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Coexpression cluster:C1066: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0151272,0.341646,0.481684,0.301904,0.480078,0.554663,0.19223,0.190005,0.0394821,0.450635,0.597407,0.152895,0.543352,0.81316,0.322799,0.774423,0.250594,0.163559,0.0766963,0.341703,0.180463,0.472508,0.805193,0.385586,0.619829,0.421276,0.470396,0.304828,0.122648,0.429397,0.810962,0.220667,0.154814,0.269459,0.0649851,0.266487,0.481208,0.685417,0.174436,0.268162,0.413601,0.0547276,0.299183,0.0775086,0.371118,0.555735,0.440085,0.416595,0.304949,0.63387,0.567337,0.639783,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.149081,0.138565,0.401476,0.730167,0.797419,0.379656,0.167664,0.745864,0.575394,0.567311,0.986227,0.0220225,0.0757344,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.644398,0.302606,0.239285,0.162291,0.87,0.664183,0.106284,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.893372,0.459808,1.17281,0.265019,0.0278613,0.428232,0.710479,0.229841,2.34551,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,2.32574,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.0833399,0.0510299,0.960402,0.53901,0.557588,1.36372,0.643609,0.288769,1.00225,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,0.146591
|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0151272,0.341646,0.481684,0.301904,0.480078,0.554663,0.19223,0.190005,0.0394821,0.450635,0.597407,0.152895,0.543352,0.81316,0.322799,0.774423,0.250594,0.163559,0.0766963,0.341703,0.180463,0.472508,0.805193,0.385586,0.619829,0.421276,0.470396,0.304828,0.122648,0.429397,0.810962,0.220667,0.154814,0.269459,0.0649851,0.266487,0.481208,0.685417,0.174436,0.268162,0.413601,0.0547276,0.299183,0.0775086,0.371118,0.555735,0.440085,0.416595,0.304949,0.63387,0.567337,0.639783,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.149081,0.138565,0.401476,0.730167,0.797419,0.379656,0.167664,0.745864,0.575394,0.567311,0.986227,0.0220225,0.0757344,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.644398,0.302606,0.239285,0.162291,0.87,0.664183,0.106284,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.893372,0.459808,1.17281,0.265019,0.0278613,0.428232,0.710479,0.229841,2.34551,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,2.32574,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.0833399,0.0510299,0.960402,0.53901,0.557588,1.36372,0.643609,0.288769,1.00225,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,0.146591
|tfbs_overrepresentation_jaspar=MA0003.1;0.00101002,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.00962431,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.0955945,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.028436,MA0056.1;0,MA0057.1;0.0912556,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.165998,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.133123,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;2.22338,MA0072.1;0.888148,MA0073.1;9.20286e-05,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.054222,MA0089.1;0,MA0090.1;0.391903,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;0.0818021,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.155155,MA0140.1;0.516266,MA0141.1;2.5401,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.623945,MA0145.1;0.0613434,MA0146.1;0.0399277,MA0147.1;0.243042,MA0148.1;1.20731,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;0.00133745,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;0.458158,MA0065.2;0.0631316,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.0799828,MA0155.1;0.0535085,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;1.23953,MA0161.1;0,MA0162.1;0.0163939,MA0163.1;0.0104024,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;1.41562e-07,MA0102.2;1.46209,MA0258.1;0.603127,MA0259.1;0.25092,MA0442.1;0
}}
}}

Revision as of 19:40, 22 January 2013


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)
MA0003.10.00101002
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.10.0912556
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.12.22338
MA0072.10.888148
MA0073.19.20286e-05
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.12.5401
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.10.0613434
MA0146.10.0399277
MA0147.10.243042
MA0148.11.20731
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.00133745
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.458158
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.11.23953
MA0161.10
MA0162.10.0163939
MA0163.10.0104024
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.21.41562e-07
MA0102.21.46209
MA0258.10.603127
MA0259.10.25092
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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