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{{Coexpression_clusters
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82,0.0167026,0.289049,0.266974,0.125746,0.112897,0.0150081,0.222091,0.0228412,0.34423,0.0936726,0.343425,0.132374,0.285122,0.0280766,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,1.23481,0.66492,0.183156,0.53106,0.0946706,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,1.03936,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;1.70187,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;1.09982,MA0145.1;0.195821,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;1.75253,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.000248021,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2666_cerebellum_hippocampus_medial_Neural_parietal_occipital_pineal
|id=C2666
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.38e-53!57;UBERON:0005068!2.38e-53!57;UBERON:0006241!2.38e-53!57;UBERON:0007135!2.38e-53!57;UBERON:0001017!1.32e-44!82;UBERON:0005743!6.28e-44!86;UBERON:0002616!3.86e-43!59;UBERON:0003075!1.59e-42!86;UBERON:0007284!1.59e-42!86;UBERON:0002780!1.80e-42!41;UBERON:0001890!1.80e-42!41;UBERON:0006240!1.80e-42!41;UBERON:0002346!5.00e-42!90;UBERON:0000073!5.86e-42!94;UBERON:0001016!5.86e-42!94;UBERON:0003080!3.02e-41!42;UBERON:0002020!1.74e-39!34;UBERON:0003528!1.74e-39!34;UBERON:0001893!7.55e-39!34;UBERON:0007023!2.53e-37!115;UBERON:0002791!3.58e-37!33;UBERON:0000955!1.28e-36!69;UBERON:0006238!1.28e-36!69;UBERON:0001869!1.30e-35!32;UBERON:0002619!1.64e-30!22;UBERON:0003056!2.23e-27!61;UBERON:0001950!1.73e-26!20;UBERON:0000956!2.71e-26!25;UBERON:0000203!2.71e-26!25;UBERON:0000924!1.38e-22!173;UBERON:0006601!1.38e-22!173;UBERON:0004121!2.42e-22!169;UBERON:0000033!2.51e-21!123;UBERON:0000153!9.31e-20!129;UBERON:0007811!9.31e-20!129;UBERON:0000025!2.77e-15!194;UBERON:0002308!7.22e-15!9;UBERON:0000125!7.22e-15!9;UBERON:0002420!7.35e-15!9;UBERON:0007245!7.35e-15!9;UBERON:0010009!7.35e-15!9;UBERON:0010011!7.35e-15!9;UBERON:0000454!7.35e-15!9;UBERON:0000200!2.62e-13!6;UBERON:0003076!7.59e-13!15;UBERON:0003057!7.59e-13!15;UBERON:0000349!1.33e-11!5;UBERON:0009663!5.08e-11!7;UBERON:0004111!6.56e-11!241;UBERON:0000064!8.17e-11!219;UBERON:0001871!9.81e-10!7;UBERON:0002298!2.35e-09!8;UBERON:0004733!2.66e-08!12;UBERON:0002028!2.66e-08!12;UBERON:0007277!2.66e-08!12;UBERON:0000477!3.54e-08!286;UBERON:0002771!1.09e-07!3;UBERON:0004732!1.46e-07!13;UBERON:0006331!1.90e-07!3;UBERON:0000988!2.30e-07!3;UBERON:0001872!3.02e-07!5;UBERON:0002021!3.50e-07!5;UBERON:0002240!5.28e-07!3
}}

Latest revision as of 12:10, 17 September 2013


Full id: C2666_cerebellum_hippocampus_medial_Neural_parietal_occipital_pineal



Phase1 CAGE Peaks

Hg19::chr2:166185518..166185522,+p@chr2:166185518..166185522
+
Hg19::chr2:39891675..39891682,+p34@TMEM178
Hg19::chr7:82583500..82583510,-p@chr7:82583500..82583510
-
Hg19::chr9:73710672..73710675,-p@chr9:73710672..73710675
-


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
neural tube6.32e-8556
neural rod6.32e-8556
future spinal cord6.32e-8556
neural keel6.32e-8556
regional part of nervous system2.46e-7953
regional part of brain2.46e-7953
central nervous system2.49e-6781
regional part of forebrain4.62e-6741
forebrain4.62e-6741
anterior neural tube4.62e-6741
future forebrain4.62e-6741
brain1.59e-6368
future brain1.59e-6368
brain grey matter1.99e-6334
gray matter1.99e-6334
nervous system5.55e-6089
telencephalon1.69e-5734
neurectoderm2.12e-5686
neural plate5.45e-5682
presumptive neural plate5.45e-5682
regional part of telencephalon7.75e-5632
cerebral hemisphere7.98e-5632
regional part of cerebral cortex2.80e-4722
pre-chordal neural plate1.93e-4361
ecto-epithelium1.09e-42104
cerebral cortex2.17e-4125
pallium2.17e-4125
neocortex2.57e-3920
adult organism1.53e-38114
structure with developmental contribution from neural crest2.19e-34132
ectoderm-derived structure8.51e-30171
ectoderm8.51e-30171
presumptive ectoderm8.51e-30171
gyrus5.41e-276
organ system subdivision1.58e-25223
neural nucleus9.02e-249
nucleus of brain9.02e-249
tube2.77e-21192
posterior neural tube2.83e-1815
chordal neural plate2.83e-1815
basal ganglion1.38e-179
nuclear complex of neuraxis1.38e-179
aggregate regional part of brain1.38e-179
collection of basal ganglia1.38e-179
cerebral subcortex1.38e-179
telencephalic nucleus7.04e-167
anatomical conduit1.62e-15240
limbic system2.62e-155
frontal cortex1.57e-143
pons2.98e-143
segmental subdivision of hindbrain2.52e-1312
hindbrain2.52e-1312
presumptive hindbrain2.52e-1312
anatomical cluster6.17e-13373
regional part of metencephalon7.16e-139
metencephalon7.16e-139
future metencephalon7.16e-139
segmental subdivision of nervous system2.98e-1213
brainstem3.87e-126
regional part of diencephalon4.04e-114
corpus striatum4.18e-114
striatum4.18e-114
ventral part of telencephalon4.18e-114
future corpus striatum4.18e-114
gland of diencephalon6.50e-114
neuroendocrine gland6.50e-114
organ part8.12e-11218
diencephalon1.00e-107
future diencephalon1.00e-107
Ammon's horn1.10e-102
lobe parts of cerebral cortex1.10e-102
hippocampal formation1.10e-102
limbic lobe1.10e-102
middle frontal gyrus1.39e-102
temporal lobe1.54e-106
epithelium1.55e-10306
cell layer2.32e-10309
pineal body2.32e-102
regional part of epithalamus2.32e-102
secretory circumventricular organ2.32e-102
circumventricular organ2.32e-102
epithalamus2.32e-102
locus ceruleus2.93e-102
brainstem nucleus2.93e-102
hindbrain nucleus2.93e-102
middle temporal gyrus3.07e-102
multi-tissue structure3.46e-10342
occipital lobe8.10e-095
parietal lobe9.50e-095
caudate-putamen2.56e-073
dorsal striatum2.56e-073
spinal cord7.60e-073
dorsal region element7.60e-073
dorsum7.60e-073


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.11.70187
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.21.75253
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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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