Bowcock AM, Shannon W, Du F, Duncan J, Cao K, Aftergut K, Catier J, Fernandez-Vina MA, Menter A. Insights into psoriasis and other inflammatory diseases from large-scale gene expression studies. Hum Mol Genet. 2001;10:1793–805.
Article
CAS
PubMed
Google Scholar
Zhou X, Krueger JGJG, Kao M-CJMC, Lee E, Du F, Menter A, Wong WHWH, Bowcock AMAM. Novel mechanisms of T-cell and dendritic cell activation revealed by profiling of psoriasis on the 63,100-element oligonucleotide array. Physiol Genomics. 2003;13:69–78.
Article
CAS
PubMed
Google Scholar
Gudjonsson JE, Ding J, Johnston A, Tejasvi T, Guzman AM, Nair RP, Voorhees JJ, Abecasis GR, Elder JT. Assessment of the psoriatic transcriptome in a large sample: additional regulated genes and comparisons with in vitro models. J Invest Dermatol. 2010;130:1829–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Elder JT, Bruce AT, Gudjonsson JE, Johnston A, Stuart PE, Tejasvi T, Voorhees JJ, Abecasis GR, Nair RP. Molecular dissection of psoriasis: integrating genetics and biology. J Invest Dermatol. 2010;130:1213–26.
Article
CAS
PubMed
Google Scholar
Li B, Tsoi LC, Swindell WR, Gudjonsson JE, Tejasvi T, Johnston A, Ding J, Stuart PE, Xing X, Kochkodan JJ, Voorhees JJ, Kang HM, Nair RP, Abecasis GR, Elder JT. Transcriptome Analysis of Psoriasis in a Large Case–control Sample: RNA-Seq Provides Insights into Disease Mechanisms. J Invest Dermatol. 2014;134:1828–38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stuart JM. A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules. Science (80-). 2003;302:249–55.
Article
CAS
Google Scholar
Schäfer J, Strimmer K. An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics. 2005;21:754–64.
Article
PubMed
Google Scholar
Cokus S, Rose S, Haynor D, Grønbech-Jensen N, Pellegrini M. Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae. BMC Bioinformatics. 2006;7:381.
Article
PubMed
PubMed Central
Google Scholar
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.
Article
PubMed
PubMed Central
Google Scholar
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102:15545–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Horvath S, Zhang B, Carlson M, Lu KV, Zhu S, Felciano RM, Laurance MF, Zhao W, Qi S, Chen Z, Lee Y, Scheck AC, Liau LM, Wu H, Geschwind DH, Febbo PG, Kornblum HI, Cloughesy TF, Nelson SF, Mischel PS. Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci U S A. 2006;103:17402–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Presson AP, Sobel EM, Papp JC, Suarez CJ, Whistler T, Rajeevan MS, Vernon SD, Horvath S. Integrated Weighted Gene Co-expression Network Analysis with an Application to Chronic Fatigue Syndrome. BMC Syst Biol. 2008;2:95.
Article
PubMed
PubMed Central
Google Scholar
Hu S, Zhou M, Jiang J, Wang J, Elashoff D, Gorr S, Michie SA, Spijkervet FKL, Bootsma H, Kallenberg CGM, Vissink A, Horvath S, Wong DT. Systems biology analysis of Sjögren’s syndrome and mucosa-associated lymphoid tissue lymphoma in parotid glands. Arthritis Rheum. 2009;60:81–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huan T, Zhang B, Wang Z, Joehanes R, Zhu J, Johnson AD, Ying S, Munson PJ, Raghavachari N, Wang R, Liu P, Courchesne P, Hwang S-JJ, Assimes TL, McPherson R, Samani NJ, Schunkert H, Meng Q, Suver C, O’Donnell CJ, Derry J, Yang X, Levy D. A systems biology framework identifies molecular underpinnings of coronary heart disease. Arterioscler Thromb Vasc Biol. 2013;33:1427–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mirza AH, Berthelsen CH, Seemann SE, Pan X, Frederiksen KS, Vilien M, Gorodkin J, Pociot F. Transcriptomic landscape of lncRNAs in inflammatory bowel disease. Genome Med. 2015;7:39.
Article
PubMed
PubMed Central
Google Scholar
Palau N, Julià A, Ferrándiz C, Puig L, Fonseca E, Fernández E, López-Lasanta M, Tortosa R, Marsal S. Genome-wide transcriptional analysis of T cell activation reveals differential gene expression associated with psoriasis. BMC Genomics. 2013;14:825.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
Article
PubMed
PubMed Central
Google Scholar
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O’Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, DiCuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014;42:D756–63.
Article
CAS
PubMed
Google Scholar
Hangauer MJ, Vaughn IW, McManus MT. Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet. 2013;9:e1003569.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol. 2013;31:46–53.
Article
CAS
PubMed
Google Scholar
Gupta R, Ahn R, Lai K, Mullins E, Debbaneh M, Dimon M, Arron S, Liao W. Landscape of Long Noncoding RNAs in Psoriatic and Healthy Skin. J Invest Dermatol. 2015;136:603–9.
Article
PubMed
Google Scholar
Iyer MK, et al. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet. 2015;47:199–208.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fatica A, Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet. 2014;15:7–21.
Article
CAS
PubMed
Google Scholar
Gudjonsson JE, Ding J, Li X, Nair RP, Tejasvi T, Qin ZS, Ghosh D, Aphale A, Gumucio DL, Voorhees JJ, Abecasis GR, Elder JT. Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin. J Invest Dermatol. 2009;129:2795–804.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang Z, Matteson EL, Goronzy JJ, Weyand CM. T-cell metabolism in autoimmune disease. Arthritis Res Ther. 2015;17:29.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cipolletta D, Feuerer M, Li A, Kamei N, Lee J, Shoelson SE, Benoist C, Mathis D. PPAR-γ is a major driver of the accumulation and phenotype of adipose tissue Treg cells. Nature. 2012;486:549–53.
