2, Dario Greco4,5,6.   

Abstract

We present manually curated transcriptomics data of psoriasis and atopic dermatitis patients retrieved from the NCBI Gene Expression Omnibus and EBI ArrayExpress repositories. We collected 39 transcriptomics datasets, deriving from DNA microarrays and RNA-Sequencing technologies, for a total of 1677 samples. We provide quality-checked, homogenised and preprocessed gene expression matrices and their corresponding metadata tables along with the estimated surrogate variables. These data represent a ready-made valuable source of knowledge for translational researchers in the dermatology field.

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Year:  2020        PMID: 33051456      PMCID: PMC7555498          DOI: 10.1038/s41597-020-00696-8

Source DB:  PubMed          Journal:  Sci Data        ISSN: 2052-4463            Impact factor:   6.444


  25 in total

1.  GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor.

Authors:  Sean Davis; Paul S Meltzer
Journal:  Bioinformatics       Date:  2007-05-12       Impact factor: 6.937

2.  HISAT: a fast spliced aligner with low memory requirements.

Authors:  Daehwan Kim; Ben Langmead; Steven L Salzberg
Journal:  Nat Methods       Date:  2015-03-09       Impact factor: 28.547

3.  INfORM: Inference of NetwOrk Response Modules.

Authors:  Veer Singh Marwah; Pia Anneli Sofia Kinaret; Angela Serra; Giovanni Scala; Antti Lauerma; Vittorio Fortino; Dario Greco
Journal:  Bioinformatics       Date:  2018-06-15       Impact factor: 6.937

4.  Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

Authors:  Mihaela Pertea; Daehwan Kim; Geo M Pertea; Jeffrey T Leek; Steven L Salzberg
Journal:  Nat Protoc       Date:  2016-08-11       Impact factor: 13.491

5.  A scaling normalization method for differential expression analysis of RNA-seq data.

Authors:  Mark D Robinson; Alicia Oshlack
Journal:  Genome Biol       Date:  2010-03-02       Impact factor: 13.583

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

Authors:  James H Bullard; Elizabeth Purdom; Kasper D Hansen; Sandrine Dudoit
Journal:  BMC Bioinformatics       Date:  2010-02-18       Impact factor: 3.169

7.  Progression of acute-to-chronic atopic dermatitis is associated with quantitative rather than qualitative changes in cytokine responses.

Authors:  Lam C Tsoi; Elke Rodriguez; Dora Stölzl; Ulrike Wehkamp; Jingru Sun; Sascha Gerdes; Mrinal K Sarkar; Matthias Hübenthal; Chang Zeng; Ranjitha Uppala; Xianying Xing; Frederieke Thielking; Allison C Billi; William R Swindell; Alanna Shefler; Jiahan Chen; Matthew T Patrick; Paul W Harms; J Michelle Kahlenberg; Bethany E Perez White; Emanual Maverakis; Johann E Gudjonsson; Stephan Weidinger
Journal:  J Allergy Clin Immunol       Date:  2019-12-28       Impact factor: 10.793

8.  NCBI GEO: archive for functional genomics data sets--update.

Authors:  Tanya Barrett; Stephen E Wilhite; Pierre Ledoux; Carlos Evangelista; Irene F Kim; Maxim Tomashevsky; Kimberly A Marshall; Katherine H Phillippy; Patti M Sherman; Michelle Holko; Andrey Yefanov; Hyeseung Lee; Naigong Zhang; Cynthia L Robertson; Nadezhda Serova; Sean Davis; Alexandra Soboleva
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971

9.  The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads.

Authors:  Yang Liao; Gordon K Smyth; Wei Shi
Journal:  Nucleic Acids Res       Date:  2019-05-07       Impact factor: 16.971

10.  eUTOPIA: solUTion for Omics data PreprocessIng and Analysis.

Authors:  Veer Singh Marwah; Giovanni Scala; Pia Anneli Sofia Kinaret; Angela Serra; Harri Alenius; Vittorio Fortino; Dario Greco
Journal:  Source Code Biol Med       Date:  2019-01-29
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  3 in total

1.  Effect of cognitive behavioral therapy on anxiety and depression in patients with psoriasis: A protocol for systematic review and meta-analysis.

Authors:  Chuan Tan; Jianmei Jiang; Xiaoling Deng; Wei Xiang; Tingting Hu
Journal:  Medicine (Baltimore)       Date:  2021-11-19       Impact factor: 1.889

2.  Nextcast: A software suite to analyse and model toxicogenomics data.

Authors:  Angela Serra; Laura Aliisa Saarimäki; Alisa Pavel; Giusy Del Giudice; Michele Fratello; Luca Cattelani; Antonio Federico; Omar Laurino; Veer Singh Marwah; Vittorio Fortino; Giovanni Scala; Pia Anneli Sofia Kinaret; Dario Greco
Journal:  Comput Struct Biotechnol J       Date:  2022-03-18       Impact factor: 7.271

3.  Finding Gene Regulatory Networks in Psoriasis: Application of a Tree-Based Machine Learning Approach.

Authors:  Jingwen Deng; Carlotta Schieler; José A M Borghans; Chuanjian Lu; Aridaman Pandit
Journal:  Front Immunol       Date:  2022-07-07       Impact factor: 8.786

  3 in total

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