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{{Coexpression_clusters
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12897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,2.52739,0.635753,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,1.53358,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.0946706,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.859396,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,1.72726,30.9323,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,1.66879,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,1.90732,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,1.41398,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,1.23342,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,3.27439,17.3972,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.08488,0.820225,1.00378|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;1.31813,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;0.709734,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;0.946082,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;16.275,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;1.54523,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;1.33363,MA0103.1;1.29536,MA0105.1;0.656404,MA0106.1;0.869173,MA0107.1;1.1497,MA0108.2;1.03412,MA0109.1;0,MA0111.1;1.57689,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;0.430413,MA0145.1;0.195821,MA0146.1;0.221129,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;0.98779,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;1.05083,MA0065.2;0.577908,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;1.21162,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;0.309472,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.122011,MA0102.2;1.75932,MA0258.1;1.07498,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2939_neuroblastoma_middle_occipital_parietal_medial_olfactory_smallcell
|id=C2939
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:3095!5.63e-08!22;DOID:2994!5.63e-08!22;DOID:171!1.14e-07!10
|ontology_enrichment_uberon=UBERON:0001049!3.55e-57!57;UBERON:0005068!3.55e-57!57;UBERON:0006241!3.55e-57!57;UBERON:0007135!3.55e-57!57;UBERON:0001017!2.19e-55!82;UBERON:0000073!8.99e-53!94;UBERON:0001016!8.99e-53!94;UBERON:0005743!3.45e-52!86;UBERON:0001893!1.90e-50!34;UBERON:0001869!2.32e-50!32;UBERON:0002020!3.10e-50!34;UBERON:0003528!3.10e-50!34;UBERON:0002780!7.02e-50!41;UBERON:0001890!7.02e-50!41;UBERON:0006240!7.02e-50!41;UBERON:0000955!1.10e-49!69;UBERON:0006238!1.10e-49!69;UBERON:0002616!3.18e-49!59;UBERON:0003080!1.76e-48!42;UBERON:0002791!2.60e-48!33;UBERON:0002619!1.34e-46!22;UBERON:0002346!1.15e-45!90;UBERON:0001950!3.07e-42!20;UBERON:0003075!1.30e-41!86;UBERON:0007284!1.30e-41!86;UBERON:0000956!2.14e-40!25;UBERON:0000203!2.14e-40!25;UBERON:0003056!1.03e-32!61;UBERON:0007023!2.39e-32!115;UBERON:0000924!1.92e-28!173;UBERON:0006601!1.92e-28!173;UBERON:0004121!1.61e-25!169;UBERON:0000153!7.02e-25!129;UBERON:0007811!7.02e-25!129;UBERON:0000033!4.00e-24!123;UBERON:0000025!5.60e-15!194;UBERON:0000200!1.56e-14!6;UBERON:0001871!1.75e-14!7;UBERON:0001872!2.21e-12!5;UBERON:0000349!3.19e-12!5;UBERON:0002021!3.42e-12!5;UBERON:0002420!1.17e-11!9;UBERON:0007245!1.17e-11!9;UBERON:0010009!1.17e-11!9;UBERON:0010011!1.17e-11!9;UBERON:0000454!1.17e-11!9;UBERON:0002308!2.80e-11!9;UBERON:0000125!2.80e-11!9;UBERON:0003076!3.25e-10!15;UBERON:0003057!3.25e-10!15;UBERON:0004111!1.26e-09!241;UBERON:0000369!2.51e-09!4;UBERON:0002435!2.51e-09!4;UBERON:0000204!2.51e-09!4;UBERON:0010082!2.51e-09!4;UBERON:0002771!2.98e-08!3;UBERON:0004733!4.53e-08!12;UBERON:0002028!4.53e-08!12;UBERON:0007277!4.53e-08!12;UBERON:0009663!7.67e-08!7;UBERON:0004732!2.31e-07!13;UBERON:0000477!2.57e-07!286;UBERON:0000483!2.81e-07!309;UBERON:0005383!2.93e-07!3;UBERON:0005382!2.93e-07!3;UBERON:0000064!3.24e-07!219;UBERON:0000988!3.96e-07!3;UBERON:0000119!4.32e-07!312
}}

