Interferome is an open access database of types i, ii and iii interferon regulated genes collected from analysing expression data sets of cells treated with ifns. Interferome is an online bioinformatics database of interferonregulated genes irgs. The data suggests that the repressed expression of interferonstimulated genes may underpin critical aspects of the profibrotic fibroblast phenotype, identifying an area in pulmonary fibrosis that requires further investigation. Liver cancer is a serious threat to public health and has fairly complicated pathogenesis. Dynamic expression of interferon lambda regulated genes in primary fibroblasts and immune organs of the chicken mehboob arslan 1. Recently, it became obvious that these cytokines have a multitude of additional functions. Interferon ifn cell signaling pathway thermo fisher.
Additionally, we found increased expression of interferon ifnregulated genes including ifi27, ifi30, mx1, irf1 and cxcl9 in scc, and to a lower extent in bcc. Full text interferon kappa is upregulated in psoriasis. This database of interferon regulated genes integrates information from high throughput experiments with annotation, ontology, orthologue. Interferon kappa is upregulated in psoriasis and it upregulates psoriasisassociated cytokines in vivo. A group of proteins, called interferons ifns,1 can directly inhibit viral replication. Irf8 plays an important role in several aspects of myeloid cells, including differentiation. Induction of interferon ifn gene expression leads to increase cellular resistance to viral. Type ii ifn is represented by a single gene encoding ifn.
Virus infection induces the production of type i interferons ifns. Il28b is associated with response to chronic hepatitis c. Protein and dna methylationbased scores as surrogate. Coexpression network analysis reveals the pivotal role of. This database of interferon regulated genes integrates information from highthroughput. Therefore, the identification of key genes and pathways is of much importance for clarifying molecular mechanism of hepatocellular carcinoma hcc initiation and progression. Due to the unique features of the chickens immune system, available data from mouse models are not easily transferable. Interferonregulated genes are upregulated in the brain following virus infection. Transcriptional dysregulation of interferome in experimental and. Isgs play very important roles in innate immunity through a variety of mechanisms. Dynamic expression of interferon lambda regulated genes in. Identification of new type i interferonstimulated genes. This database of interferon regulated genes integrates information from highthroughput experiments with annotation, ontology, orthologue sequences from 37 species, tissue expression patterns and gene regulatory information to enable a detailed investigation of the molecular mechanisms underlying ifn biology. A and c were analyzed using interferome, string and gorilla databases.
Tissue and time specific expression pattern of interferon. Type i interferonregulated gene expression and signaling. In order to obtain a more comprehensive understanding of the genes regulated by ifns we have used different microarray formats to identify over 400 interferon stimulated genes isg. Dynamic expression of interferon lambda regulated genes in primary fibroblasts and immune organs of the chicken. Levydifferential viral induction of distinct interferon. Type i ifns are encoded by a family of closely related. The proteins encoded by these genes enhance recognition of the infected cells by the host immune system. To directly characterize the effects of ifnalpha in humans, we used microarrays to profile gene expression in peripheral blood mononuclear cells pbmcs from hepatitis c patients treated with ifnalpha. Dna microarrays were analyzed by different software, including mas5 affymetrixkegg and gsea gene set enrichment analysis to identify specific pathways both up regulated and down regulated. Il28b is associated with response to chronic hepatitis c interferon. Ifnregulated genes were identified through the interferome v. Using interferome searching interferon regulated gene signatures. Gene ontology go term enrichment analysis and kyoto encyclopedia of genes and genomes kegg pathway analysis, based on r software, were. This database of interferon regulated genes integrates information from.
