Chromosome contacts in activated T cells identify autoimmune disease candidate genes
Open accessPublished version of a preprint
Abstract
BACKGROUND: T cells. Linking such regulatory regions to gene promoters in disease-relevant cell contexts facilitates identification of candidate disease genes. RESULTS: T cells invokes changes in histone modifications and enhancer RNA transcription that correspond to altered expression of the interacting genes identified by promoter capture Hi-C. By integrating promoter capture Hi-C data with genetic associations for five autoimmune diseases, we prioritised 245 candidate genes with a median distance from peak signal to prioritised gene of 153 kb. Just under half (108/245) prioritised genes related to activation-sensitive interactions. This included IL2RA, where allele-specific expression analyses were consistent with its interaction-mediated regulation, illustrating the utility of the approach. CONCLUSIONS: Our systematic experimental framework offers an alternative approach to candidate causal gene identification for variants with cell state-specific functional effects, with achievable sample sizes.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Variants associated with type 1 diabetes were strongly enriched at promoter-connected active enhancers in activated, compared with resting, CD4+ T cells.
“Likewise, variants associated with type 1 diabetes were strongly enriched at promoter-connected active enhancers in activated, compared with resting, CD4+ T cells [229].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [229]
The Results section (‘PCHi-C-facilitated mapping of candidate disease-causal genes’; page unavailable) reports overlap between fine-mapped autoimmune-disease variants and expressed enhancer RNAs at promoter-interacting regions. The paper also compares activated and non-activated CD4+ T cells, but the passages available do not establish that type 1 diabetes variants were strongly enriched at those enhancers in activated cells relative to resting cells. (LLM, conf=0.74)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works
limma powers differential expression analyses for RNA-sequencing and microarray studies
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458 · see citing works
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889 · see citing works
WGCNA: an R package for weighted correlation network analysis
Langfelder, P., & Horvath, S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-559 · Cited by 27,252 · see citing works
HTSeq—a Python framework to work with high-throughput sequencing data
Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464 · see citing works
Interleukin-10 and the Interleukin-10 Receptor
Moore, K. W., de Waal Malefyt, R., Coffman, R. L., & O'Garra, A. (2001) · Annual Review of Immunology · doi:10.1146/annurev.immunol.19.1.683 · Cited by 6,737 · see citing works
Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease
The International IBD Genetics Consortium (IIBDGC), Jostins, L., Ripke, S., Weersma, R. K., Duerr, R. H., McGovern, D. P., Hui, K. Y., Lee, J. C., Philip Schumm, L., Sharma, Y., et al. (2012) · Nature · doi:10.1038/nature11582 · Cited by 4,722 · see citing works
Giambartolomei, C., Vukcevic, D., Schadt, E. E., Franke, L., Hingorani, A. D., Wallace, C., & Plagnol, V. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004383 · Cited by 4,261 · see citing works
Self-citationSystematic Localization of Common Disease-Associated Variation in Regulatory DNA
Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716 · see citing works
Super-enhancers in the control of cell identity and disease
Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.09.053 · Cited by 3,662 · see citing works
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis
The International Multiple Sclerosis Genetics Consortium & The Wellcome Trust Case Control Consortium 2 (2011) · Nature · doi:10.1038/nature10251 · Cited by 2,697 · see citing works
