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Coexpression cluster:C1567: Difference between revisions

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5,0.108081,0.123829,0.205215,0.175247,6.69639e-05,0.109077,0.144842,0.0604892,2.24936e-07,0.316879,3.36211e-05,0.0196242,0.0354176,0.224871,0.398887,0.000160964,0.00651415,0.00964357,0.445995,0.385709,0.278202,0.426488,0.0152991,1.93612e-07,0.0351523,3.25334e-06,0.309489,0.0196661,7.82111e-06,0.480785,0.185476,0.00847033,0.0676318,0.184651,2.27555e-06,0.00565016,0.106207,0.425912,0.0128718,0.0035934,0.345068,0.000647553,0.0047298,0.00941969,0.00730933,0.15463,0.000500369,0.0267252,0.269432,0.250466,0.0986342,0.115686,0.0164276,3.5895e-05,5.29441e-06,0.27567,0.248127,0.33299,0.0133264,0.319112,0.00104951
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,1.02276,0.287891,0.969147,0.500405,0.121147,1.55551,1.14094,0.549618,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,1.68319,0.27659,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.414516,0.451846,0.476793,0.533483,0.734485,0.609718,1.85968,0.458489,0.817229,1.76707,1.06581,1.08035,1.2359,0.724351,1.17039,0.689906,0.659455,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,0.189341,1.23387,0.741483,0.255232,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.873042,1.18161,0.0719601,0.166306,0.647361,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,1.01093,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,1.11542,0.512457,1.05402,1.23742,0.631235,1.37132,1.05995,0.597842,0.596731,0.897476,0.370186,1.22546,0.841768,2.64959,3.02031,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,2.41357,0.363423,0.526389,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0938701
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,1.02276,0.287891,0.969147,0.500405,0.121147,1.55551,1.14094,0.549618,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,1.68319,0.27659,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.414516,0.451846,0.476793,0.533483,0.734485,0.609718,1.85968,0.458489,0.817229,1.76707,1.06581,1.08035,1.2359,0.724351,1.17039,0.689906,0.659455,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,0.189341,1.23387,0.741483,0.255232,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.873042,1.18161,0.0719601,0.166306,0.647361,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,1.01093,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,1.11542,0.512457,1.05402,1.23742,0.631235,1.37132,1.05995,0.597842,0.596731,0.897476,0.370186,1.22546,0.841768,2.64959,3.02031,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,2.41357,0.363423,0.526389,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0938701
|tfbs_overrepresentation_jaspar=MA0003.1;0.136928,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.0418333,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;1.18667,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;1.73592,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,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;0.00220137,MA0074.1;0.730989,MA0076.1;1.33654,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;1.2972,MA0083.1;5.82067,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,MA0089.1;0,MA0090.1;1.36977,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;1.77562,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.175503,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;1.87149,MA0144.1;0.356507,MA0145.1;0.442008,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;1.57313,MA0149.1;0.681935,MA0062.2;0.777733,MA0035.2;0.691506,MA0039.2;0.0575907,MA0138.2;0.837782,MA0002.2;0.83106,MA0137.2;1.20193,MA0104.2;0.320919,MA0047.2;1.80892,MA0112.2;0.425004,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;0.130813,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.0592265,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;3.83292e-05,MA0102.2;1.66336,MA0258.1;0.914277,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:01, 22 January 2013


Full id: C1567_Neural_pituitary_caudate_spinal_Neurons_parietal_putamen



Phase1 CAGE Peaks

Hg19::chr10:123951927..123951952,+p17@TACC2
Hg19::chr10:123951957..123951980,+p18@TACC2
Hg19::chr17:61194527..61194561,+p@chr17:61194527..61194561
+
Hg19::chr17:61194578..61194599,+p@chr17:61194578..61194599
+
Hg19::chr17:61194620..61194635,+p@chr17:61194620..61194635
+


