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Job Description Region-Gene Association Graphs Global Controls Overview News Use GREAT Demo Video How to Cite Help Forum Bejerano Lab, Stanford University GREAT version 3.0.0 current (02/15/2015 to now) Job Description Region-Gene Association Graphs Number of associated genes per region Binned by orientation and distance to TSS Binned by absolute distance to TSS What do these graphs illustrate? Download as PDF. Download as PDF. Download as PDF. Global Controls Global Export Which data is exported by each option? GO Molecular Function (3 terms) Global controls Table controls: Export Shown top rows in this table: 20 Set Term annotation count: Min: 1 Max: Inf Set Visualize this table: [select one] Binom Binom Hyper Hyper Binom Binom Binom Binom Binom Hyper Hyper Hyper Hyper Hyper Hyper Term Term Binom Binom Observed Region Hyper Hyper Observed Term Raw Bonferroni FDR Q- Fold Genome Raw Bonferroni FDR Q- Fold Total Gene Set Name ID Rank Expected Region Set Rank Expected Gene Gene P-Value P-Value Val Enrichment Fraction P-Value P-Value Val Enrichment Genes Coverage Hits Coverage Hits Coverage sequence-specific DNA binding GO:0043565 2 5.7476e- 2.1197e-6 1.0598e- 2.0959 36.2619 76 0.0935 19.59% 2 4.7470e- 1.7507e-13 8.7535e- 3.1263 21.7511 68 697 12.08% 9.76% 10 6 17 14 HMG box domain binding GO:0071837 5 8.0649e- 2.9743e-3 5.9486e- 7.9439 1.2588 10 0.0032 2.58% 9 1.7248e- 6.3610e-2 7.0678e- 10.1193 0.5929 6 19 1.07% 31.58% 7 4 5 3 regulatory region DNA binding GO:0000975 6 7.9757e- 2.9414e-2 4.9024e- 2.0768 20.2232 42 0.0521 10.82% 5 5.4813e- 2.0215e-4 4.0430e- 2.8814 11.4529 33 367 5.86% 8.99% 6 3 8 5 The test set of 388 genomic regions picked 563 (3%) of all 18,041 genes. GO Molecular Function has 3,688 terms covering 15,090 (84%) of all 18,041 genes, and 189,388 term - gene associations. 3,688 ontology terms (100%) were tested using an annotation count range of [1, Inf]. GO Biological Process (17 terms) Global controls Table controls: Export Shown top rows in this table: 20 Set Term annotation count: Min: 1 Max: Inf Set Visualize this table: [select one] Binom Binom Hyper Hyper Binom Binom Binom Binom Binom Hyper Hyper Hyper Hyper Hyper Hyper Term Term Binom Binom Observed Region Hyper Hyper Observed Term Raw Bonferroni FDR Q- Fold Genome Raw Bonferroni FDR Q- Fold Total Gene Set Name ID Rank Expected Region Set Rank Expected Gene Gene P-Value P-Value Val Enrichment Fraction P-Value P-Value Val Enrichment Genes Coverage Hits Coverage Hits Coverage skeletal system development GO:0001501 1 8.8312e- 9.2198e-7 9.2198e- 2.5437 22.8016 58 0.0588 14.95% 2 2.9408e- 3.0702e-12 1.5351e- 3.8962 12.5763 49 403 8.70% 12.16% 11 7 16 12 Binom Binom Hyper Hyper Binom Binom Binom Binom Binom Hyper Hyper Hyper Hyper Hyper Hyper Term Term Binom Binom Observed Region Hyper Hyper Observed Term Raw Bonferroni FDR Q- Fold Genome Raw Bonferroni FDR Q- Fold Total Gene Set Name ID Rank Expected Region Set Rank Expected Gene Gene P-Value P-Value Val Enrichment Fraction P-Value P-Value Val Enrichment Genes Coverage Hits Coverage Hits Coverage embryonic morphogenesis GO:0048598 2 5.2786e- 5.5108e-6 2.7554e- 2.2762 28.5569 65 0.0736 16.75% 4 2.8600e- 2.9858e-11 7.4645e- 3.4063 