The interferome database was used to identify ifnregulated genes that were upregulated in the brain following infection with jev, wnv, or reovirus. One of the many responses to the viral invasion is the induction of a family of pleiotropic cytokines known as interferons ifn1. Vastly improved computational infrastructure now enables more complex and faster queries, and supports more data sets from types i. Interferon regulated genes irgs were identified from experiments where cells or organisms were treated with an ifn. Finally, ex vivo and in vitro experiments established that ifnbeta. Definitions interferon regulated genes irgs were identified from multiple microarray and proteomic experiments where cells were treated with ifns. Genes that were significantly up or down regulated relative to control samples were defined as irgs, annotated and uploaded into the database. Tissue and time specific expression pattern of interferon regulated. Enrichment of interferonregulated genes was computed using the hypergeometric test implemented in the r software. Celfiles were further processed using the chipster software, version 3. Circadian control of interferonsensitive gene expression. This database of ifn regulated genes is an attempt at integrating information from highthroughput experiments to gain a detailed understanding of ifn biology. Interferon regulatory factor 8 regulates pathways for. Although interferon was discovered in chicken cells, details of the response, particularly the identity of hundreds of stimulated genes, are far better described in mammals.
We show timeofdaydependent activation of the interferon pathway, a key pathway involved in the host defense response. This database of interferon regulated genes integrates information from highthroughput experiments with annotation, ontology, orthologue sequences from 37 species, tissue expression patterns and. C i d how to find meaningful information interferome v2. Suppression of ribosomal protein synthesis and protein. This database is an upgrade of the original database and contains type i, ii and iii interferon ifn regulated genes. Ifns bind to their heterodimeric receptors to initiate downstream cascade of signaling, leading to the upregulation of interferonstimulated genes isgs. Stimulator of interferon genes sting, also known as transmembrane protein 173 tmem173 and mpysmitaeris is a protein that in humans is encoded by the tmem173 gene. Interactions among type i and type ii interferon, tumor necrosis factor, and. Hccassociated gene expression dataset was downloaded from gene expression omnibus database. Interferome is a database that enables the reliable identification of interferon. Pdf interferome is an open access database of types i, ii and iii interferon regulated genes collected from analysing. Type i and type ii interferon responses in two human liver cell lines huh7 and huh6. Virusinduced transcriptional changes in the brain include.
Interactions among type i and type ii interferon, tumor. The parameters were set with 20,900 as total number of genes in the human genome based on data from the ensembl database release 64 and 2,000 as the number of interferonregulated genes as stated in the interferome web site. Almost as many genes are down regulated suppressed during interferonribavirin treatment as are up regulated. Type i interferons are major players against viral infections and mediate their function by the induction of interferon regulated genes irgs. The identification of novel ifnregulated genes in our study may lead to improved therapeutic uses for ifns in different ways. Although hundreds of isgs have been identified, it is commonly recognized that more. Interferon alfa ifnalpha is an approved therapeutic agent for chronic hepatitis c. The main functionality of this database is to enable the identification interferon regulated genes in a gene list generated from a highthroughput microarray or proteomic experiment. Here, we show that expression of key circadian clock genes in the skin is altered by acute inflammation in mice treated topically with the immune activator imiquimod and by chronic inflammation in human psoriatic lesions. Identification of genes differentially regulated by. Viruses induce interferonstimulated genes but they also regulate the expression of many hundreds of cellular metabolic and structural genes to facilitate their replication. A total of 2,834 differentially expressed genes between jdm and hc were identified, including 1,888 downregulated genes and 946 upregulated genes.
To facilitate the dissemination of this data we have compiled a database comprising the. In addition, we used the top 500 pm genes for each leprosy state for the analysis of the specific interferon regulated genes. Type i and type ii interferon responses in two human liver. The gene expression profiles of all tissue samples were analyzed based on the platform of the affymetrix human genome u3 plus 2. Regulation of type i interferon gene expression by. Author summary irf8 is a member of the interferon regulatory factor family that is expressed in myeloid cells such as macrophages and dendritic cells and that activates or represses gene transcription upon stimulation with interferon gamma ifn. Quantification of the autoradiographs was performed by densitometry using nih image software version 1. The interferome and isg databases 11, 12, 3639 were used as sources for. Stabilization of ifnar1 improves cytotoxic t lymphocyte survival and suppresses tumor growth. Affymetrix gene chip operating software was used to extract the raw. Article dynamic expression of interferon lambda regulated. Following viral infection, the human body triggers a complex regulatory system of innate and adaptive immune responses designed to defend against these foreign invaders.
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