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Coexpression cluster:C1064: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.600139,0.905112,0.481684,0.301904,0.480078,0.554663,0.561282,1.05889,1.41657,0.450635,0.597407,0.465048,0.543352,0.300614,0.322799,1.82405,1.29227,0.951811,0.0766963,0.341703,0.180463,0.472508,0.29709,0.385586,0.619829,0.833436,0.470396,0.304828,0.388322,0.429397,0.810962,0.220667,0.469827,0.742281,0.0649851,0.266487,1.20926,0.244807,0.996317,0.268162,1.06332,0.0547276,0.299183,0.0775086,0.970329,1.36786,1.12076,0.0498256,2.27437,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.388089,0.513089,0.85167,0.558065,1.06063,0.746929,0.575742,1.69656,1.12756,1.49516,0.800646,1.33315,1.82757,0.197328,2.77815,1.03748,2.05941,1.36791,0.799673,0.730167,0.797419,0.379656,0.50159,0.745864,0.575394,0.19474,0.986227,2.95029,2.54786,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.817658,0.239285,0.162291,0.87,0.664183,0.106284,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,1.00159,1.42617,0.352381,0.861701,0.336372,0.459808,1.17281,0.265019,4.45915,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,1.76429,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.637373,0.0833399,1.14002,0.960402,0.53901,0.557588,1.36372,0.643609,0.288769,0.385642,0.941217,1.15277,0.941964,0.796636,0.36101,0.71907,1.40773,0.611402,0.553354,0.446088
|tfbs_overrepresentation_jaspar=MA0003.1;0.248189,MA0004.1;0.455723,MA0006.1;4.06209,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;4.32519,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;0.524515,MA0056.1;0,MA0057.1;2.14064,MA0058.1;0.362328,MA0059.1;1.69011,MA0060.1;0.190336,MA0061.1;0.165998,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.415214,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.215282,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;3.00258,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;1.44231,MA0105.1;4.02822,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;1.84219,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;6.23103,MA0140.1;0.516266,MA0141.1;0.944441,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;0.830366,MA0146.1;0.00761723,MA0147.1;1.26392,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;0.284736,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;1.05746,MA0047.2;0.586412,MA0112.2;1.21228,MA0065.2;0.0631316,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.974997,MA0155.1;1.16939,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;9.38516,MA0163.1;1.06699,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;0.916243,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.699589,MA0442.1;0
}}
}}

Revision as of 19:40, 22 January 2013


Full id: C1064_carcinoid_neuroectodermal_amygdala_insula_temporal_frontal_hippocampus



Phase1 CAGE Peaks

Hg19::chr1:20813796..20813807,-p@chr1:20813796..20813807
-
Hg19::chr1:20813828..20813867,-p@chr1:20813828..20813867
-
Hg19::chr2:119916074..119916122,-p4@C1QL2
Hg19::chr2:119916311..119916368,-p1@C1QL2
Hg19::chr2:119916446..119916455,-p9@C1QL2
Hg19::chr2:119916459..119916470,-p3@C1QL2
Hg19::chr2:119916474..119916485,-p5@C1QL2
Hg19::chr2:119916486..119916506,-p2@C1QL2


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
embryonic stem cell1.32e-105
Uber Anatomy
Ontology termp-valuen
neural tube1.14e-8456
neural rod1.14e-8456
future spinal cord1.14e-8456
neural keel1.14e-8456
regional part of nervous system7.96e-8153
regional part of brain7.96e-8153
telencephalon1.14e-7934
brain grey matter4.17e-7934
gray matter4.17e-7934
regional part of forebrain1.30e-7441
forebrain1.30e-7441
anterior neural tube1.30e-7441
future forebrain1.30e-7441
cerebral hemisphere1.33e-7332
regional part of telencephalon3.78e-7332
regional part of cerebral cortex1.11e-7122
central nervous system3.56e-6881
neocortex1.29e-6420
brain6.78e-6468
future brain6.78e-6468
nervous system1.20e-6389
cerebral cortex1.03e-6225
pallium1.03e-6225
neurectoderm1.10e-6186
neural plate1.46e-6182
presumptive neural plate1.46e-6182
pre-chordal neural plate8.45e-5561
ecto-epithelium3.83e-49104
adult organism2.09e-44114
structure with developmental contribution from neural crest1.08e-38132
ectoderm-derived structure9.54e-36171
ectoderm9.54e-36171
presumptive ectoderm9.54e-36171
organ system subdivision4.53e-22223
gyrus8.18e-226
temporal lobe1.39e-186
limbic system1.59e-185
parietal lobe3.02e-185
tube3.40e-18192
basal ganglion3.64e-189
nuclear complex of neuraxis3.64e-189
aggregate regional part of brain3.64e-189
collection of basal ganglia3.64e-189
cerebral subcortex3.64e-189
occipital lobe1.36e-175
neural nucleus1.49e-179
nucleus of brain1.49e-179
brainstem1.58e-136
anatomical conduit1.04e-12240
posterior neural tube1.55e-1215
chordal neural plate1.55e-1215
telencephalic nucleus4.32e-127
organ part4.59e-12218
frontal cortex9.73e-123
anatomical cluster1.56e-10373
pons1.91e-103
epithelium3.28e-10306
cell layer5.11e-10309
segmental subdivision of hindbrain3.24e-0912
hindbrain3.24e-0912
presumptive hindbrain3.24e-0912
Ammon's horn1.20e-082
lobe parts of cerebral cortex1.20e-082
hippocampal formation1.20e-082
limbic lobe1.20e-082
middle temporal gyrus1.49e-082
corpus striatum1.76e-084
striatum1.76e-084
ventral part of telencephalon1.76e-084
future corpus striatum1.76e-084
segmental subdivision of nervous system1.85e-0813
amygdala2.47e-082
middle frontal gyrus2.96e-082
meninx1.16e-072
membrane organ1.16e-072
meningeal cluster1.16e-072
locus ceruleus1.63e-072
brainstem nucleus1.63e-072
hindbrain nucleus1.63e-072
multi-tissue structure1.64e-07342


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)
MA0003.10.248189
MA0004.10.455723
MA0006.14.06209
MA0007.10.437331
MA0009.10.918715
MA0014.14.32519
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
MA0055.10.524515
MA0056.10
MA0057.12.14064
MA0058.10.362328
MA0059.11.69011
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.415214
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.215282
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
MA0091.13.00258
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.11.44231
MA0105.14.02822
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.11.84219
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
MA0139.16.23103
MA0140.10.516266
MA0141.10.944441
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.830366
MA0146.10.00761723
MA0147.11.26392
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.284736
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.21.05746
MA0047.20.586412
MA0112.21.21228
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.974997
MA0155.11.16939
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.19.38516
MA0163.11.06699
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.916243
MA0102.21.46209
MA0258.10.209744
MA0259.10.699589
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
CTCF#1066464.020192279806270.0008334820206774180.00628959745357867
EGR1#195853.117611934256340.01051390990388360.0389231943728226
RAD21#588556.47189618466020.0003657753484789720.0036496810566347
SUZ12#23512637.58683568329721.70067604697628e-091.49007471199795e-07



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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