CAS
PubMed
PubMed Central
Google Scholar
Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J, DeRoos P. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature. 2013;504:451–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haghikia A, Jörg S, Duscha A, Berg J, Manzel A, Waschbisch A, Hammer A, Lee D-H, May C, Wilck N, Balogh A, Ostermann AI, Schebb NH, Akkad DA, Grohme DA, Kleinewietfeld M, Kempa S, Thöne J, Demir S, Müller DN, Gold R, Linker RA. Dietary Fatty Acids Directly Impact Central Nervous System Autoimmunity via the Small Intestine. Immunity. 2015;43:817–29.
Article
CAS
PubMed
Google Scholar
Rodriguez RS, Pauli M, Neuhaus I, Al E. Memory regulatory T cells reside in human skin. J Clin Invest. 2014;124:1027–36.
Article
CAS
Google Scholar
Busse D, Kudella P, Grüning N-M, Gisselmann G, Ständer S, Luger T, Jacobsen F, Steinsträßer L, Paus R, Gkogkolou P, Böhm M, Hatt H, Benecke H. A Synthetic Sandalwood Odorant Induces Wound-Healing Processes in Human Keratinocytes via the Olfactory Receptor OR2AT4. J Invest Dermatol. 2014;134:2823–32.
Article
CAS
PubMed
Google Scholar
Jabbari A, Suárez-Fariñas M, Dewell S, Krueger JG. Transcriptional profiling of psoriasis using RNA-seq reveals previously unidentified differentially expressed genes. J Invest Dermatol. 2012;132:246–9.
Article
CAS
PubMed
Google Scholar
Swindell WR, Xing X, Voorhees JJ, Elder JT, Johnston A, Gudjonsson JE. Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome. Physiol Genomics. 2014;46:533–46.
Article
PubMed
PubMed Central
Google Scholar
Kallen AN, Haines K, Taylor HS. HOXA10 regulates expression of cytokeratin 15 in endometrial epithelial cytoskeletal remodeling. Reprod Sci. 2014;21:892–7.
Article
PubMed
PubMed Central
Google Scholar
Bei L, Shah C, Wang H, Huang W, Platanias LC, Eklund EA. Regulation of CDX4 gene transcription by HoxA9, HoxA10, the Mll-Ell oncogene and Shp2 during leukemogenesis. Oncogenesis. 2014;3:e135.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang H, Bei L, Shah CA, Hu L, Eklund EA. HoxA10 Terminates Emergency Granulopoiesis by Increasing Expression of Triad1. J Immunol. 2015;194:5375–87.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yasmeen R, Meyers JM, Alvarez CE, Thomas JL, Bonnegarde-Bernard A, Alder H, Papenfuss TL, Benson DM, Boyaka PN, Ziouzenkova O. Aldehyde dehydrogenase-1a1 induces oncogene suppressor genes in B cell populations. Biochim Biophys Acta - Mol Cell Res. 1833;2013:3218–27.
Google Scholar
Rosenblum MD, Olasz EB, Yancey KB, Woodliff JE, Lazarova Z, Gerber KA, Truitt RL. Expression of CD200 on epithelial cells of the murine hair follicle: a role in tissue-specific immune tolerance? J Invest Dermatol. 2004;123:880–7.
Article
CAS
PubMed
Google Scholar
Mukhopadhyay S, Plüddemann A, Hoe JC, Williams KJ, Varin A, Makepeace K, Aknin M-L, Bowdish DME, Smale ST, Barclay AN, Gordon S. Immune Inhibitory Ligand CD200 Induction by TLRs and NLRs Limits Macrophage Activation to Protect the Host from Meningococcal Septicemia. Cell Host Microbe. 2010;8:236–47.
Article
CAS
PubMed
Google Scholar
Ruse M, Broome A-M, Eckert RL. S100A7 (Psoriasin) Interacts with Epidermal Fatty Acid Binding Protein and Localizes in Focal Adhesion-Like Structures in Cultured Keratinocytes. J Invest Dermatol. 2003;121:132–41.
Article
CAS
PubMed
Google Scholar
Dallaglio K, Marconi A, Truzzi F, Lotti R, Palazzo E, Petrachi T, Saltari A, Coppini M, Pincelli C. E-FABP induces differentiation in normal human keratinocytes and modulates the differentiation process in psoriatic keratinocytes in vitro. Exp Dermatol. 2013;22:255–61.
Article
CAS
PubMed
Google Scholar
Naitza S, Porcu E, Steri M, Taub DD, Mulas A, Xiao X, Strait J, Dei M, Lai S, Busonero F, Maschio A, Usala G, Zoledziewska M, Sidore C, Zara I, Pitzalis M, Loi A, Virdis F, Piras R, Deidda F, Whalen MB, Crisponi L, Concas A, Podda C, Uzzau S, Scheet P, Longo DL, Lakatta E, Abecasis GR, Cao A, et al. A Genome-Wide Association Scan on the Levels of Markers of Inflammation in Sardinians Reveals Associations That Underpin Its Complex Regulation. PLoS Genet. 2012;8:e1002480.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lande R, Botti E, Jandus C, Dojcinovic D, Fanelli G, Conrad C, Chamilos G, Feldmeyer L, Marinari B, Chon S, Vence L, Riccieri V, Guillaume P, Navarini AA, Romero P, Costanzo A, Piccolella E, Gilliet M, Frasca L. The antimicrobial peptide LL37 is a T-cell autoantigen in psoriasis. Nat Commun. 2014;5(May):1–15.
Google Scholar