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{{Coexpression_clusters
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204,0.00153667,7.35559e-05,0.356232,3.09176e-06,0.813041,0.318338,0.0422834,0.126433,0.417412,0.0570477,0.0555558,3.2958e-05,0.000170953,0.000461533,0.116969,0.000193394,0.255983,0.297663,0.256708,2.72726e-11,0.322052,0.145568,0.153833,0.00369306,0.000148689,1.91094e-06,1.29128e-05,1.6824e-14,0.627637,0.280757,0.050816,0.340343,0.343265,0.501812,0.462092,2.69579e-07,0.308589,0.291523,0.19697,0.309816,0.0537285,0.15063,0.198077,0.0439565,0.348739,0.419895,0.138495,0.208834,0.32256,7.06662e-07,0.342366,0.109684,0.00738257,0.403482,2.25947e-06,0.230841,8.98985e-05,0.255358,0.351665,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.0160823,0.312881,0.512825,7.42687e-10,3.09042e-06,0.158985,0.174153,8.59485e-08,0.333309,0.249919,0.339517,0.303699,0.0211134,0.00176446,0.000435878,0.282501,0.0348179,0.390891,0.238377,0.334983,0.197875,0.287909,2.92062e-05,0.117618,0.392533,1.08084e-06,0.316002,0.330317,5.29416e-05,0.225079,1.08288e-07,0.379651,0.185715,0.345505,0.00140931,0.271405,0.00654668,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,7.69637e-05,0.270094,0.276922,0.156279,0.0067183,0.461742,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.0311458,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,9.4585e-08,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,3.01375e-07,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.0248943,0.316879,2.0109e-07,0.000295973,0.508546,0.224871,1.56404e-05,0.389061,0.0542381,0.0698238,0.445995,0.385709,0.0428885,0.426488,0.00190533,4.96156e-06,0.253154,0.319519,0.309489,0.00268888,0.000105534,0.480785,0.185476,0.336314,0.344469,6.14916e-05,1.1673e-07,0.297596,0.018596,0.00254622,0.380826,0.259046,0.000955184,0.151046,0.000611206,0.347171,0.321735,0.15463,0.13907,0.0267252,0.269432,0.250466,0.409882,0.115686,8.69504e-16,0.000816283,0.342661,0.27567,0.248127,5.60868e-10,0.384731,0.319112,0.526476|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,2.9874,1.57264,0.733342,0.324142,0.321368,0.106358,0.621241,0.778743,0.274093,0.721271,1.14971,0.478935,0.963929,0.395009,0.287891,0.167776,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.758594,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.132849,0.451846,0.0606304,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,1.72052,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,1.57121,1.18161,0.0719601,0.166306,0.647361,3.26181,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.606298,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,1.23742,0.631235,1.37132,0.412056,0.084145,0.596731,3.42732,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,2.06113,0.680988,0.87256,2.09294,0.577088,2.55945,0.526389,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572|tfbs_overrepresentation_jaspar=MA0003.1;0.00991994,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.0418333,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;2.63789,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;0.554727,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;2.92423,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.00220137,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;2.45206,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;3.29691,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;1.65391,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.6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|full_id=C1803_heart_melanoma_nonsmall_left_Fibroblast_substantia_Melanocyte
|id=C1803
}}

Latest revision as of 11:52, 17 September 2013


Full id: C1803_heart_melanoma_nonsmall_left_Fibroblast_substantia_Melanocyte



Phase1 CAGE Peaks

Hg19::chr18:64271316..64271334,-p1@CDH19
Hg19::chr18:64271339..64271357,-p3@CDH19
Hg19::chr18:64271363..64271390,-p2@CDH19
Hg19::chr18:64271391..64271398,-p5@CDH19
Hg19::chr18:64271403..64271414,-p4@CDH19


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

No GOStat results

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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism7.64e-92114
neural tube1.80e-4356
neural rod1.80e-4356
future spinal cord1.80e-4356
neural keel1.80e-4356
regional part of nervous system1.40e-3953
regional part of brain1.40e-3953
neurectoderm1.06e-3686
neural plate2.01e-3682
presumptive neural plate2.01e-3682
brain1.19e-3368
future brain1.19e-3368
central nervous system1.32e-3381
structure with developmental contribution from neural crest1.28e-32132
regional part of forebrain9.34e-3241
forebrain9.34e-3241
anterior neural tube9.34e-3241
future forebrain9.34e-3241
nervous system3.42e-3089
ecto-epithelium2.16e-29104
brain grey matter2.22e-2734
gray matter2.22e-2734
telencephalon5.35e-2734
regional part of telencephalon1.14e-2432
cerebral hemisphere2.36e-2432
organ system subdivision1.61e-23223
pre-chordal neural plate2.42e-2261
ectoderm-derived structure3.12e-21171
ectoderm3.12e-21171
presumptive ectoderm3.12e-21171
tube8.37e-20192
anatomical conduit4.22e-19240
regional part of cerebral cortex6.92e-1922
anatomical cluster6.97e-18373
neocortex1.91e-1620
multi-tissue structure4.85e-16342
cerebral cortex5.18e-1625
pallium5.18e-1625
neural nucleus5.38e-149
nucleus of brain5.38e-149
basal ganglion1.78e-139
nuclear complex of neuraxis1.78e-139
aggregate regional part of brain1.78e-139
collection of basal ganglia1.78e-139
cerebral subcortex1.78e-139
organ2.22e-13503
posterior neural tube1.49e-1215
chordal neural plate1.49e-1215
telencephalic nucleus4.20e-117
epithelium4.87e-11306
cell layer9.97e-11309
primary circulatory organ1.26e-1027
segmental subdivision of nervous system4.07e-1013
embryonic structure9.55e-10564
brainstem1.05e-096
germ layer1.34e-09560
germ layer / neural crest1.34e-09560
embryonic tissue1.34e-09560
presumptive structure1.34e-09560
germ layer / neural crest derived structure1.34e-09560
epiblast (generic)1.34e-09560
embryo1.61e-09592
developing anatomical structure6.01e-09581
segmental subdivision of hindbrain6.41e-0912
hindbrain6.41e-0912
presumptive hindbrain6.41e-0912
organ part7.84e-09218
gyrus1.03e-086
multi-cellular organism3.84e-08656
compound organ3.92e-0868
heart7.93e-0824
primitive heart tube7.93e-0824
primary heart field7.93e-0824
anterior lateral plate mesoderm7.93e-0824
heart tube7.93e-0824
heart primordium7.93e-0824
cardiac mesoderm7.93e-0824
cardiogenic plate7.93e-0824
heart rudiment7.93e-0824
limbic system8.23e-085
regional part of diencephalon1.68e-074
anatomical system8.38e-07624
anatomical group9.62e-07625


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)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.12.63789
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.12.92423
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.12.45206
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.13.29691
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.11.65391
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.83292e-05
MA0102.21.66336
MA0258.10.914277
MA0259.11.02361
MA0442.10



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

This analysis result is provided for C0 - C305 clusters.

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