A new multipoint method for genome-wide association studies by imputation of genotypes
Marchini, J., Howie, B., Myers, S., McVean, G., & Donnelly, P. (2007) · Nature Genetics · doi:10.1038/ng2088 · Cited by 2,609 · see citing works
An atlas of active enhancers across human cell types and tissues
The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550 · see citing works
ChromHMM: automating chromatin-state discovery and characterization
Ernst, J., & Kellis, M. (2012) · Nature Methods · doi:10.1038/nmeth.1906 · Cited by 2,489 · see citing works
Huber, W., von Heydebreck, A., Sültmann, H., Poustka, A., & Vingron, M. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s96 · Cited by 2,440 · see citing works
Genetics of rheumatoid arthritis contributes to biology and drug discovery
the RACI consortium, Okada, Y., the GARNET consortium, Wu, D., Trynka, G., Raj, T., Terao, C., Ikari, K., Kochi, Y., Ohmura, K., et al. (2014) · Nature · doi:10.1038/nature12873 · Cited by 2,310 · see citing works
Genetic and epigenetic fine mapping of causal autoimmune disease variants
Farh, K. K.-H., Marson, A., Zhu, J., Kleinewietfeld, M., Housley, W. J., Beik, S., Shoresh, N., Whitton, H., Ryan, R. J. H., Shishkin, A. A., et al. (2015) · Nature · doi:10.1038/nature13835 · Cited by 1,956 · see citing works
The long-range interaction landscape of gene promoters
Sanyal, A., Lajoie, B. R., Jain, G., & Dekker, J. (2012) · Nature · doi:10.1038/nature11279 · Cited by 1,489 · see citing works
Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci
BIRAC Consortium, Stahl, E. A., YEAR Consortium, Raychaudhuri, S., Remmers, E. F., Xie, G., Eyre, S., Thomson, B. P., Li, Y., Kurreeman, F. A. S., et al. (2010) · Nature Genetics · doi:10.1038/ng.582 · Cited by 1,253 · see citing works
Obesity-associated variants within FTO form long-range functional connections with IRX3
Smemo, S., Tena, J. J., Kim, K.-H., Gamazon, E. R., Sakabe, N. J., Gómez-Marín, C., Aneas, I., Credidio, F. L., Sobreira, D. R., Wasserman, N. F., et al. (2014) · Nature · doi:10.1038/nature13138 · Cited by 1,219 · see citing works
Histocompatibility-Linked Immune Response Genes
D, B. B. M., & McDevitt, H. O. (1972) · Science · doi:10.1126/science.175.4019.273 · Cited by 1,181 · see citing works
Interleukin-2 at the Crossroads of Effector Responses, Tolerance, and Immunotherapy
Liao, W., Lin, J., & Leonard, W. J. (2013) · Immunity · doi:10.1016/j.immuni.2013.01.004 · Cited by 1,077 · see citing works
Javierre, B. M., Burren, O. S., Wilder, S. P., Kreuzhuber, R., Hill, S. M., Sewitz, S., Cairns, J., Wingett, S. W., Várnai, C., Thiecke, M. J., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.037 · Cited by 1,046 · see citing works
Self-citationMapping long-range promoter contacts in human cells with high-resolution capture Hi-C
Mifsud, B., Tavares-Cadete, F., Young, A. N., Sugar, R., Schoenfelder, S., Ferreira, L., Wingett, S. W., Andrews, S., Grey, W., Ewels, P. A., et al. (2015) · Nature Genetics · doi:10.1038/ng.3286 · Cited by 990 · see citing works
Self-citationA compendium of chromatin contact maps reveals spatially active regions in the human genome
Schmitt, A. D., Hu, M., Jung, I., Xu, Z., Qiu, Y., Tan, C. L., Li, Y., Lin, S., Lin, Y., Barr, C. L., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.10.061 · Cited by 866 · see citing works
Trynka, G., PreventCD Study Group, Hunt, K. A., Bockett, N. A., Romanos, J., Mistry, V., Szperl, A., Bakker, S. F., Bardella, M. T., Bhaw, L., et al. (2011) · Nature Genetics · doi:10.1038/ng.998 · Cited by 825 · see citing works
Self-citationA Versatile Gene-Based Test for Genome-wide Association Studies
Liu, J. Z., McRae, A. F., Nyholt, D. R., Medland, S. E., Wray, N. R., Brown, K. M., Hayward, N. K., Montgomery, G. W., Visscher, P. M., Martin, N. G., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.06.009 · Cited by 791 · see citing works
