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Fig. 5 | Clinical Epigenetics

Fig. 5

From: Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

Fig. 5

Genomic context for investigated SNPs and CpGs. This figure shows the genetic organization of the MAD1L1 gene and the location of investigated SNPs and their dependent CpGs. Ideogram and genome axis tracks were available natively in the R package “gviz.” Data for gene sequences, CpG islands, histone modifications, and transcription factor binding were obtained from the UCSC genome browser. Only depression-related transcription factors (PAX5, ESR1, FOXP2, TAL1, EBF1, SP4, and MEF2C) that were identified using GWAS Catalog were selected. For further information please refer to “materials and methods.” RefSeq track shows neighboring genes. CpGIsl track, H3k27ac, H3 methyl, and Txn_ChIP show CpG islands, histone H3 acetylation, histone H3 methylation, and transcription factor binding, respectively. The last eight tracks (BRAG to BRSN) show chromatin states for the investigated gene region. For color codes, please refer to Additional file 18: Table S10. SNP, single nucleotide polymorphism; TFAMP1, transcription factor A, mitochondrial pseudogene 1; ELFN1, extracellular leucine-rich repeat and fibronectin type III domain containing 1; ELFN1-AS1, ELFN1 antisense RNA 1; MAD1L1, mitotic arrest deficient 1 like 1; SNORA114, small nucleolar RNA, H/ACA Box 114; LOC105375303, homo sapiens uncharacterized LOC105375303; MIR4655, microRNA 4655; MRM2, mitochondrial RRNA methyltransferase 2; NUDT1, nudix hydrolase 1; MIR6836, microRNA 6836; SNX8, sorting nexin 8; EIF3B, eukaryotic translation initiation factor 3 subunit B; CHST12, carbohydrate sulfotransferase 12; GRIFIN, galectin-related inter-fiber protein; PAX5, paired box 5; ESR1, estrogen receptor 1; FOXP2, forkhead box P2; TAL1, T-cell acute lymphocytic leukemia protein 1; EBF1, early b cell factor 1; MEF2C, myocyte enhancer factor 2C; SP4, sp4 transcription factor; BRAG, brain angular gyrus; BRAC, brain anterior caudate; BRCG, brain cingulate gyrus; BRGM, brain germinal matrix; BRHM, brain hippocampus middle; BITL, brain inferior temporal lobe; BDPC, brain dorsolateral prefrontal cortex; BRSN, brain substantia nigra

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