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Method: Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus
- Bharat Panwar,
- Benjamin J. Schmiedel,
- Shu Liang,
- Brandie White,
- Enrique Rodriguez,
- Kenneth Kalunian,
- Andrew J. McKnight,
- Rachel Soloff,
- Gregory Seumois,
- Pandurangan Vijayanand,
- and Ferhat Ay
Genome Res. April 2021 31: 659-676; Published in Advance March 5, 2021, doi:10.1101/gr.265249.120
.... S1F). Particularly, IFI6 and LY6E, both well-known type I interferon-related genes (Zhang et al. 2015a), are highly expressed in most cMos across different patients (violin plot, Supplemental Fig. S1F). A recent high-throughput 10x Genomics–based single-cell study also showed an expansion...
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Research: A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection
- Katherine J. Siddle,
- Matthieu Deschamps,
- Ludovic Tailleux,
- Yohann Nédélec,
- Julien Pothlichet,
- Geanncarlo Lugo-Villarino,
- Valentina Libri,
- Brigitte Gicquel,
- Olivier Neyrolles,
- Guillaume Laval,
- Etienne Patin,
- Luis B. Barreiro,
- and Lluís Quintana-Murci
Genome Res. May 2014 24: 850-859; Published in Advance January 30, 2014, doi:10.1101/gr.161471.113
...miR-eQTLs in cis for miR-326 and miR-1260, in non-infected and infected samples. (B) Regional association plot for miR-582-5p and genotyped SNPs in the region of the gene PDE4D showing the location of a cluster of significantly associated SNPs ;500 kb upstream of the miRNA in infected samples...
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LETTER: Identification of New Herpesvirus Gene Homologs in the Human Genome
- Ria Holzerlandt,
- Christine Orengo,
- Paul Kellam,
- and M. Mar Albà
Genome Res. November 1, 2002 12: 1739-1748; Published in Advance October 15, 2002, doi:10.1101/gr.334302
...the former. In other homolog cases, a single event of gene acquisition is easier to delineate; for example, the interferon regulatory factor and the macrophage inflammatory protein families are only found in RRV and HHV-8; they are at the same loci in both s and hence were presumably captured before host...
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ARTICLE: The Genexpress Index: a resource for gene discovery and the genic map of the human genome.
- R Houlgatte,
- R Mariage-Samson,
- S Duprat,
- A Tessier,
- S Bentolila,
- B Lamy,
- and C Auffray
Genome Res. October 1995 5: 272-304; doi:10.1101/gr.5.3.272
...signatures over 5750 distinct human gene transcripts. About half of these genes have been assigned to specific chromosomes utilizing 2733 eSTS markers, the polymerase chain reaction, and DNA from human-rodent somatic cell hybrids. Sequence and clone clustering and a functional classification together...
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Research: Cell type–specific DNA methylation at intragenic CpG islands in the immune system
- Aimée M. Deaton,
- Shaun Webb,
- Alastair R.W. Kerr,
- Robert S. Illingworth,
- Jacky Guy,
- Robert Andrews,
- and Adrian Bird
Genome Res. July 2011 21: 1074-1086; Published in Advance May 31, 2011, doi:10.1101/gr.118703.110
...) Transcription factor regulating IL-2 production early in T-cell activation (Wu and Lingrel 2005) Il10ra CD4 (vs. B cell) Interleukin-10 receptor, regulation of immune response. (Pils et al. 2010) Tnfaip2 DC (vs. Th1/Th2) Pro-inflammatory gene (Mookherjee et al. 2006) Cxcr5 CD4 (vs. B cell) Chemokine receptor...
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ARTICLE: Cytokine-Related Genes Identified From the RIKEN Full-Length Mouse cDNA Data Set
- Vladimir Brusic,
- Rekha S. Pillai,
- Diego G. Silva,
- Nikolai Petrovsky,
- RIKEN GER Group,
- GSL Members,
- and Christian Schönbach
Genome Res. June 2003 13: 1307-1317; doi:10.1101/gr.1016503
...and cytokine-related products such as cytokine receptors, cytokine-associated genes, or their products (enhancers, accessory proteins, cytokine-induced genes). We found 15 clusters of FANTOM2 clones that are candidates for novel cytokine-related genes. These encoded products with strong sequence similarity...
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LETTER: The Mouse Secretome: Functional Classification of the Proteins Secreted Into the Extracellular Environment
- Sean M. Grimmond,
- Kevin C. Miranda,
- Zheng Yuan,
- Melissa J. Davis,
- David A. Hume,
- Ken Yagi,
- Naoko Tominaga,
- Hidemasa Bono,
- Yoshihide Hayashizaki,
- Yasushi Okazaki,
- RIKEN GER Group,
- GSL Members,
- and Rohan D. Teasdale
Genome Res. June 2003 13: 1350-1359; doi:10.1101/gr.983703
...EST clustering and gene predictions within genomic sequences. Only through the generation and sequencing of full-length cDNAs on a large scale, such as that conducted by RIKEN, has this type of analysis been allowed to be performed. Properties of the Mouse Secretome Having defined the secretome, we...
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Method: A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma
- Jan Müller,
- Christina Hartwig,
- Mirko Sonntag,
- Lisa Bitzer,
- Christopher Adelmann,
- Yevhen Vainshtein,
- Karolina Glanz,
- Sebastian O. Decker,
- Thorsten Brenner,
- Georg F. Weber,
- Arndt von Haeseler,
- and Kai Sohn
Genome Res. August 2024 34: 1185-1195; Published in Advance September 13, 2024, doi:10.1101/gr.279326.124
...dendritic cells (Reizis 2010). TCF4 also regulates the immune response as a downstream target of toll-like receptor 2 (TLR2) signaling to induce the expression of immunoregulatory genes such as interleukin 10 (IL10) (Manoharan et al. 2014). The identified transcription factor zinc finger protein X...
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Research: Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules
- Jonathon L. Baker,
- James T. Morton,
- Márcia Dinis,
- Ruth Alvarez,
- Nini C. Tran,
- Rob Knight,
- and Anna Edlund
Genome Res. January 2021 31: 64-74; Published in Advance November 25, 2020, doi:10.1101/gr.265645.120
...protein-1 alpha), C-C motif chemokine ligand 4 (CCL4, formerly, macrophage inflammatory protein-1 beta), interferon alpha 2 (IFNA2), interferon gamma (IFNG), interleukin 1 alpha (IL1A), interleukin 1 beta (IL1B), interleukin 1 receptor antagonist (IL1RN), interleukin 2 (IL2), interleukin 3 (IL3...
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RESOURCE: A Consensus Linkage Map of the Chicken Genome
- Martien A.M. Groenen,
- Hans H. Cheng,
- Nat Bumstead,
- Bernard F. Benkel,
- W. Elwood Briles,
- Terry Burke,
- Dave W. Burt,
- Lyman B. Crittenden,
- Jerry Dodgson,
- Jossi Hillel,
- Sue Lamont,
- Abel Ponce de Leon,
- Morris Soller,
- Hideaki Takahashi,
- and Alain Vignal
Genome Res. January 1, 2000 10: 137-147; doi:10.1101/gr.10.1.137
.... , Gardiner K. , Monneron D. , Uzé G. , Lutfalla G. ( 1999 ) Comparative genomic analysis of the interferon/interleukin-10 receptor gene cluster. Genome Res. 9 : 242 – 250 . ↵ Rodionov A.V. , Myakoshina Y.A. , Chelysheva L.A. , Solovei I.V. , Gaginskaya E.R. ( 1992 ) Chiasmata in the lambrush chromosomes...

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