Shared and Distinct Genetic Variants in Type 1 Diabetes and Celiac Disease
Smyth, D. J., Plagnol, V., Walker, N. M., Cooper, J. D., Downes, K., Yang, J. H. M., Howson, J. M. M., Stevens, H. E., McManus, R., Wijmenga, C., et al. (2008) · New England Journal of Medicine · doi:10.1056/nejmoa0807917 · Cited by 738 · see citing works
Self-citationHiCUP: pipeline for mapping and processing Hi-C data
Wingett, S., Ewels, P., Furlan-Magaril, M., Nagano, T., Schoenfelder, S., Fraser, P., & Andrews, S. (2015) · F1000Research · doi:10.12688/f1000research.7334.1 · Cited by 724 · see citing works
Self-citationEnhancers as non-coding RNA transcription units: recent insights and future perspectives
Li, W., Notani, D., & Rosenfeld, M. G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.4 · Cited by 710 · see citing works
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
Chen, L., Ge, B., Casale, F. P., Vasquez, L., Kwan, T., Garrido-Martín, D., Watt, S., Yan, Y., Kundu, K., Ecker, S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.10.026 · Cited by 679 · see citing works
Self-citationÖnengüt-Gümüşcü, S., Chen, W., Burren, O. S., Cooper, N. J., Quinlan, A. R., Mychaleckyj, J. C., Farber, E., Bonnie, J. K., Szpak, M., Schofield, E. C., et al. (2015) · Nature Genetics · doi:10.1038/ng.3245 · Cited by 675 · see citing works
Self-citationIRF8 Mutations and Human Dendritic-Cell Immunodeficiency
Hambleton, S., Salem, S., Bustamante, J. C., Bigley, V., Boisson‐Dupuis, S., Azevedo, J., Fortin, A., Haniffa, M. A., Ceron‐Gutierrez, L., Bacon, C. M., et al. (2011) · New England Journal of Medicine · doi:10.1056/nejmoa1100066 · Cited by 609 · see citing works
Single-cell genomics unveils critical regulators of Th17 cell pathogenicity
Gaublomme, J. T., Yosef, N., Lee, Y., Gertner, R. S., Yang, L. V., Wu, C., Pandolfi, P. P., Mak, T., Satija, R., Shalek, A. K., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.009 · Cited by 575 · see citing works
Enhancer RNAs and regulated transcriptional programs
Lam, M. T. Y., Li, W., Rosenfeld, M. G., & Glass, C. K. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.02.007 · Cited by 502 · see citing works
Th17 Cell Pathway in Human Immunity: Lessons from Genetics and Therapeutic Interventions
Patel, D. D., & Kuchroo, V. K. (2015) · Immunity · doi:10.1016/j.immuni.2015.12.003 · Cited by 481 · see citing works
Bayesian refinement of association signals for 14 loci in 3 common diseases
Maller, J., McVean, G., Byrnes, J., Vukcevic, D., Palin, K., Su, Z., Howson, J. M. M., Auton, A., Myers, S. R., Morris, A. P., et al. (2012) · Nature Genetics · doi:10.1038/ng.2435 · Cited by 481 · see citing works
Self-citationLooping Back to Leap Forward: Transcription Enters a New Era
Levine, M., Cattoglio, C., & Tjian, R. (2014) · Cell · doi:10.1016/j.cell.2014.02.009 · Cited by 481 · see citing works
Disease variants alter transcription factor levels and methylation of their binding sites
Bonder, M. J., Luijk, R., Zhernakova, D. V., Moed, M., Deelen, P., Vermaat, M., van Iterson, M., van Dijk, F., van Galen, M., Bot, J. J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3721 · Cited by 462 · see citing works
Hughes, J. R., Roberts, N., McGowan, S., Hay, D., Giannoulatou, E., Lynch, M., De Gobbi, M., Taylor, S., Gibbons, R., & Higgs, D. R. (2014) · Nature Genetics · doi:10.1038/ng.2871 · Cited by 461 · see citing works
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
Cairns, J., Freire-Pritchett, P., Wingett, S. W., Várnai, C., Dimond, A., Plagnol, V., Zerbino, D., Schoenfelder, S., Javierre, B.-M., Osborne, C., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0992-2 · Cited by 417 · see citing works
Self-citationChapman, J. M., Cooper, J. D., Todd, J. A., & Clayton, D. G. (2003) · Human Heredity · doi:10.1159/000073729 · Cited by 414 · see citing works
