Coexpression cluster:C36: Difference between revisions
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|ontology_enrichment_disease=DOID:0060058!2.58e-07!10;DOID:2531!2.60e-07!51;DOID:0060083!2.60e-07!51 | |ontology_enrichment_disease=DOID:0060058!2.58e-07!10;DOID:2531!2.60e-07!51;DOID:0060083!2.60e-07!51 | ||
|ontology_enrichment_uberon=UBERON:0002390!3.63e-18!102;UBERON:0003061!3.63e-18!102;UBERON:0007023!8.91e-18!115;UBERON:0002193!8.61e-17!112;UBERON:0000178!1.64e-09!15;UBERON:0000179!1.64e-09!15;UBERON:0000463!1.64e-09!15;UBERON:0002371!8.28e-09!80;UBERON:0002405!9.79e-09!115;UBERON:0001474!1.43e-07!86 | |ontology_enrichment_uberon=UBERON:0002390!3.63e-18!102;UBERON:0003061!3.63e-18!102;UBERON:0007023!8.91e-18!115;UBERON:0002193!8.61e-17!112;UBERON:0000178!1.64e-09!15;UBERON:0000179!1.64e-09!15;UBERON:0000463!1.64e-09!15;UBERON:0002371!8.28e-09!80;UBERON:0002405!9.79e-09!115;UBERON:0001474!1.43e-07!86 | ||
|tfbs_overrepresentation=0.997003,0.95136,1,0.853364,0.939497,1,0.947428,1,0.36332,0.989418,0.910251,0.999995,0.999993,0.896946,0.994877,0.995647,0.999993,0.985065,0.833845,0.960522,0.999455,0.859766,0.961365,0.751169,0.937525,0.999997,0.936475,0.999944,0.901968,0.99496,1,0.997474,0.95834,0.966527,0.999922,0.985856,1,0.999534,0.934013,0.91299,0.999978,0.987127,0.978682,0.989663,0.994208,0.623318,0.804949,0.999881,0.99999,0.999998,0.327782,0.996545,0.93714,0.72305,0.969467,0.966635,0.988319,1,0.999924,0.918683,0.764204,0.99763,0.962382,0.880605,0.856825,0.299851,0.999984,0.99858,0.998313,0.973257,1,0.677431,0.991593,0.974715,0.730375,0.803196,0.982154,0.996406,0.960927,0.719558,0.584845,0.988199,0.944103,0.96211,1,1,0.892332,0.999778,1,0.999073,0.230087,0.662279,0.999973,0.999792,0.778371,0.472124,1,0.85278,0.99457,0.999994,0.944764,0.999917,0.981904,0.959953,0.998934,0.97638,0.852114,0.843967,0.999996,1,1,0.939855,0.692301,0.204713,0.998085,0.848549,0.972377,0.990991,0.938708,0.997725,0.994415,0.999996,0.999911,0.697405,0.990438,0.869653,0.993069,0.264698,0.997878,0.966888,0.998483,0.981715,0.943156,0.0526976,0.999786,0.997889,0.288644,0.866226,0.980581,0.153106,0.765422,0.978711,0.935184,0.424323,1,0.994832,0.803137,0.898374,0.968943,0.325715,0.999868,0.995615,0.925357,0.506461,0.999511,0.99936,0.79418,0.964922,0.994992,0.392456,0.995744,0.961066,0.990872,0.969181,0.999997,0.994402,0.925059,0.592381,0.993849,0.890478,0.889184,0.98504,1,0.96501,0.214318,0.983199,0.944459,0.952189,0.999971,0.987024,0.89245,0.596232,0.992201,0.980231,0.857651,0.973451,0.609794,0.993671,0.88677,0.994797,0.987934,0.999977,0.999998,1,0.98627,0.997927,0.99848,0.915477,0.982454,0.99076,0.828353,0.525895,0.972755,0.851552,0.997776,0.989477,1,0.992936,0.543355,1,0.204546,0.801076,0.903688,1,0.999986,0.999456,1,0.884883,0.999857,0.273269,0.950832,0.807769,0.355973,1,0.997203,0.999983,1,0.233371,0.916827,0.395471,1,1,0.979198,0.998059,0.893153,0.999367,0.997979,0.998082,1,0.999996,0.933566,1,0.985372,0.983512,0.981531,0.999954,0.719858,0.751798,0.999999,0.591756,1,0.999824,0.99716,0.99303,0.0287728,0.999995,0.766701,0.999979,0.998559,1,0.986491,0.999998,1,0.999559,0.0935163,0.614151,0.958159,0.972059,0.998445,0.999999,1,0.970891,1,1,0.975751,0.805482,0.983213,0.999986,1,1,0.999999,1,1,1,1,1,0.928569,1,0.872265,0.937889,0.999157,0.999664,1,0.999378,0.999961,1,0.857755,0.999976,1,1,1,1,0.828365,0.995582,0.656861,1,0.991065,0.999457,0.998846,1,0.943355,0.999999,1,0.999913,1,0.999755,1,1,0.999981,1,0.967979,0.998882,0.999992,0.998768,1,1,0.902822,0.996033,1,0.994408,0.999999,1,1,0.152603,1,0.91486,1,0.999999,1,0.997858,1,1,1,0.998393