0000000000409225
AUTHOR
Enrique Muro
MOESM2 of The distributions of protein coding genes within chromatin domains in relation to human disease
Additional file 2: Figure S2. Distribution of the distances from the TSS of the genes to their closest TAD borders depending on the gene association with disease. The TAD border is represented with a vertical black line. Blue and salmon color represent genes associated and not with disease, respectively. If the TSS is within a TAD a negative distance is calculated, otherwise the distance is positive. a. HK genes. b. non-HK genes. Insets: The densities for the same data is shown. Genes not associated with disease have higher preference for TAD borders but this is only significant for non-HK genes (p-value = 9 × 10−11, Wilcoxon rank test).
MOESM9 of The distributions of protein coding genes within chromatin domains in relation to human disease
Additional file 9: Figure S8. Distribution of TAD lengths depending on the number of TSSs they contain. An horizontal black line indicates the median for each TAD category.
MOESM5 of The distributions of protein coding genes within chromatin domains in relation to human disease
Additional file 5: Figure S4. Fraction of genes for HK and non-HK genes associated with disease (ordinates) depending on the number of genes contained within the TADs (n; abscissas); the numbers have been aggregated for n ≥ 6. The lower the number of genes inside the TAD the higher fraction of the genes associated with disease: a. HK genes; a p-value = 3.6 × 10−5 from a Chi-square test, comparing the number of genes associated and non-associated with disease for the six TAD categories, was obtained. The green dotted line represents the genome-wide fraction of HK genes associated with disease (0.309). b. non-HK genes; a p-value = 1.2 × 10−43 from a Chi-square test has been obtained. The gree…
MOESM8 of The distributions of protein coding genes within chromatin domains in relation to human disease
Additional file 8: Figure S7. Mean ratios of the number of enhancers per gene within the TADs versus the number of genes within the TAD associated with disease (0 ≤ k ≤ n), where n is the total number of genes within the TAD. The value of n, which determines the TAD category, is represented for TADs with n = 1, 2, 3, and 4 genes (red, blue, green and purple lines, respectively). TADs with fewer TSSs have higher ratios of enhancers to TSSs. Moreover, for each TAD category, the higher the number of genes associated with disease, the higher the average number of enhancers per gene.
MOESM3 of The distributions of protein coding genes within chromatin domains in relation to human disease
Additional file 3: Figure S3. Number of TADs depending on the number of genes within the TADs. The counts are displayed behind each bar. Many TADs contain few genes and from a total of 9274 TADs, 2017 TADs (21.7%) have no gene within them.
MOESM1 of The distributions of protein coding genes within chromatin domains in relation to human disease
Additional file 1: Figure S1. Distribution of the distances from the TSS of genes to their closest TAD borders. The TAD borders are represented with a vertical black line. Blue and salmon color represent HK and non-HK genes, respectively. If the TSS is within a TAD a negative distance is calculated, otherwise the distance is positive. Each bin represents 500 nt. Inset: the density for the same data is shown. The preference of HKs toward the TAD borders is significant (p-value = 3 × 10−4, Wilcoxon rank test).
MOESM7 of The distributions of protein coding genes within chromatin domains in relation to human disease
Additional file 7: Figure S6. Distribution of the ratios of the number of enhancers to genes depending on the number of genes within a TAD. Mean and median values of each boxplot are shown by white diamonds and black horizontal lines, respectively.
MOESM6 of The distributions of protein coding genes within chromatin domains in relation to human disease
Additional file 6: Figure S5. Distribution of the number of enhancers within TADs versus the number of genes contained within the TADs. Mean and median values of each boxplot are shown by white diamonds and black horizontal lines, respectively. The more genes within a TAD, the larger the number of enhancers.
MOESM12 of The distributions of protein coding genes within chromatin domains in relation to human disease
Additional file 12: Table S3. Distance of each TSS to the closest TAD border. The distance (negative) has been calculated for each TAD where the TSS is contained. If the TSS is within no TAD the closest distance (positive) to a TAD border has been calculated. Each entry of the table displays the following information by columns: geneId, gene strand, gene locus, TSS of gene, distance to the TAD border, and TAD.
MOESM11 of The distributions of protein coding genes within chromatin domains in relation to human disease
Additional file 11: Table S2. The 3650 different protein coding HKs.
MOESM4 of The distributions of protein coding genes within chromatin domains in relation to human disease
Additional file 4: Table S4. TADs that contain only one gene.
MOESM10 of The distributions of protein coding genes within chromatin domains in relation to human disease
Additional file 10: Table S1. The 18,141 different protein coding genes. Each row has the following information in the columns: geneid, gene locus, transcription starting site (TSS), and CTD gene association or not with disease.