15.8530 54 508 9.59% 10.63% 10 6 15 12 anterior/posterior pattern specification GO:0009952 3 6.9152e- 7.2195e-6 2.4065e- 3.3730 10.3765 35 0.0267 9.02% 18 2.7401e- 2.8607e-8 1.5893e- 4.7656 6.0853 29 195 5.15% 14.87% 10 6 12 9 embryonic organ development GO:0048568 5 1.8247e- 1.9050e-5 3.8101e- 2.4148 22.7760 55 0.0587 14.18% 20 3.1036e- 3.2401e-8 1.6201e- 3.4333 12.2330 42 392 7.46% 10.71% 9 6 12 9 embryonic organ morphogenesis GO:0048562 6 5.4845e- 5.7258e-5 9.5431e- 2.7034 15.9061 43 0.0410 11.08% 25 1.4103e- 1.4723e-7 5.8893e- 3.9754 8.3010 33 266 5.86% 12.41% 9 6 11 9 regionalization GO:0003002 9 4.0631e- 4.2419e-4 4.7132e- 2.5182 17.0755 43 0.0440 11.08% 30 1.9585e- 2.0447e-7 6.8157e- 3.7385 9.3620 35 300 6.22% 11.67% 8 5 11 9 pattern specification process GO:0007389 13 1.6930e- 1.7675e-3 1.3596e- 2.1457 24.7002 53 0.0637 13.66% 12 7.0261e- 7.3353e-9 6.1127e- 3.4009 13.2316 45 424 7.99% 10.61% 7 4 13 10 skeletal system morphogenesis GO:0048705 28 9.7855e- 1.0216e-2 3.6486e- 2.7370 10.9607 30 0.0282 7.73% 23 9.3387e- 9.7496e-8 4.2390e- 4.6976 5.9605 28 191 4.97% 14.66% 7 4 12 9 embryonic skeletal system morphogenesis GO:0048704 33 2.2968e- 2.3979e-2 7.2664e- 3.6094 5.2640 19 0.0136 4.90% 47 1.9138e- 1.9980e-6 4.2511e- 6.5545 2.7462 18 88 3.20% 20.45% 6 4 10 8 embryonic skeletal system development GO:0048706 41 4.5261e- 4.7252e-2 1.1525e- 2.9918 7.6876 23 0.0198 5.93% 15 1.3688e- 1.4290e-8 9.5269e- 6.2993 3.6512 23 117 4.09% 19.66% 6 3 12 10 ossification GO:0001503 52 1.1910e- 1.2434e-1 2.3912e- 2.6096 9.9634 26 0.0257 6.70% 92 3.7858e- 3.9524e-2 4.2961e- 3.2532 6.1477 20 197 3.55% 10.15% 5 3 6 4 muscle organ development GO:0007517 67 5.3845e- 5.6215e-1 8.3903e- 2.2155 13.5410 30 0.0349 7.73% 111 2.9925e- 3.1241e-1 2.8145e- 2.6704 8.2386 22 264 3.91% 8.33% 5 3 5 3 chondroblast differentiation GO:0060591 69 6.1310e- 6.4007e-1 9.2764e- 41.0115 0.0732 3 0.0002 0.77% 131 1.1812e- 1.0000 9.4136e- 24.0333 0.1248 3 4 0.53% 75.00% 5 3 4 3 negative regulation of myeloid cell GO:0045638 83 1.5678e- 1.0000 1.9720e- 3.6344 3.3018 12 0.0085 3.09% 143 1.5114e- 1.0000 1.1034e- 4.1083 2.4341 10 78 1.78% 12.82% differentiation 4 2 4 2 positive regulation of steroid biosynthetic GO:0010893 89 2.3134e- 1.0000 2.7137e- 9.3321 0.5358 5 0.0014 1.29% 158 3.8036e- 1.0000 2.5133e- 10.6815 0.3745 4 12 0.71% 33.33% process 4 2 4 2 osteoblast development GO:0002076 94 3.2381e- 1.0000 3.5963e- 5.5549 1.2601 7 0.0032 1.80% 148 2.3507e- 1.0000 1.6582e- 8.4327 0.5929 5 19 0.89% 26.32% 4 2 4 2 artery morphogenesis GO:0048844 103 4.8435e- 1.0000 4.9093e- 3.4182 3.2181 11 0.0083 2.84% 172 6.7334e- 1.0000 4.0870e- 4.6731 1.4979 7 48 1.24% 14.58% 4 2 4 2 The test set of 388 genomic regions picked 563 (3%) of all 18,041 genes. GO Biological Process has 10,440 terms covering 15,441 (86%) of all 18,041 genes, and 950,065 term - gene associations. 