Latest revision as of 12:16, 17 September 2013


Full id: C2939_neuroblastoma_middle_occipital_parietal_medial_olfactory_smallcell



Phase1 CAGE Peaks

Hg19::chr9:136465122..136465132,-p2@AK124587
Hg19::chr9:136465213..136465223,-p@chr9:136465213..136465223
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Hg19::chr9:136465441..136465483,-p@chr9:136465441..136465483
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Hg19::chr9:136465528..136465544,-p@chr9:136465528..136465544
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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 tube3.55e-7756
neural rod3.55e-7756
future spinal cord3.55e-7756
neural keel3.55e-7756
regional part of nervous system2.39e-7353
regional part of brain2.39e-7353
telencephalon5.00e-6634
brain grey matter1.13e-6534
gray matter1.13e-6534
cerebral hemisphere2.17e-6532
brain8.90e-6568
future brain8.90e-6568
regional part of cerebral cortex4.57e-6322
regional part of forebrain2.42e-6241
forebrain2.42e-6241
anterior neural tube2.42e-6241
future forebrain2.42e-6241
regional part of telencephalon3.60e-6032
central nervous system4.37e-5981
nervous system2.13e-5889
neocortex6.97e-5720
neurectoderm3.71e-5686
cerebral cortex4.08e-5525
pallium4.08e-5525
neural plate7.12e-5382
presumptive neural plate7.12e-5382
pre-chordal neural plate1.12e-4261
ecto-epithelium4.19e-42104
adult organism2.43e-31114
structure with developmental contribution from neural crest3.20e-31132
ectoderm-derived structure7.99e-31171
ectoderm7.99e-31171
presumptive ectoderm7.99e-31171
organ system subdivision1.43e-23223
gyrus6.84e-216
tube1.20e-19192
occipital lobe9.89e-185
parietal lobe1.30e-175
posterior neural tube1.25e-1515
chordal neural plate1.25e-1515
anatomical conduit9.26e-14240
temporal lobe6.08e-136
brainstem1.28e-126
neural nucleus2.18e-129
nucleus of brain2.18e-129
segmental subdivision of hindbrain3.50e-1212
hindbrain3.50e-1212
presumptive hindbrain3.50e-1212
limbic system2.00e-115
frontal cortex2.26e-113
organ part2.62e-11218
segmental subdivision of nervous system3.60e-1113
epithelium3.42e-10306
cell layer5.35e-10309
pons8.14e-103
anatomical cluster9.32e-10373
basal ganglion3.53e-099
nuclear complex of neuraxis3.53e-099
aggregate regional part of brain3.53e-099
collection of basal ganglia3.53e-099
cerebral subcortex3.53e-099
regional part of metencephalon7.00e-099
metencephalon7.00e-099
future metencephalon7.00e-099
middle temporal gyrus2.69e-082
middle frontal gyrus4.24e-082
corpus striatum4.77e-084
striatum4.77e-084
ventral part of telencephalon4.77e-084
future corpus striatum4.77e-084
Ammon's horn9.03e-082
lobe parts of cerebral cortex9.03e-082
hippocampal formation9.03e-082
limbic lobe9.03e-082
telencephalic nucleus1.11e-077
dorsal plus ventral thalamus1.65e-072
thalamic complex1.65e-072
multi-tissue structure1.81e-07342
locus ceruleus3.41e-072
brainstem nucleus3.41e-072
hindbrain nucleus3.41e-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)
MA0003.10.0214529
MA0004.10.71247
MA0006.11.31813
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
MA0048.10.709734
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
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.116.275
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
MA0090.11.54523
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.11.29536
MA0105.10.656404
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.11.57689
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
MA0144.10.430413
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.21.05083
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.122011
MA0102.21.75932
MA0258.11.07498
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

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

TF#promotersEnrichmentp-valueq-value
SUZ12#23512225.05789045553150.002325256716520610.0131881984477406



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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