,0.97171,0.763374,1,0.999833,0.815604,1,0.999999,1,1,0.626651,0.504966,1,0.392194,0.997915,0.996894,0.207274,1,1,1,1,1,1,0.999998,1,0.800942,0.999998,1,0.986897,0.868664,0.977003,1,1,1,1,0.998419,1,1,1,1,0.999872,1,1,0.997574,0.998715,0.994945,0.829058,1,0.999129,0.999897,0.999998,1,1,0.999999,0.999159,0.999958,0.999482,1,1,0.985889,0.981454,0.988169,0.837154,0.895037,1,0.829051,0.94819,0.999794,0.999578,0.978929,0.999986,0.992048,0.84968,1,0.999759,1,0.959698,0.999999,0.999961,0.999746,0.999999,1,0.999959,0.999997,1,0.999692,1,1,1,0.560233,0.985319,1,0.999486,0.888359,0.995111,1,0.993903,0.666896,0.99947,0.795698,0.99807,0.962832,0.838229,0.989376,1,0.999739,0.997046,0.999932,1,0.999987,1,1,0.108983,0.995134,0.989719,1,0.899044,0.997934,0.99206,0.999983,0.999994,1,1,1,0.996758,0.999992,0.950716,0.999249,0.799133,0.999999,0.956265,1,0.996163,1,0.957434,1,1,0.999995,0.989246,0.624854,0.717122,0.946556,0.674328,0.712274,0.859844,0.886679,0.890503,0.149187,0.998072,0.947042,1,0.999997,0.999941,0.789075,0.82273,0.992692,0.999999,0.872441,0.999864,0.999998,1,0.97529,1,0.930981,1,1,0.999836,0.999462,0.999988,0.999999,0.978264,0.931007,0.861536,0.99584,0.88613,0.999681,0.569471,0.999946,0.967324,0.998737,0.995169,0.956246,0.80463,0.956962,0.999539,0.891054,0.996124,0.13955,0.982094,0.998057,0.984192,0.934039,1,1,0.930584,0.47374,0.146288,0.999839,0.995044,0.860331,0.930472,0.99509,0.908116,0.860988,0.754794,0.876033,0.864355,0.984614,0.914263,1,0.360612,0.999729,0.265521,0.999994,1,0.238914,1,1,0.00252067,0.508973,1,0.981021,0.850263,0.128889,1,0.744491,1,0.999996,0.968543,0.998601,0.862512,0.935342,0.914024,0.999915,0.851911,0.892587,1,0.000310537,1,0.411514,0.999638,0.526232,0.873994,1,0.999406,0.78559,0.958959,0.879957,0.56012,1,0.999995,0.471956,0.884507,1,0.999378,0.894248,0.998155,0.997528,0.973607,1,1,0.901217,0.73532,0.943876,0.927257,0.715099,0.000219148,0.995795,0.561622,0.0111273,0.987512,1,0.999987,0.98926,0.999879,0.999825,0.999971,0.999117,1,0.162916,0.479214,1,0.765276,0.812057,1,0.896717,0.999359,0.999902,0.756511,0.99978,0.893575,1,1,0.999858,0.999994,0.844354,0.993292,0.785885,0.779227,0.999975,0.856794,0.929134,0.987883,0.999998,0.987192,1,0.999987,0.234049,0.860132,0.902798,0.964088,0.712261,0.994704,0.936994,0.0149448,0.97296,0.975655,0.999991,0.8109,1,1,0.999999,1,0.960379,1,0.999941,0.999937,0.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}} | }} | ||
Revision as of 19:23, 8 August 2012
Full id: C36_B_b_splenic_plasma_xeroderma_adrenal_Burkitt
Phase1 CAGE Peaks
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
No results for this coexpression
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0032502 | developmental process | 0.00219476440964271 |
| GO:0005515 | protein binding | 0.00219476440964271 |
| GO:0042330 | taxis | 0.00219476440964271 |
| GO:0006935 | chemotaxis | 0.00219476440964271 |
| GO:0007275 | multicellular organismal development | 0.00219476440964271 |
| GO:0048513 | organ development | 0.00219476440964271 |
| GO:0048856 | anatomical structure development | 0.00256244224350349 |
| GO:0048731 | system development | 0.00256244224350349 |
| GO:0007626 | locomotory behavior | 0.00256244224350349 |
| GO:0008009 | chemokine activity | 0.00384522098278705 |
| GO:0042379 | chemokine receptor binding | 0.00384522098278705 |
| GO:0032501 | multicellular organismal process | 0.00505004133334144 |
| GO:0030426 | growth cone | 0.00687927808508844 |
| GO:0030427 | site of polarized growth | 0.00687927808508844 |
| GO:0001664 | G-protein-coupled receptor binding | 0.00687927808508844 |