10,440 ontology terms (100%) were tested using an annotation count range of [1, Inf]. GO Cellular Component (1 term) Global controls Table controls: Export Shown top rows in this table: 20 Set Term annotation count: Min: 1 Max: Inf Set Visualize this table: [select one] Binom Binom Hyper Hyper Binom Binom Binom Binom Binom Hyper Hyper Hyper Hyper Hyper Hyper Term Term Binom Binom Observed Region Hyper Hyper Observed Term Raw Bonferroni FDR Q- Fold Genome Raw Bonferroni FDR Q- Fold Total Gene Set Name ID Rank Expected Region Set Rank Expected Gene Gene P-Value P-Value Val Enrichment Fraction P-Value P-Value Val Enrichment Genes Coverage Hits Coverage Hits Coverage PcG protein complex GO:0031519 4 2.6739e- 3.3825e-2 8.4563e- 5.9780 1.5055 9 0.0039 2.32% 2 2.2406e- 2.8344e-2 1.4172e- 6.5732 1.2171 8 39 1.42% 20.51% 5 3 5 2 The test set of 388 genomic regions picked 563 (3%) of all 18,041 genes. GO Cellular Component has 1,265 terms covering 16,807 (93%) of all 18,041 genes, and 277,316 term - gene associations. 1,265 ontology terms (100%) were tested using an annotation count range of [1, Inf]. Mouse Phenotype (20+ terms) Global controls Table controls: Export Shown top rows in this table: 20 Set Term annotation count: Min: 1 Max: Inf Set Visualize this table: [select one] Binom Binom Hyper Hyper Binom Binom Binom Binom Binom Hyper Hyper Hyper Hyper Hyper Hyper Term Term Binom Binom Observed Region Hyper Hyper Observed Term Raw Bonferroni FDR Q- Fold Genome Raw Bonferroni FDR Q- Fold Total Gene Set Name ID Rank Expected Region Set Rank Expected Gene Gene P-Value P-Value Val Enrichment Fraction P-Value P-Value Val Enrichment Genes Coverage Hits Coverage Hits Coverage thoracic vertebral transformation MP:0004618 1 4.4458e- 3.5202e-10 3.5202e- 11.9222 1.5098 18 0.0039 4.64% 17 6.0629e- 4.8006e-7 2.8239e- 8.9012 1.6852 15 54 2.66% 27.78% 14 10 11 8 abnormal sternebra morphology MP:0004322 2 2.7539e- 2.1806e-7 1.0903e- 6.5333 3.2143 21 0.0083 5.41% 22 2.4197e- 1.9159e-6 8.7088e- 8.1469 1.8412 15 59 2.66% 25.42% 11 7 10 8 abnormal rib development MP:0002823 3 2.8995e- 2.2958e-7 7.6527e- 11.9491 1.1716 14 0.0030 3.61% 126 4.7384e- 3.7518e-1 2.9776e- 7.0097 0.9986 7 32 1.24% 21.88% 11 8 5 3 abnormal cervical vertebrae morphology MP:0003048 4 4.5629e- 3.6129e-6 9.0323e- 4.4541 5.8374 26 0.0150 6.70% 12 1.0731e- 8.4969e-8 7.0808e- 6.0254 3.6512 22 117 3.91% 18.80% 10 7 11 9 abnormal vertebrae morphology MP:0000137 5 5.8125e- 4.6024e-6 9.2047e- 2.6774 18.3013 49 0.0472 12.63% 9 3.5959e- 2.8472e-8 3.1636e- 3.5506 11.2656 40 361 7.10% 11.08% 10 7 12 9 vertebral transformation MP:0003036 6 7.7012e- 6.0978e-6 1.0163e- 5.4186 3.8756 21 0.0100 5.41% 35 3.8747e- 3.0680e-5 8.7657e- 5.4933 3.2767 18 105 3.20% 17.14% 10 6 9 7 abnormal rib morphology MP:0000150 7 8.4592e- 6.6980e-6 9.5686e- 3.0860 12.6378 39 0.0326 10.05% 30 1.1165e- 8.8401e-6 2.9467e- 3.7321 7.7705 29 249 5.15% 11.65% 10 7 9 7 abnormal thoracic cage morphology MP:0004624 8 9.3369e- 7.3929e-6 9.2412e- 2.6059 19.1869 50 0.0495 12.89% 8 2.5109e- 1.9881e-8 2.4851e- 3.6649 10.6415 39 341 6.93% 11.44% 10 7 12 9 abnormal sternum morphology MP:0000157 9 1.1460e- 9.0737e-6 1.0082e- 3.0522 12.7775 39 0.0329 10.05% 13 1.1043e- 8.7435e-8 6.7258e- 4.5111 6.4286 29 206 5.15% 14.08% 9 6 11 9 abnormal presacral vertebrae morphology MP:0000459 10 1.4313e- 1.1333e-5 1.1333e- 3.2783 10.6764 35 0.0275 9.02% 14 1.2473e- 9.8759e-8 7.0542e- 4.4893 6.4598 29 207 5.15% 14.01% 9 6 11 9 abnormal rib attachment MP:0004625 11 3.4050e- 2.6961e-5 2.4510e- 4.7393 4.6421 22 0.0120 5.67% 28 7.1791e- 5.6844e-6 2.0302e- 6.0716
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