Self-citationDuhen, T., Duhen, R., Lanzavecchia, A., Sallusto, F., & Campbell, D. J. (2012) · Blood · doi:10.1182/blood-2011-11-392324 · Cited by 413 · see citing works
Identification of context-dependent expression quantitative trait loci in whole blood
Zhernakova, D. V., Deelen, P., Vermaat, M., van Iterson, M., van Galen, M., Arindrarto, W., Hof, P. V. ‘., Mei, H., van Dijk, F., Westra, H.-J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3737 · Cited by 405 · see citing works
Bayes factors for genome‐wide association studies: comparison with P ‐values
Wakefield, J. (2008) · Genetic Epidemiology · doi:10.1002/gepi.20359 · Cited by 397 · see citing works
Super-enhancers delineate disease-associated regulatory nodes in T cells
Vahedi, G., Kanno, Y., Furumoto, Y., Jiang, K., Parker, S. C. J., Erdos, M. R., Davis, S. R., Roychoudhuri, R., Restifo, N. P., Gadina, M., et al. (2015) · Nature · doi:10.1038/nature14154 · Cited by 369 · see citing works
Heritability and genomics of gene expression in peripheral blood
Wright, F. A., Sullivan, P. F., Brooks, A. I., Zou, F., Sun, W., Xia, K., Madar, V., Jansen, R., Chung, W., Zhou, Y.-H., et al. (2014) · Nature Genetics · doi:10.1038/ng.2951 · Cited by 362 · see citing works
Coit, P., Jeffries, M. A., Altorok, N., Dozmorov, M. G., Koelsch, K. A., Wren, J. D., Merrill, J. T., McCune, W. J., & Sawalha, A. H. (2013) · Journal of Autoimmunity · doi:10.1016/j.jaut.2013.04.003 · Cited by 306 · see citing works
Dendrou, C. A., Plagnol, V., Fung, E., Yang, J. H. M., Downes, K., Cooper, J. D., Nutland, S., Coleman, G., Himsworth, M., Hardy, M., et al. (2009) · Nature Genetics · doi:10.1038/ng.434 · Cited by 274 · see citing works
Self-citationFine-mapping cellular QTLs with RASQUAL and ATAC-seq
Kumasaka, N., Knights, A. J., & Gaffney, D. J. (2015) · Nature Genetics · doi:10.1038/ng.3467 · Cited by 259 · see citing works
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression
Hung, T., Pratt, G. A., Sundararaman, B., Townsend, M. J., Chaivorapol, C., Bhangale, T., Graham, R., Ortmann, W. A., Criswell, L. A., Yeo, G. W.-M., et al. (2015) · Science · doi:10.1126/science.aac7442 · Cited by 255 · see citing works
Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-CPreprint
Dryden, N. H., Broome, L. R., Dudbridge, F., Johnson, N., Orr, N., Schoenfelder, S., Nagano, T., Andrews, S., Wingett, S., Kozarewa, I., et al. (2014) · Genome Research · doi:10.1101/gr.175034.114 · Cited by 254 · see citing works
Self-citationChepelev, I., Wei, G., Wangsa, D., Tang, Q., & Zhao, K. (2012) · Cell Research · doi:10.1038/cr.2012.15 · Cited by 253 · see citing works
Intersection of population variation and autoimmunity genetics in human T cell activation
Ye, C. J., Feng, T., Kwon, H.-K., Raj, T., Wilson, M. T., Asinovski, N., McCabe, C., Lee, M. H., Frohlich, I., Paik, H.-I., et al. (2014) · Science · doi:10.1126/science.1254665 · Cited by 236 · see citing works
Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes
Raghavan, A. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf682 · Cited by 233 · see citing works
Martin, P., McGovern, A., Orozco, G., Duffus, K., Yarwood, A., Schoenfelder, S., Cooper, N. J., Barton, A., Wallace, C., Fraser, P., et al. (2015) · Nature Communications · doi:10.1038/ncomms10069 · Cited by 213 · see citing works
Self-citationGarg, G., Tyler, J. R., Yang, J. H. M., Cutler, A. J., Downes, K., Pękalski, M. Ł., Bell, G. L., Nutland, S. L., Peakman, M., Todd, J. A., et al. (2012) · The Journal of Immunology · doi:10.4049/jimmunol.1100272 · Cited by 202 · see citing works
Self-citationBowes, J., Budu‐Aggrey, A., Hüffmeier, U., Uebe, S., Steel, K. J. A., Hébert, H. L., Wallace, C., Massey, J., Bruce, I. N., Bluett, J., et al. (2015) · Nature Communications · doi:10.1038/ncomms7046 · Cited by 186 · see citing works
Self-citationThe deubiquitinating enzyme UCH37 interacts with Smads and regulates TGF-β signalling