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
neuronal stem cell6.06e-108
astrocyte of the cerebral cortex1.06e-083
Uber Anatomy
Ontology termp-valuen
neural tube5.56e-12556
neural rod5.56e-12556
future spinal cord5.56e-12556
neural keel5.56e-12556
central nervous system5.02e-11881
regional part of nervous system3.78e-11653
regional part of brain3.78e-11653
regional part of forebrain9.97e-11141
forebrain9.97e-11141
anterior neural tube9.97e-11141
future forebrain9.97e-11141
nervous system3.99e-10589
brain4.16e-9968
future brain4.16e-9968
telencephalon1.16e-9034
brain grey matter1.64e-9034
gray matter1.64e-9034
cerebral hemisphere2.12e-8532
regional part of telencephalon3.27e-8532
neural plate4.05e-8582
presumptive neural plate4.05e-8582
neurectoderm1.31e-8086
pre-chordal neural plate6.05e-7561
cerebral cortex1.54e-6525
pallium1.54e-6525
ecto-epithelium1.46e-64104
regional part of cerebral cortex2.55e-5822
adult organism5.84e-58114
neocortex1.69e-5220
ectoderm-derived structure6.86e-51171
ectoderm6.86e-51171
presumptive ectoderm6.86e-51171
structure with developmental contribution from neural crest1.79e-50132
organ system subdivision6.55e-39223
tube3.00e-29192
neural nucleus1.07e-259
nucleus of brain1.07e-259
basal ganglion1.32e-259
nuclear complex of neuraxis1.32e-259
aggregate regional part of brain1.32e-259
collection of basal ganglia1.32e-259
cerebral subcortex1.32e-259
anatomical conduit4.55e-23240
anatomical cluster1.96e-22373
telencephalic nucleus1.15e-207
diencephalon1.22e-207
future diencephalon1.22e-207
gyrus1.65e-176
posterior neural tube2.44e-1715
chordal neural plate2.44e-1715
brainstem1.24e-166
parietal lobe7.16e-165
occipital lobe1.82e-155
limbic system2.68e-155
epithelium1.78e-14306
cell layer3.27e-14309
temporal lobe5.51e-146
multi-tissue structure1.10e-13342
corpus striatum6.53e-134
striatum6.53e-134
ventral part of telencephalon6.53e-134
future corpus striatum6.53e-134
gland of diencephalon2.50e-124
neuroendocrine gland2.50e-124
organ part3.48e-12218
regional part of diencephalon9.51e-124
segmental subdivision of hindbrain1.44e-1012
hindbrain1.44e-1012
presumptive hindbrain1.44e-1012
caudate-putamen5.53e-103
dorsal striatum5.53e-103
spinal cord5.87e-103
dorsal region element5.87e-103
dorsum5.87e-103
frontal cortex9.76e-103
segmental subdivision of nervous system1.12e-0913
embryo2.61e-09592
medulla oblongata2.97e-093
myelencephalon2.97e-093
future myelencephalon2.97e-093
developing anatomical structure3.98e-09581
organ4.43e-09503
pons4.44e-093
germ layer9.31e-09560
germ layer / neural crest9.31e-09560
embryonic tissue9.31e-09560
presumptive structure9.31e-09560
germ layer / neural crest derived structure9.31e-09560
epiblast (generic)9.31e-09560
embryonic structure1.37e-08564
anatomical system4.63e-08624
anatomical group5.04e-08625
pituitary gland8.88e-082
Ammon's horn2.01e-072
lobe parts of cerebral cortex2.01e-072
hippocampal formation2.01e-072
limbic lobe2.01e-072
caudate nucleus3.50e-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)
MA0003.10.136928
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.11.18667
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
MA0051.11.73592
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.11.33654
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.15.82067
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.11.36977
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.11.77562
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
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
MA0143.11.87149
MA0144.10.356507
MA0145.10.442008
MA0146.10.0359558
MA0147.10.386018
MA0148.11.57313
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.20.0575907
MA0138.20.837782
MA0002.20.83106
MA0137.21.20193
MA0104.20.320919
MA0047.21.80892
MA0112.20.425004
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.83292e-05
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
RAD21#588536.21302033727380.007751055068811640.0318818652408971
SRF#672238.278306957300690.003404846073776150.0173538977648288



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:C1567&oldid=2570078"