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Coexpression cluster:C1066: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
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.125132,0.401145,0.708839,0.0857811,0.681349,0.48369,0.101821,0.151258,0.765247,0.294186,0.264629,0.267153,0.554314,0.0744668,0.88063,0.340579,0.10027,0.216542,0.140095,0.339551,0.541739,0.479289,0.429978,0.312506,0.737097,0.514064,0.594251,0.190339,0.39643,0.203718,0.416086,0.66316,0.346997,0.33418,0.386217,0.332439,0.219989,0.627646,0.594435,0.121222,0.233436,0.792498,0.316293,0.193405,0.265337,0.307168,0.313275,0.95497,0.795728,0.132332,0.243599,0.127929,0.1565,0.188908,0.230656,0.339566,0.0881682,0.18579,0.579058,0.972382,0.941584,0.479647,0.597758,0.28717,0.434522,0.407023,0.879571,0.146252,0.12193,0.735829,0.154198,0.401916,0.614575,0.179067,0.491271,0.600481,0.0920973,0.300879,0.40148,0.998435,0.999352,0.460251,0.48128,0.0381891,0.169668,0.264355,0.126386,0.235621,0.45894,0.189069,0.117159,0.267581,0.1766,0.495277,0.358721,0.0973803,0.315733,0.115553,0.13739,0.276387,0.229078,0.396303,0.255961,0.487366,0.145278,0.509288,0.190011,0.59406,0.356502,0.439115,0.481419,0.248532,0.652258,0.397384,0.671042,0.354931,0.158525,0.43239,0.348785,0.846337,0.36346,0.180408,0.226687,0.152678,0.340038,0.35297,0.239072,0.361869,0.39215,0.436719,0.325366,0.498702,0.538083,0.595929,0.28677,0.208355,0.658265,0.273994,0.272914,0.423557,0.400864,0.233355,0.558548,0.534095,0.332254,0.24444,0.548105,0.253118,0.273827,0.0667061,0.387479,0.223866,0.904489,0.385626,0.427353,0.202588,0.420356,0.364345,0.630887,0.852275,0.149927,0.531236,0.407834,0.481345,0.503758,0.752108,0.924193,0.0933565,0.757541,0.312516,0.111737,0.317827,0.76404,0.707417,0.795985,0.752206,0.504402,0.877369,0.786493,0.708393,0.772671,0.795749,0.443827,0.74047,0.697643,0.750697,0.721788,0.901346,0.936229,0.445023,0.967131,0.732791,0.832307,0.842996,0.790157,0.861021,0.99617,0.995774,0.496897,0.85764,0.923096,0.728237,0.590655,0.846474,0.882448,0.969291,0.597402,0.380163,0.809189,0.595604,0.897663,0.823504,0.664803,0.814591,0.549112,0.793528,0.524662,0.981789,0.733501,0.970984,0.953366,0.375011,0.975506,0.936699,0.839155,0.986171,0.712705,0.983429,0.822762,0.983171,0.974383,0.980597,0.454729,0.44937,0.458665,0.614438,0.546419,0.772399,0.681923,0.724441,0.364029,0.333879,0.757271,0.236293,0.63458,0.689159,0.379433,0.502911,0.289349,0.590067,0.889628,0.634568,0.413633,0.587076,0.911143,0.922307,0.753368,0.856,0.645528,0.941952,0.66902,0.918981,0.729164,0.860789,0.986712,0.87196,0.488054,0.762387,0.420398,0.809211,0.685922,0.900712,0.457276,0.799317,0.328805,0.949451,0.385504,0.444467,0.207197,0.637438,0.825729,0.401684,0.660264,0.71269,0.861581,0.753866,0.702714,0.870027,0.733391,0.699838,0.162041,0.45485,0.573299,0.715409,0.79357,0.684354,0.576345,0.933166,0.622298,0.520881,0.710061,0.62342,0.619131,0.839028,0.728293,0.849193,0.537256,0.724424,0.804607,0.846436,0.484879,0.850008,0.442887,0.432731,0.810194,0.914222,0.624396,0.806372,0.588879,0.890421,0.818739,0.743413,0.573115,0.705962,0.575942,0.72599,0.823302,0.694833,0.669433,0.44442,0.917799,0.72892,0.293277,0.865189,0.613531,0.931641,0.45836,0.403985,0.194485,0.578712,0.458152,0.0873966,0.42925,0.55014,0.426623,0.180477,0.559835,0.376936,0.431837,0.377907,0.483463,0.463074,0.222529,0.234528,0.383967,0.539263,0.718529,0.544718,0.462199,0.794152,0.409798,0.436622,0.486064,0.489702,0.672033,0.629206,0.480957,0.445913,0.42387,0.296003,0.447485,0.0845698,0.229886,0.297555,0.410714,0.49649,0.581581,0.212206,0.31257,0.463718,0.531673,0.488584,0.169631,0.4639,0.56248,0.273878,0.342908,0.500922,0.376098,0.500105,0.389123,0.0993883,0.1667,0.133211,0.116907,0.565967,0.451406,0.683557,0.361689,0.289284,0.241971,0.263726,0.151053,0.477267,0.368791,0.485034,0.43963,0.297904,0.551399,0.625257,0.412086,0.371597,0.547611,0.353179,0.479366,0.297272,0.41916,0.42109,0.18144,0.54956,0.554803,0.455388,0.473509,0.462252,0.335015,0.435559,0.53418,0.28015,0.492484,0.529209,0.397471,0.449258,0.330704,0.443138,0.519779,0.364755,0.312488,0.547073,0.48939,0.395736,0.404755,0.238065,0.452384,0.62882,0.585012,0.481224,0.204547,0.452254,0.259924,0.136638,0.137048,0.353983,0.194753,0.104944,0.136955,0.642324,0.554772,0.469052,0.425619,0.50814,0.429061,0.202353,0.240717,0.162041,0.292976,0.161384,0.255196,0.167238,0.190639,0.307532,0.265287,0.113346,0.168727,0.221472,0.095012,0.320667,0.456504,0.607439,0.5938,0.679098,0.334729,0.557075,0.545435,0.448658,0.497569,0.611294,0.541437,0.406439,0.589165,0.559083,0.313926,0.373141,0.459861,0.447066,0.594101,0.512982,0.649607,0.279812,0.481032,0.491197,0.278645,0.439191,0.431751,0.586217,0.588503,0.535591,0.381036,0.491941,0.230489,0.653021,0.494548,0.462673,0.23568,0.213047,0.638022,0.394858,0.369527,0.569966,0.178571,0.568909,0.247225,0.48895,0.403105,0.366377,0.476867,0.540268,0.459344,0.697624
}}
}}