Wicks, S. J., Haros, K., Maillard, M., Song, L., Cohen, R. E., ten Dijke, P., & Chantry, A. (2005) · Oncogene · doi:10.1038/sj.onc.1208944 · Cited by 183 · see citing works
Brown, C. D., Mangravite, L. M., & Engelhardt, B. E. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003649 · Cited by 173 · see citing works
Increased DNA methylation variability in type 1 diabetes across three immune effector cell types
Paul, D. S., Teschendorff, A. E., Dang, M. N., Lowe, R., Hawa, M. I., Ecker, S., Beyan, H., Cunningham, S. L., Fouts, A., Ramelius, A., et al. (2016) · Nature Communications · doi:10.1038/ncomms13555 · Cited by 170 · see citing works
Self-citationGuo, H., Fortune, M. D., Burren, O. S., Schofield, E. C., Todd, J. A., & Wallace, C. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv077 · Cited by 149 · see citing works
Self-citationFerreira, R. C., Simons, H. Z., Thompson, W. S., Cutler, A. J., Dopico, X. C., Smyth, D. J., Mashar, M., Schuilenburg, H., Walker, N. M., Dunger, D. B., et al. (2015) · Diabetologia · doi:10.1007/s00125-015-3509-8 · Cited by 143 · see citing works
Self-citationTranscription factor IRF8 directs a silencing programme for TH17 cell differentiation
Ouyang, X., Zhang, R., Yang, J., Li, Q., Qin, L., Zhu, C. Y., Liu, J., Ning, H., Shin, M. S., Gupta, M., et al. (2011) · Nature Communications · doi:10.1038/ncomms1311 · Cited by 119 · see citing works
Trynka, G., Westra, H.-J., Slowikowski, K., Hu, X., Xu, H., Stranger, B. E., Klein, R. J., Han, B., & Raychaudhuri, S. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.05.016 · Cited by 114 · see citing works
McGovern, A., Schoenfelder, S., Martin, P., Massey, J., Duffus, K., Plant, D., Yarwood, A., Pratt, A. G., Anderson, A. E., Isaacs, J. D., et al. (2016) · Genome biology · doi:10.1186/s13059-016-1078-x · Cited by 91 · see citing works
Self-citationThe enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations
Schmidl, C., Hansmann, L., Lassmann, T., Balwierz, P. J., Kawaji, H., Itoh, M., Kawai, J., Nagao-Sato, S., Suzuki, H., Andreesen, R., et al. (2014) · Blood · doi:10.1182/blood-2013-02-486944 · Cited by 86 · see citing works
Gustafsson, M., Gawel, D. R., Alfredsson, L. S., Baranzini, S. E., Björkander, J., Blomgran, R., Hellberg, S., Eklund, D., Ernerudh, J., Kockum, I. S., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aad2722 · Cited by 67 · see citing works
Pękalski, M. Ł., Ferreira, R. C., Coulson, R., Cutler, A. J., Guo, H., Smyth, D. J., Downes, K., Dendrou, C. A., Dopico, X. C., Esposito, L., et al. (2013) · The Journal of Immunology · doi:10.4049/jimmunol.1202914 · Cited by 56 · see citing works
Self-citationAryl hydrocarbon receptor antagonism and its role in rheumatoid arthritis
Kishimoto, T., Nguyen, N., Nakahama, T., Nguyen, H. C., Tran, T. T., Le, V. S., & Hà, C. H. (2015) · Journal of Experimental Pharmacology · doi:10.2147/jep.s63549 · Cited by 53 · see citing works
Wallace, C., Cutler, A. J., Pontikos, N., Pękalski, M. Ł., Burren, O. S., Cooper, J. D., García, A. R., Ferreira, R. C., Guo, H., Walker, N. M., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005272 · Cited by 50 · see citing works
Self-citationMeddens, C., Harakaľová, M., van den Dungen, N. A. M., Asl, H. F., Hijma, H. J., Cuppen, E. P. J. G., Björkegren, J., Asselbergs, F. W., Nieuwenhuis, E. E. S., & Mokrý, M. (2016) · Genome biology · doi:10.1186/s13059-016-1100-3 · Cited by 48 · see citing works
Ling, N., Jacko, A. M., Tan, J., Wang, D., Zhao, J., Kass, D. J., Ma, H., & Zhao, Y. (2016) · Scientific Reports · doi:10.1038/srep33116 · Cited by 48 · see citing works
The autoimmunity-associated gene RGS1 affects the frequency of T follicular helper cells
Caballero‐Franco, C., & Kissler, S. (2016) · Genes and Immunity · doi:10.1038/gene.2016.16 · Cited by 38 · see citing works
Ballesteros‐Tato, A. (2014) · Immunotherapy · doi:10.2217/imt.14.83 · Cited by 35 · see citing works
