Journal: Journal of applied statistical science

Article Title: Estimating a scale-change effect for time-varying phenotypes in genome-wide association studies

doi:

Figure Lengend Snippet: Association Results

Article Snippet: For PHM model, both NFDs are less than 1. table ft1 table-wrap mode="anchored" t5 caption a7 AHM PHM SNP Chrom Position Alleles g-freq a p-geno b exp(β) 95% CI −log 10 p exp(β) 95% CI −log 10 p rs6531130 2 16492896 C/T 0.058 99.9% 0.26 (0.14,0.48) 4.71 2.32 (1.67,3.21) 6.32 c rs4832615 2 16494265 C/T 0.058 100% 0.24 (0.14,0.42) 6.44 c 2.38 (1.72,3.01) 6.70 c Relapse rs9868748 3 182965497 C/T 0.053 100% 0.26 (0.16,0.43) 7.10 c 2.08 (1.45,2.99) 4.16 rs7336528 13 101178168 C/G 0.07 100% 0.28 (0.17,0.45) 6.56 c 2.06 (1.51,2.83) 5.22 rs7903420 10 9615684 A/T 0.167 100% 0.51 (0.40,0.67) 6.18 c 1.56 (1.32,1.87) 6.32 c Mortality rs4812426 20 38145076 C/T 0.06 99.9% 0.28 (0.16,0.50) 4.78 2.05 (1.59,2.65) 7.5 c rs6028880 20 38174681 A/G 0.069 99.9% 0.32 (0.22,0.46) 9.01 c 1.99 (1.56,2.52) 7.74 c Open in a separate window a frequency of homogeneous minor allele. b frequency of genotyping call. c significant association using threshold of the negative of logistic p-value as 6.

Techniques:

Journal: Journal of applied statistical science

Article Title: Estimating a scale-change effect for time-varying phenotypes in genome-wide association studies

doi:

Figure Lengend Snippet: Log of negative log of survival functions of (a) rs4832615,(b) rs6531130, (c) rs7336528, (d) rs9868748. Genotype 0/1/2 denotes homozygous major/heterozygous/homozygous rare alleles respectively

Article Snippet: For PHM model, both NFDs are less than 1. table ft1 table-wrap mode="anchored" t5 caption a7 AHM PHM SNP Chrom Position Alleles g-freq a p-geno b exp(β) 95% CI −log 10 p exp(β) 95% CI −log 10 p rs6531130 2 16492896 C/T 0.058 99.9% 0.26 (0.14,0.48) 4.71 2.32 (1.67,3.21) 6.32 c rs4832615 2 16494265 C/T 0.058 100% 0.24 (0.14,0.42) 6.44 c 2.38 (1.72,3.01) 6.70 c Relapse rs9868748 3 182965497 C/T 0.053 100% 0.26 (0.16,0.43) 7.10 c 2.08 (1.45,2.99) 4.16 rs7336528 13 101178168 C/G 0.07 100% 0.28 (0.17,0.45) 6.56 c 2.06 (1.51,2.83) 5.22 rs7903420 10 9615684 A/T 0.167 100% 0.51 (0.40,0.67) 6.18 c 1.56 (1.32,1.87) 6.32 c Mortality rs4812426 20 38145076 C/T 0.06 99.9% 0.28 (0.16,0.50) 4.78 2.05 (1.59,2.65) 7.5 c rs6028880 20 38174681 A/G 0.069 99.9% 0.32 (0.22,0.46) 9.01 c 1.99 (1.56,2.52) 7.74 c Open in a separate window a frequency of homogeneous minor allele. b frequency of genotyping call. c significant association using threshold of the negative of logistic p-value as 6.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Genome-wide Association Study Identifies New Loci for Resistance to Leptosphaeria maculans in Canola

doi: 10.3389/fpls.2016.01513

Figure Lengend Snippet: Manhattan plots showing genome-wide P values for associations between SNP markers and resistance to L. maculans evaluated with ascospore shower test under greenhouse conditions in 179 canola accessions. Stubble was collected from different canola varieties: (A) ATR-Cobbler, (B) AV-Garnet, (C) ATR-JardeeHT, and (D) Monola76TT. Different colors represent different chromosomes (A01–A10, C01–C9). Significant associations were tested at – log10( p ) value of ≥3.

Article Snippet: Utilizing a linkage map previously constructed for SASDH population , resistance to L. maculans isolate 06MGPP041 was remapped using a cotyledon lesion scores on chromosome A01 near Infinium 6K SNP markers UQnapus0918/UQnapus3827 [–log10( p ) > 2.5, favorable resistance allele: Ag-Spectrum].

Techniques: Genome Wide

Journal: Frontiers in Plant Science

Article Title: Genome-wide Association Study Identifies New Loci for Resistance to Leptosphaeria maculans in Canola

doi: 10.3389/fpls.2016.01513

Figure Lengend Snippet: Genome-wide significant SNP associated with variation in resistance to L. maculans at the cotyledon stage (cs).

Article Snippet: Utilizing a linkage map previously constructed for SASDH population , resistance to L. maculans isolate 06MGPP041 was remapped using a cotyledon lesion scores on chromosome A01 near Infinium 6K SNP markers UQnapus0918/UQnapus3827 [–log10( p ) > 2.5, favorable resistance allele: Ag-Spectrum].

Techniques: Genome Wide

Journal: BMC Genomics

Article Title: Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model

doi: 10.1186/s12864-018-5274-9

Figure Lengend Snippet: Emission probabilities of ( a ) a 30-state model for Roadmap Epigenomics dataset and ( b ) a 20-state model for group “HSC & B cell”. Each column stands for a cell-mark combination. The group information comes from Roadmap Epigenomics Consortium. Exxx stands for the EID for each cell type or tissue (Additional file : Table S1). PB, peripheral blood; CB, cord blood; HSC, hematopoietic stem cells; NK cells, nature killer cells

Article Snippet: We downloaded the signals of epigenomic modification tracks [−log 10 ( P -value)] for five histone marks of 127 tissues and cell types (Additional file : Table S1) generated by the Roadmap Epigenomics Consortium at http://egg2.wustl.edu/roadmap/data/ .

Techniques: