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{{Coexpression_clusters
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31474,0.137231,0.562305,0.528646,0.075058,0.31558,0.412744,0.185983,0.0777665,0.163034,0.415367,0.0290437,0.45585,0.36864,0.538745,0.456862,0.453004,0.316163,0.196391,0.693441,0.382214,0.553161,0.639572,0.11429,0.339393,0.332211,0.306231,0.298354,0.646049,0.199987,0.457741,0.0851712,0.426239,0.401917,0.656093,0.572661,0.412586,0.534679,0.41502,0.55475,0.294859,0.170461,0.499347,0.307426,0.0736126,0.557732,0.490527,0.356232,0.44799,0.813041,0.318338,0.276338,0.126433,0.417412,0.318174,0.0555558,0.295666,0.393022,0.293641,0.116969,0.401231,0.255983,0.297663,0.256708,0.338258,0.322052,0.145568,0.153833,0.261242,0.38389,0.54721,0.388459,0.321362,0.627637,0.280757,0.301366,0.340343,0.343265,0.501812,0.462092,0.336254,0.308589,0.291523,0.19697,0.309816,0.0537285,0.15063,0.198077,0.281455,0.348739,0.419895,0.138495,0.208834,0.32256,0.377566,0.342366,0.109684,0.322704,0.403482,0.181288,0.230841,0.352328,0.255358,0.351665,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.312881,0.512825,0.244656,0.192188,0.158985,0.174153,0.0972854,0.333309,0.249919,0.339517,0.303699,0.198326,0.394084,0.458518,0.282501,0.252005,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.117618,0.0897364,0.396962,0.316002,0.330317,0.321404,0.225079,0.300542,0.379651,0.0184244,0.345505,0.375521,0.271405,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.343014,0.270094,0.276922,0.156279,0.313647,0.461742,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.508546,0.224871,0.398887,0.389061,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.297596,0.42392,0.425912,0.380826,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,0.13907,0.470121,0.269432,0.250466,0.409882,0.115686,0.408975,0.162633,0.342661,0.27567,0.248127,0.33299,0.384731,0.319112,0.526476|tfbs_overrepresentation_for_novel_motifs=0.508327,0.787587,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.859849,0.703495,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.501863,0.500405,0.770467,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,0.94379,0.27659,0.417272,0.432883,1.06371,0.654459,0.388123,0.301779,0.415749,0.580638,0.132849,0.451846,0.476793,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,1.64902,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.330474,3.13794,1.23387,1.36104,0.709554,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,3.82149,0.49825,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,1.11542,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,1.49495,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,1.00998,5.71749,1.15522,1.51895,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.923751,0.731946,2.92355|tfbs_overrepresentation_jaspar=MA0003.1;3.78382,MA0004.1;0.626788,MA0006.1;2.97829,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;5.09469,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;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;1.7027,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;2.06887,MA0056.1;0,MA0057.1;3.97654,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,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;5.50918,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;1.3271,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.520776,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;0.994489,MA0117.1;1.1512,MA0119.1;1.25946,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;1.99092,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;2.13391,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.442008,MA0146.1;0.6031,MA0147.1;2.66688,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;2.38271,MA0138.2;1.95446,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;2.35335,MA0047.2;0.767096,MA0112.2;1.35805,MA0065.2;2.03954,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.98952,MA0155.1;0.409315,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;5.73519,MA0163.1;7.5271,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;22.1863,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;1.80881,MA0442.1;0}}
|full_id=C1756_cerebellum_small_merkel_putamen_caudate_pineal_occipital
|id=C1756
}}

Latest revision as of 11:51, 17 September 2013


Full id: C1756_cerebellum_small_merkel_putamen_caudate_pineal_occipital



Phase1 CAGE Peaks

Hg19::chr16:2198604..2198644,+p1@RAB26
Hg19::chr19:42817614..42817625,+p7@TMEM145
Hg19::chr19:51198850..51198862,+p@chr19:51198850..51198862
+
Hg19::chr21:34697083..34697182,-p@chr21:34697083..34697182
-
Hg19::chr7:75831181..75831236,+p1@SRRM3