Identifying Causal Genes at the Multiple Sclerosis Associated Region 6q23 Using Capture Hi-C
Martin, P., McGovern, A., Massey, J., Schoenfelder, S., Duffus, K., Yarwood, A., Barton, A. C., Worthington, J., Fraser, P., Eyre, S., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0166923 · Cited by 32 · see citing works
Self-citationEpigenetic analysis of regulatory T cells using multiplex bisulfite sequencing
Rainbow, D. B., Yang, X., Burren, O., Pekalski, M. L., Smyth, D. J., Klarqvist, M. D. R., Penkett, C. J., Brugger, K., Martin, H., Todd, J. A., et al. (2015) · European Journal of Immunology · doi:10.1002/eji.201545646 · Cited by 26 · see citing works
Self-citationHua, J., Davis, S. P., Hill, J. A., & Yamagata, T. (2015) · The Journal of Immunology · doi:10.4049/jimmunol.1500349 · Cited by 23 · see citing works
Xu, Z. Q., Zhang, G., Duan, Q., Chai, S., Zhang, B., Wu, C., Jin, F., Yue, F., Li, Y., & Hu, M. (2016) · BMC Research Notes · doi:10.1186/s13104-016-1947-0 · Cited by 11 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [69]Li H Durbin R Fast and accurate long-read alignment with Burrows-Wheeler transform Bioinformatics. 2010 26 589 95 10.1093/bioinformatics/btp698 20080505 PMC2828108 · DOI · Paper page
Cited by
Sorted by citations
Biology and regulation of IL-2: from molecular mechanisms to human therapy
Spolski, R., Li, P., & Leonard, W. J. (2018) · Nature Reviews Immunology · doi:10.1038/s41577-018-0046-y · Cited by 637 · see citing works
Robertson, C. C., Inshaw, J. R. J., Onengut-Gumuscu, S., Chen, W.-M., Santa Cruz, D. F., Yang, H., Cutler, A. J., Crouch, D. J. M., Farber, E., Bridges, S. L., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00880-5 · Cited by 302 · see citing works
Self-citationTranscriptional enhancers and their communication with gene promoters
Ray-Jones, H., & Spivakov, M. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03903-w · Cited by 81 · see citing works
Self-citationApproaches and advances in the genetic causes of autoimmune disease and their implications
Inshaw, J. R. J., Cutler, A. J., Burren, O. S., Stefana, M. I., & Todd, J. A. (2018) · Nature Immunology · doi:10.1038/s41590-018-0129-8 · Cited by 70 · see citing works
Self-citation
- Authors
- Burren, O. S., Rubio García, A., Javierre, B.-M., Rainbow, D. B., Cairns, J., Cooper, N. J., Lambourne, J. J., Schofield, E., Castro Dopico, X., Ferreira, R. C., Coulson, R., Burden, F., Rowlston, S. P., Downes, K., Wingett, S. W., Frontini, M., Ouwehand, W. H., Fraser, P., Spivakov, M., Todd, J. A., Wicker, L. S., Cutler, A. J., & Wallace, C.
- Affiliations
- University of Cambridge (GB)
- Babraham Institute (GB)
- Centre for Human Genetics (GB)
- National Health Service (GB)
- Corresponding author
- Wallace, Chris
- ORCID
- Venue
- Genome Biology
- Published
- 2017-09-04
- Volume
- 18
- Issue
- 1
- Pages
- 165-165
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC5584004
- OpenAlex
- W2949341516
- Cited by
- 80
- References
- 81
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 9 · 2023: 8 · 2022: 8 · 2021: 14 · 2020: 13 · 2019: 12 · 2018: 7
- FWCI
- 3.58
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- JDRF (US) (9-2011-253)
- Wellcome Trust (089989, 091157, 107881, 100140)
- Medical Research Council (MR/L007150/1, MC_UP_1302/5)
- Biotechnology and Biological Sciences Research Council (BB/J004480/)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- T cell activation, promoter capture Hi-C, enhancer-promoter interactions, histone modifications, enhancer RNA, allele-specific expression, IL2RA, causal gene prioritization
- MeSH terms
- Autoimmune Diseases, Chromatin, Chromosome Mapping, Enhancer Elements, Genetic, Humans, Lymphocyte Activation, Promoter Regions, Genetic, CD4-Positive T-Lymphocytes, Interleukin-2 Receptor alpha Subunit, Transcriptome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