Revision as of 10:47, 19 October 2012


Full id: C1066_heart_neuroblastoma_caudate_hippocampus_umbilical_occipital_cerebellum



Phase1 CAGE Peaks

Hg19::chr1:237209194..237209198,+p@chr1:237209194..237209198
+
Hg19::chr1:237210706..237210709,+p@chr1:237210706..237210709
+
Hg19::chr1:237228081..237228086,+p@chr1:237228081..237228086
+
Hg19::chr1:237231349..237231352,+p@chr1:237231349..237231352
+
Hg19::chr1:237255831..237255843,+p@chr1:237255831..237255843
+
Hg19::chr1:237350761..237350764,+p@chr1:237350761..237350764
+
Hg19::chr1:237599779..237599780,+p@chr1:237599779..237599780
+
Hg19::chr1:237747972..237747976,+p@chr1:237747972..237747976
+


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 organism2.98e-67114
regional part of nervous system5.79e-6553
regional part of brain5.79e-6553
neural tube6.40e-6156
neural rod6.40e-6156
future spinal cord6.40e-6156
neural keel6.40e-6156
central nervous system1.13e-5481
regional part of forebrain2.35e-5441
forebrain2.35e-5441
anterior neural tube2.35e-5441
future forebrain2.35e-5441
brain7.15e-5368
future brain7.15e-5368
nervous system1.32e-5089
brain grey matter2.07e-5034
gray matter2.07e-5034
cerebral hemisphere2.97e-5032
neurectoderm8.10e-5086
neural plate4.86e-4882
presumptive neural plate4.86e-4882
telencephalon6.57e-4734
regional part of telencephalon1.53e-4632
regional part of cerebral cortex6.07e-4022
pre-chordal neural plate5.94e-3661
ecto-epithelium2.49e-35104
neocortex2.85e-3520
structure with developmental contribution from neural crest5.60e-35132
cerebral cortex1.20e-3425
pallium1.20e-3425
ectoderm-derived structure2.62e-28171
ectoderm2.62e-28171
presumptive ectoderm2.62e-28171
tube4.47e-22192
organ system subdivision5.52e-22223
neural nucleus3.57e-179
nucleus of brain3.57e-179
anatomical conduit1.03e-16240
anatomical cluster4.71e-16373
gyrus6.46e-156
basal ganglion9.38e-149
nuclear complex of neuraxis9.38e-149
aggregate regional part of brain9.38e-149
collection of basal ganglia9.38e-149
cerebral subcortex9.38e-149
telencephalic nucleus2.28e-137
parietal lobe1.03e-125
organ part3.64e-12218
segmental subdivision of hindbrain1.17e-1112
hindbrain1.17e-1112
presumptive hindbrain1.17e-1112
corpus striatum2.26e-114
striatum2.26e-114
ventral part of telencephalon2.26e-114
future corpus striatum2.26e-114
multi-tissue structure2.70e-11342
segmental subdivision of nervous system1.19e-1013
epithelium2.91e-10306
cell layer4.89e-10309
valve1.86e-093
cardiac mesenchyme1.86e-093
cardial valve1.86e-093
tunica intima1.86e-093
heart layer1.86e-093
endocardium1.86e-093
endocardial cushion1.86e-093
presumptive endocardium1.86e-093
regional part of metencephalon2.10e-099
metencephalon2.10e-099
future metencephalon2.10e-099
brainstem2.83e-096
caudate-putamen3.62e-093
dorsal striatum3.62e-093
posterior neural tube4.83e-0915
chordal neural plate4.83e-0915
cardiac chamber5.96e-093
temporal lobe6.18e-096
diencephalon9.77e-097
future diencephalon9.77e-097
limbic system9.82e-095
frontal cortex1.23e-083
occipital lobe1.32e-085
organ3.57e-08503
germ layer4.30e-08560
germ layer / neural crest4.30e-08560
embryonic tissue4.30e-08560
presumptive structure4.30e-08560
germ layer / neural crest derived structure4.30e-08560
epiblast (generic)4.30e-08560
embryonic structure6.51e-08564
developing anatomical structure1.02e-07581
pons1.98e-073
embryo3.01e-07592
atrioventricular valve7.73e-072


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

This analysis result is provided for C0 - C305 clusters.

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