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{{Coexpression_clusters
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0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.0458843,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.0386145,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,1.10579,0.344471,0.49475,0.598278,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.0946706,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.859396,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,0.109222,0.6318,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,1.12407,0.535192,2.0177,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,0.516141,1.44917,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,1.63159,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.08488,0.820225,0.0401987|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;0.841508,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.100363,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;1.4709,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;2.61689,MA0091.1;0.715356,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;0.656404,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;2.2938,MA0143.1;0.887001,MA0144.1;0.430413,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;0.10559,MA0138.2;0.928035,MA0002.2;0.98779,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;0.0626799,MA0102.2;1.75932,MA0258.1;1.07498,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2292_corpus_brain_diencephalon_thalamus_parietal_cerebral_medulla
|id=C2292
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!7.61e-68!57;UBERON:0005068!7.61e-68!57;UBERON:0006241!7.61e-68!57;UBERON:0007135!7.61e-68!57;UBERON:0001017!3.06e-66!82;UBERON:0005743!2.07e-65!86;UBERON:0000073!3.74e-58!94;UBERON:0001016!3.74e-58!94;UBERON:0002616!1.05e-54!59;UBERON:0003075!3.89e-54!86;UBERON:0007284!3.89e-54!86;UBERON:0000955!9.19e-54!69;UBERON:0006238!9.19e-54!69;UBERON:0002346!3.14e-51!90;UBERON:0002780!8.77e-49!41;UBERON:0001890!8.77e-49!41;UBERON:0006240!8.77e-49!41;UBERON:0003080!1.86e-47!42;UBERON:0001893!9.74e-47!34;UBERON:0002020!5.00e-46!34;UBERON:0003528!5.00e-46!34;UBERON:0002791!3.84e-44!33;UBERON:0001869!1.32e-41!32;UBERON:0007023!1.97e-40!115;UBERON:0003056!1.42e-37!61;UBERON:0000033!1.76e-32!123;UBERON:0000153!1.84e-30!129;UBERON:0007811!1.84e-30!129;UBERON:0004121!3.99e-30!169;UBERON:0000924!3.79e-29!173;UBERON:0006601!3.79e-29!173;UBERON:0002619!7.39e-26!22;UBERON:0000956!1.52e-25!25;UBERON:0000203!1.52e-25!25;UBERON:0001950!7.84e-25!20;UBERON:0002308!2.75e-24!9;UBERON:0000125!2.75e-24!9;UBERON:0003076!9.39e-21!15;UBERON:0003057!9.39e-21!15;UBERON:0009663!1.58e-19!7;UBERON:0002420!1.86e-19!9;UBERON:0007245!1.86e-19!9;UBERON:0010009!1.86e-19!9;UBERON:0010011!1.86e-19!9;UBERON:0000454!1.86e-19!9;UBERON:0000025!1.45e-17!194;UBERON:0004111!1.85e-14!241;UBERON:0004733!7.59e-14!12;UBERON:0002028!7.59e-14!12;UBERON:0007277!7.59e-14!12;UBERON:0000483!4.96e-13!309;UBERON:0000119!8.77e-13!312;UBERON:0002298!1.02e-12!8;UBERON:0000477!1.04e-12!286;UBERON:0004732!1.14e-12!13;UBERON:0000200!1.67e-12!6;UBERON:0000369!6.45e-12!4;UBERON:0002435!6.45e-12!4;UBERON:0000204!6.45e-12!4;UBERON:0010082!6.45e-12!4;UBERON:0002680!1.62e-10!9;UBERON:0001895!1.62e-10!9;UBERON:0010092!1.62e-10!9;UBERON:0000475!1.63e-10!365;UBERON:0000064!1.80e-10!219;UBERON:0002021!8.92e-10!5;UBERON:0002771!1.75e-09!3;UBERON:0002240!1.96e-09!3;UBERON:0000988!3.66e-09!3;UBERON:0006331!3.99e-09!3;UBERON:0001871!4.04e-09!7;UBERON:0005383!4.46e-09!3;UBERON:0005382!4.46e-09!3;UBERON:0000062!2.60e-08!511;UBERON:0001897!1.93e-07!2;UBERON:0000467!3.98e-07!625;UBERON:0000480!4.33e-07!626;UBERON:0000922!5.00e-07!612;UBERON:0001873!7.80e-07!2;UBERON:0010122!7.80e-07!2;UBERON:0002360!8.51e-07!2;UBERON:0000094!8.51e-07!2;UBERON:0007645!8.51e-07!2;UBERON:0000923!9.06e-07!604;UBERON:0005291!9.06e-07!604;UBERON:0006598!9.06e-07!604;UBERON:0002532!9.06e-07!604;UBERON:0002050!9.85e-07!605;UBERON:0005423!9.85e-07!605
}}