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 IDGO nameFDR corrected p-value
GO:0035272exocrine system development0.0295770902979239
GO:0017157regulation of exocytosis0.0295770902979239



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
nervous system3.63e-7289
neural tube6.67e-7056
neural rod6.67e-7056
future spinal cord6.67e-7056
neural keel6.67e-7056
central nervous system1.47e-6981
regional part of nervous system1.71e-6553
regional part of brain1.71e-6553
brain2.73e-5968
future brain2.73e-5968
neurectoderm1.17e-5786
regional part of forebrain1.22e-5541
forebrain1.22e-5541
anterior neural tube1.22e-5541
future forebrain1.22e-5541
neural plate7.37e-5582
presumptive neural plate7.37e-5582
brain grey matter5.43e-4534
gray matter5.43e-4534
ecto-epithelium5.61e-45104
telencephalon6.45e-4534
pre-chordal neural plate6.81e-4461
cerebral hemisphere1.77e-4232
regional part of telencephalon5.18e-4232
ectoderm-derived structure1.14e-40171
ectoderm1.14e-40171
presumptive ectoderm1.14e-40171
adult organism9.23e-39114
regional part of cerebral cortex2.62e-3622
neocortex8.12e-3320
cerebral cortex3.17e-3125
pallium3.17e-3125
organ system subdivision5.85e-31223
structure with developmental contribution from neural crest4.96e-30132
basal ganglion1.49e-159
nuclear complex of neuraxis1.49e-159
aggregate regional part of brain1.49e-159
collection of basal ganglia1.49e-159
cerebral subcortex1.49e-159
neural nucleus3.53e-159
nucleus of brain3.53e-159
posterior neural tube5.51e-1515
chordal neural plate5.51e-1515
anatomical cluster3.31e-14373
tube1.14e-13192
segmental subdivision of nervous system2.22e-1213
telencephalic nucleus2.67e-127
diencephalon6.05e-127
future diencephalon6.05e-127
gyrus1.39e-116
segmental subdivision of hindbrain4.48e-1112
hindbrain4.48e-1112
presumptive hindbrain4.48e-1112
organ part4.51e-10218
brainstem4.54e-106
limbic system4.62e-105
parietal lobe5.64e-105
occipital lobe6.40e-105
temporal lobe8.10e-106
anatomical conduit4.98e-09240
corpus striatum3.26e-084
striatum3.26e-084
ventral part of telencephalon3.26e-084
future corpus striatum3.26e-084
epithelium5.49e-08306
gland of diencephalon8.80e-084
neuroendocrine gland8.80e-084
regional part of diencephalon9.12e-084
cell layer9.30e-08309
multi-tissue structure9.55e-08342
regional part of metencephalon2.93e-079
metencephalon2.93e-079
future metencephalon2.93e-079
Disease
Ontology termp-valuen
neuroectodermal tumor7.18e-0910


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)
MA0003.13.78382
MA0004.10.626788
MA0006.12.97829
MA0007.10.606704
MA0009.11.11255
MA0014.15.09469
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
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.7027
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.12.06887
MA0056.10
MA0057.13.97654
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.15.50918
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.11.25946
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.11.99092
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.12.13391
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.6031
MA0147.12.66688
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.22.38271
MA0138.21.95446
MA0002.20.30855
MA0137.20.47779
MA0104.22.35335
MA0047.20.767096
MA0112.21.35805
MA0065.22.03954
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.15.73519
MA0163.17.5271
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.222.1863
MA0102.21.66336
MA0258.10.345771
MA0259.11.80881
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
REST#597835.790017229676810.009468788694433940.0356955971144234
ZBTB7A#5134145.881527446300720.001524947561042230.00971418105078925



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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