| GO:0050794 | regulation of cellular process | 0.00852004298658917 |
| GO:0007610 | behavior | 0.00876268216484562 |
| GO:0007267 | cell-cell signaling | 0.0167305732280785 |
| GO:0006366 | transcription from RNA polymerase II promoter | 0.0167305732280785 |
| GO:0065007 | biological regulation | 0.0192382479609515 |
| GO:0050789 | regulation of biological process | 0.0205303385264814 |
| GO:0045610 | regulation of hemocyte differentiation | 0.0242188905245067 |
| GO:0008349 | MAP kinase kinase kinase kinase activity | 0.0242188905245067 |
| GO:0006357 | regulation of transcription from RNA polymerase II promoter | 0.0242188905245067 |
| GO:0001501 | skeletal development | 0.0314270170411542 |
| GO:0050793 | regulation of developmental process | 0.0360978928605626 |
| GO:0016533 | cyclin-dependent protein kinase 5 activator complex | 0.0360978928605626 |
| GO:0035235 | ionotropic glutamate receptor signaling pathway | 0.0360978928605626 |
| GO:0016534 | cyclin-dependent protein kinase 5 activator activity | 0.0360978928605626 |
| GO:0043539 | protein serine/threonine kinase activator activity | 0.0360978928605626 |
| GO:0005153 | interleukin-8 receptor binding | 0.0360978928605626 |
| GO:0044459 | plasma membrane part | 0.043073508145334 |
| GO:0044421 | extracellular region part | 0.043073508145334 |
| GO:0005887 | integral to plasma membrane | 0.043073508145334 |
| GO:0048869 | cellular developmental process | 0.043073508145334 |
| GO:0030154 | cell differentiation | 0.043073508145334 |
| GO:0031226 | intrinsic to plasma membrane | 0.043073508145334 |
| GO:0001958 | endochondral ossification | 0.0438517780456094 |
| GO:0003702 | RNA polymerase II transcription factor activity | 0.0438517780456094 |
| GO:0043005 | neuron projection | 0.0438517780456094 |
| GO:0002376 | immune system process | 0.0438517780456094 |
| GO:0022610 | biological adhesion | 0.0438517780456094 |
| GO:0007155 | cell adhesion | 0.0438517780456094 |
| GO:0042221 | response to chemical stimulus | 0.0438517780456094 |
| GO:0031214 | biomineral formation | 0.0465434875206655 |
| GO:0001503 | ossification | 0.0465434875206655 |
| GO:0045091 | regulation of retroviral genome replication | 0.0465770583515556 |
| GO:0004992 | platelet activating factor receptor activity | 0.0465770583515556 |
| GO:0009888 | tissue development | 0.046601283594754 |
| GO:0005125 | cytokine activity | 0.0477817720982678 |
| GO:0009605 | response to external stimulus | 0.0487789974952223 |
| GO:0046849 | bone remodeling | 0.0487789974952223 |
| GO:0000185 | activation of MAPKKK activity | 0.0499910146372366 |
| GO:0007413 | axonal fasciculation | 0.0499910146372366 |
| GO:0019863 | IgE binding | 0.0499910146372366 |
| GO:0007050 | cell cycle arrest | 0.0499910146372366 |
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| hematopoietic system | 3.63e-18 | 102 |
| blood island | 3.63e-18 | 102 |
| adult organism | 8.91e-18 | 115 |
| hemolymphoid system | 8.61e-17 | 112 |
| blood | 1.64e-09 | 15 |
| haemolymphatic fluid | 1.64e-09 | 15 |
| organism substance | 1.64e-09 | 15 |
| bone marrow | 8.28e-09 | 80 |
| immune system | 9.79e-09 | 115 |
| bone element | 1.43e-07 | 86 |
| Ontology term | p-value | n |
|---|---|---|
| lymphoma | 2.58e-07 | 10 |
| hematologic cancer | 2.60e-07 | 51 |
| immune system cancer | 2.60e-07 | 51 |
Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
|
{{{tfbs_overrepresentation_jaspar}}} |
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
No analysis results for this cluster
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.
