scholarly journals Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities

2012 ◽  
Vol 29 (4) ◽  
pp. 468-475 ◽  
Author(s):  
Rosario M. Piro ◽  
Ivan Molineris ◽  
Ferdinando Di Cunto ◽  
Roland Eils ◽  
Rainer König
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Disease Gene ◽  
Gene Discovery ◽  
Transcription Factor Binding ◽  
Binding Affinities ◽  
Factor Binding ◽  
Disease Gene Discovery ◽  
3D Gene

scholarly journals Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

2016 ◽  
Vol 45 (1) ◽  
pp. 54-66 ◽  
Author(s):  
Florian Schmidt ◽  
Nina Gasparoni ◽  
Gilles Gasparoni ◽  
Kathrin Gianmoena ◽  
Cristina Cadenas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Open Chromatin ◽  
Binding Affinities ◽  
Factor Binding

scholarly journals Bioinformatics Analysis of SNPs in IL-6 Gene Promoter of Jinghai Yellow Chickens

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 446 ◽  
Author(s):  
Shijie Xin ◽  
Xiaohui Wang ◽  
Guojun Dai ◽  
Jingjing Zhang ◽  
Tingting An ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Binding Sites ◽  
Promoter Region ◽  
Bioinformatics Analysis ◽  
Cpg Islands ◽  
Regulatory Region ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Factor Binding

The proinflammatory cytokine, interleukin-6 (IL-6), plays a critical role in many chronic inflammatory diseases, particularly inflammatory bowel disease. To investigate the regulation of IL-6 gene expression at the molecular level, genomic DNA sequencing of Jinghai yellow chickens (Gallus gallus) was performed to detect single-nucleotide polymorphisms (SNPs) in the region −2200 base pairs (bp) upstream to 500 bp downstream of IL-6. Transcription factor binding sites and CpG islands in the IL-6 promoter region were predicted using bioinformatics software. Twenty-eight SNP sites were identified in IL-6. Four of these 28 SNPs, three [−357 (G > A), −447 (C > G), and −663 (A > G)] in the 5′ regulatory region and one in the 3′ non-coding region [3177 (C > T)] are not labelled in GenBank. Bioinformatics analysis revealed 11 SNPs within the promoter region that altered putative transcription factor binding sites. Furthermore, the C-939G mutation in the promoter region may change the number of CpG islands, and SNPs in the 5′ regulatory region may influence IL-6 gene expression by altering transcription factor binding or CpG methylation status. Genetic diversity analysis revealed that the newly discovered A-663G site significantly deviated from Hardy-Weinberg equilibrium. These results provide a basis for further exploration of the promoter function of the IL-6 gene and the relationships of these SNPs to intestinal inflammation resistance in chickens.

MGMT DNA repair gene promoter/enhancer haplotypes alter transcription factor binding and gene expression

2016 ◽  
Vol 39 (5) ◽  
pp. 435-447 ◽  
Author(s):  
Meixiang Xu ◽  
Courtney E. Cross ◽  
Jordan T. Speidel ◽  
Sherif Z. Abdel-Rahman
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Transcription Factor ◽  
Gene Promoter ◽  
Transcription Factor Binding ◽  
Repair Gene ◽  
Factor Binding ◽  
Dna Repair Gene

scholarly journals Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression

PLoS Genetics ◽  
2013 ◽  
Vol 9 (9) ◽  
pp. e1003748 ◽  
Author(s):  
Mathilde Paris ◽  
Tommy Kaplan ◽  
Xiao Yong Li ◽  
Jacqueline E. Villalta ◽  
Susan E. Lott ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Factor Binding ◽  
Conserved Gene ◽  
Drosophila Embryos

scholarly journals Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

PLoS Genetics ◽  
2014 ◽  
Vol 10 (9) ◽  
pp. e1004663 ◽  
Author(s):  
Nicholas E. Banovich ◽  
Xun Lan ◽  
Graham McVicker ◽  
Bryce van de Geijn ◽  
Jacob F. Degner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Histone Modifications ◽  
Transcription Factor Binding ◽  
Expression Levels ◽  
Factor Binding ◽  
Gene Expression Levels
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