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Coexpression cluster:C1804: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.205703,0.500341,0.654974,0.454983,1.57264,0.733342,0.324142,0.321368,0.703495,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.501863,1.25032,0.121147,0.645033,0.44943,0.549618,0.802434,0.700122,0.642741,2.02225,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.195238,1.87167,0.654459,0.388123,0.301779,0.415749,0.580638,0.132849,2.00042,0.218848,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.330474,0.189341,1.23387,0.741483,0.255232,0.240727,0.917983,0.987729,0.543014,0.796279,0.934302,1.78477,0.327263,1.18161,0.536557,0.49825,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.99322,0.28626,1.06255,0.849074,1.78691,1.01093,1.01316,2.40164,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,1.52665,1.37132,0.412056,0.597842,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.443702
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.205703,0.500341,0.654974,0.454983,1.57264,0.733342,0.324142,0.321368,0.703495,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.501863,1.25032,0.121147,0.645033,0.44943,0.549618,0.802434,0.700122,0.642741,2.02225,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.195238,1.87167,0.654459,0.388123,0.301779,0.415749,0.580638,0.132849,2.00042,0.218848,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.330474,0.189341,1.23387,0.741483,0.255232,0.240727,0.917983,0.987729,0.543014,0.796279,0.934302,1.78477,0.327263,1.18161,0.536557,0.49825,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.99322,0.28626,1.06255,0.849074,1.78691,1.01093,1.01316,2.40164,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,1.52665,1.37132,0.412056,0.597842,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.443702
|tfbs_overrepresentation_jaspar=MA0003.1;1.04569,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;1.02528,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.603517,MA0056.1;0,MA0057.1;0.554727,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;1.74614,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.782425,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.412364,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;1.00065,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.442008,MA0146.1;0.143081,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.0575907,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.839774,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.409315,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.81299,MA0163.1;0.168633,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;2.12087,MA0102.2;1.66336,MA0258.1;0.914277,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:12, 22 January 2013


Full id: C1804_hippocampus_temporal_duodenum_amygdala_brain_merkel_Neurons



Phase1 CAGE Peaks

Hg19::chr18:67068228..67068257,+p2@DOK6
Hg19::chr22:26779052..26779057,+p@chr22:26779052..26779057
+
Hg19::chr5:175223625..175223636,+p15@CPLX2
Hg19::chr8:65492915..65492932,+p1@BHLHE22
Hg19::chr8:65492973..65492989,+p5@BHLHE22


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

GO IDGO nameFDR corrected p-value
GO:0002448mast cell mediated immunity0.00402637148661542
GO:0043303mast cell degranulation0.00402637148661542
GO:0045576mast cell activation0.00402637148661542
GO:0043299leukocyte degranulation0.00402637148661542
GO:0002444myeloid leukocyte mediated immunity0.00402637148661542
GO:0019905syntaxin binding0.00642968469553287
GO:0000149SNARE binding0.00642968469553287
GO:0005158insulin receptor binding0.00642968469553287
GO:0002274myeloid leukocyte activation0.00670884107822723
GO:0006904vesicle docking during exocytosis0.00708040750904987
GO:0048278vesicle docking0.00708040750904987
GO:0022406membrane docking0.00708040750904987
GO:0045055regulated secretory pathway0.00911365272578224
GO:0006836neurotransmitter transport0.011619925588591
GO:0002443leukocyte mediated immunity0.011619925588591
GO:0032403protein complex binding0.0137733392856842
GO:0002252immune effector process0.0137733392856842
GO:0006887exocytosis0.0137733392856842
GO:0045321leukocyte activation0.0211380868929689
GO:0001775cell activation0.0233065056081194
GO:0045045secretory pathway0.0254773357295268
GO:0032940secretion by cell0.0300697653881253
GO:0046903secretion0.0371399017736141



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>disease_data<br>

Cell Type
Ontology termp-valuen
neuronal stem cell1.03e-078
Uber Anatomy
Ontology termp-valuen
nervous system7.98e-8189
central nervous system1.53e-7581
neural tube5.48e-6856
neural rod5.48e-6856
future spinal cord5.48e-6856
neural keel5.48e-6856
regional part of nervous system1.83e-6553
regional part of brain1.83e-6553
brain5.27e-6268
future brain5.27e-6268
brain grey matter2.32e-5234
gray matter2.32e-5234
telencephalon4.52e-5234
cerebral hemisphere7.41e-5232
regional part of forebrain3.71e-5141
forebrain3.71e-5141
anterior neural tube3.71e-5141
future forebrain3.71e-5141
neurectoderm4.82e-5186
neural plate2.81e-4982
presumptive neural plate2.81e-4982
regional part of cerebral cortex2.20e-4822
regional part of telencephalon4.87e-4832
ectoderm-derived structure1.70e-44171
ectoderm1.70e-44171
presumptive ectoderm1.70e-44171
neocortex1.97e-4320
adult organism3.33e-42114
cerebral cortex5.33e-4225
pallium5.33e-4225
ecto-epithelium2.64e-40104
pre-chordal neural plate4.91e-3861
organ system subdivision3.13e-36223
structure with developmental contribution from neural crest1.13e-28132
posterior neural tube3.30e-1715
chordal neural plate3.30e-1715
anatomical cluster6.40e-17373
segmental subdivision of hindbrain6.37e-1512
hindbrain6.37e-1512
presumptive hindbrain6.37e-1512
gyrus4.14e-146
brainstem6.00e-146
tube6.40e-14192
segmental subdivision of nervous system1.27e-1313
limbic system2.39e-135
temporal lobe6.28e-136
occipital lobe7.35e-135
parietal lobe1.59e-125
basal ganglion4.63e-129
nuclear complex of neuraxis4.63e-129
aggregate regional part of brain4.63e-129
collection of basal ganglia4.63e-129
cerebral subcortex4.63e-129
neural nucleus8.93e-129
nucleus of brain8.93e-129
organ part1.76e-11218
sympathetic nervous system2.18e-115
autonomic nervous system2.18e-115
anatomical conduit4.41e-10240
germ layer1.19e-09560
germ layer / neural crest1.19e-09560
embryonic tissue1.19e-09560
presumptive structure1.19e-09560
germ layer / neural crest derived structure1.19e-09560
epiblast (generic)1.19e-09560
embryonic structure1.90e-09564
regional part of metencephalon2.12e-099
metencephalon2.12e-099
future metencephalon2.12e-099
embryo3.13e-09592
developing anatomical structure3.65e-09581
frontal cortex5.81e-083
pons6.69e-083
telencephalic nucleus7.36e-087
medulla oblongata1.02e-073
myelencephalon1.02e-073
future myelencephalon1.02e-073
epithelium1.54e-07306
cell layer2.37e-07309
multi-tissue structure3.21e-07342
Disease
Ontology termp-valuen
neuroectodermal tumor2.84e-1010
neuroendocrine tumor2.00e-096


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)
MA0003.11.04569
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.02528
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.11.74614
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.782425
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.11.00065
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.143081
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0575907
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.839774
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.81299
MA0163.10.168633
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.22.12087
MA0102.21.66336
MA0258.10.914277
MA0259.10.395396
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#23512220.04631236442520.003824075654154750.0188735238053149



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1804&oldid=2570315"