Latest revision as of 12:02, 17 September 2013


Full id: C2292_corpus_brain_diencephalon_thalamus_parietal_cerebral_medulla



Phase1 CAGE Peaks

Hg19::chr14:36462898..36462917,+p@chr14:36462898..36462917
+
Hg19::chr17:65474624..65474629,-p@chr17:65474624..65474629
-
Hg19::chr6:163681762..163681767,+p@chr6:163681762..163681767
+
Hg19::chr7:124405418..124405429,-p14@GPR37


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 tube4.26e-8956
neural rod4.26e-8956
future spinal cord4.26e-8956
neural keel4.26e-8956
regional part of nervous system5.21e-7753
regional part of brain5.21e-7753
central nervous system1.33e-7681
nervous system1.77e-6889
brain3.53e-6768
future brain3.53e-6768
regional part of forebrain1.80e-6241
forebrain1.80e-6241
anterior neural tube1.80e-6241
future forebrain1.80e-6241
neural plate3.06e-5982
presumptive neural plate3.06e-5982
telencephalon2.19e-5634
neurectoderm3.14e-5686
adult organism7.26e-51114
brain grey matter2.65e-5034
gray matter2.65e-5034
cerebral hemisphere3.14e-4832
regional part of telencephalon6.63e-4832
ecto-epithelium1.64e-45104
regional part of cerebral cortex2.33e-4222
pre-chordal neural plate1.10e-4061
neocortex3.67e-4020
structure with developmental contribution from neural crest1.15e-39132
cerebral cortex3.96e-3725
pallium3.96e-3725
ectoderm-derived structure4.04e-33171
ectoderm4.04e-33171
presumptive ectoderm4.04e-33171
posterior neural tube1.73e-2615
chordal neural plate1.73e-2615
organ system subdivision1.55e-25223
gyrus6.09e-226
tube7.51e-22192
anatomical conduit3.28e-16240
spinal cord4.64e-163
dorsal region element4.64e-163
dorsum4.64e-163
segmental subdivision of hindbrain3.76e-1512
hindbrain3.76e-1512
presumptive hindbrain3.76e-1512
brainstem2.04e-146
neural nucleus2.27e-149
nucleus of brain2.27e-149
basal ganglion2.77e-149
nuclear complex of neuraxis2.77e-149
aggregate regional part of brain2.77e-149
collection of basal ganglia2.77e-149
cerebral subcortex2.77e-149
segmental subdivision of nervous system6.06e-1413
anatomical cluster1.21e-12373
temporal lobe3.19e-126
dorsal plus ventral thalamus3.37e-122
thalamic complex3.37e-122
telencephalic nucleus4.16e-127
meninx1.38e-112
membrane organ1.38e-112
meningeal cluster1.38e-112
epithelium2.52e-11306
middle temporal gyrus2.75e-112
cell layer3.76e-11309
parietal lobe2.46e-105
occipital lobe2.79e-105
limbic system3.37e-105
organ part1.14e-09218
regional part of metencephalon2.19e-099
metencephalon2.19e-099
future metencephalon2.19e-099
frontal cortex4.25e-083
medulla oblongata4.72e-083
myelencephalon4.72e-083
future myelencephalon4.72e-083
pons4.89e-083
diencephalon8.84e-087
future diencephalon8.84e-087
multi-tissue structure9.07e-08342
corpus callosum4.09e-071
central nervous system cell part cluster4.09e-071
axon tract4.09e-071
intercerebral commissure4.09e-071
dorsal telencephalic commissure4.09e-071
brain white matter4.09e-071
brain commissure4.09e-071
white matter4.09e-071
nervous system commissure4.09e-071
cerebral hemisphere white matter4.09e-071
paracentral gyrus6.08e-071
nucleus accumbens6.43e-071
ventral striatum6.43e-071
postcentral gyrus7.19e-071
organ7.94e-07503
occipital pole8.49e-071
pole of cerebral hemisphere8.49e-071
olfactory region9.48e-071
primary subdivision of skull9.48e-071
cranium9.48e-071


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
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.12.61689
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
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
MA0142.12.2938
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.98779
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
MA0079.20.0626799
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
POU5F1#5460183.85980036297640.01187154239091560.0432365746884096



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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