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Coexpression cluster:C1652: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,1.15291,0.653236,0.733342,0.866061,0.321368,3.71916,0.621241,0.778743,1.37937,0.721271,0.453496,1.20439,0.963929,1.02276,0.287891,0.501863,0.500405,0.384437,0.645033,1.14094,0.549618,0.802434,0.700122,0.642741,1.16016,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,1.06799,0.580638,0.132849,0.451846,0.218848,1.32072,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,1.67994,1.08035,1.2359,0.724351,1.17039,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,2.08177,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,1.05625,1.23387,0.741483,0.709554,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,1.57121,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,1.35434,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.597842,2.47721,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,1.55197,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,2.90914,0.233587
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,1.15291,0.653236,0.733342,0.866061,0.321368,3.71916,0.621241,0.778743,1.37937,0.721271,0.453496,1.20439,0.963929,1.02276,0.287891,0.501863,0.500405,0.384437,0.645033,1.14094,0.549618,0.802434,0.700122,0.642741,1.16016,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,1.06799,0.580638,0.132849,0.451846,0.218848,1.32072,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,1.67994,1.08035,1.2359,0.724351,1.17039,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,2.08177,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,1.05625,1.23387,0.741483,0.709554,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,1.57121,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,1.35434,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.597842,2.47721,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,1.55197,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,2.90914,0.233587
|tfbs_overrepresentation_jaspar=MA0003.1;0.737422,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.161847,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;0.569896,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;6.52915,MA0056.1;0,MA0057.1;2.36624,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;2.35759,MA0061.1;0.791444,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;0.0469445,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;1.92154,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;0.520776,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;3.1147,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;2.64838,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;1.65391,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;3.47082,MA0145.1;0.442008,MA0146.1;0.333008,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.311551,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;2.08722,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;1.96224,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;1.66846,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.813062,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;1.23503,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;3.15891,MA0102.2;1.66336,MA0258.1;1.63655,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:05, 22 January 2013


Full id: C1652_normal_brain_cerebellum_occipital_postcentral_temporal_amygdala



Phase1 CAGE Peaks

Hg19::chr12:101188502..101188513,+p13@ANO4
Hg19::chr12:101188514..101188532,+p8@ANO4
Hg19::chr12:101188547..101188565,+p5@ANO4
Hg19::chr12:101188608..101188621,+p7@ANO4
Hg19::chr5:137774709..137774806,+p1@REEP2


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>

Uber Anatomy
Ontology termp-valuen
neural tube4.51e-9756
neural rod4.51e-9756
future spinal cord4.51e-9756
neural keel4.51e-9756
regional part of nervous system2.45e-9153
regional part of brain2.45e-9153
neural plate1.70e-8182
presumptive neural plate1.70e-8182
central nervous system4.91e-7981
neurectoderm5.89e-7786
brain9.03e-7768
future brain9.03e-7768
regional part of forebrain2.18e-7541
forebrain2.18e-7541
anterior neural tube2.18e-7541
future forebrain2.18e-7541
nervous system1.09e-7489
telencephalon7.41e-7034
brain grey matter1.23e-6934
gray matter1.23e-6934
pre-chordal neural plate4.02e-6761
cerebral hemisphere1.20e-6532
regional part of telencephalon1.70e-6532
ecto-epithelium8.01e-61104
cerebral cortex2.97e-5125
pallium2.97e-5125
structure with developmental contribution from neural crest4.27e-48132
regional part of cerebral cortex8.90e-4622
adult organism2.07e-45114
ectoderm-derived structure3.54e-43171
ectoderm3.54e-43171
presumptive ectoderm3.54e-43171
neocortex1.73e-4120
organ system subdivision2.35e-32223
tube5.63e-23192
posterior neural tube1.05e-2115
chordal neural plate1.05e-2115
basal ganglion1.07e-199
nuclear complex of neuraxis1.07e-199
aggregate regional part of brain1.07e-199
collection of basal ganglia1.07e-199
cerebral subcortex1.07e-199
anatomical cluster1.33e-19373
anatomical conduit1.73e-19240
neural nucleus2.36e-199
nucleus of brain2.36e-199
epithelium3.40e-17306
cell layer7.39e-17309
organ part1.37e-16218
segmental subdivision of hindbrain1.52e-1612
hindbrain1.52e-1612
presumptive hindbrain1.52e-1612
telencephalic nucleus2.09e-157
segmental subdivision of nervous system4.29e-1513
gyrus4.50e-146
multi-tissue structure1.48e-13342
brainstem2.94e-136
organ5.72e-13503
parietal lobe1.60e-125
limbic system3.40e-125
occipital lobe3.48e-125
temporal lobe5.92e-126
regional part of metencephalon2.74e-119
metencephalon2.74e-119
future metencephalon2.74e-119
embryonic structure6.39e-10564
anatomical system1.18e-09624
anatomical group1.32e-09625
germ layer1.54e-09560
germ layer / neural crest1.54e-09560
embryonic tissue1.54e-09560
presumptive structure1.54e-09560
germ layer / neural crest derived structure1.54e-09560
epiblast (generic)1.54e-09560
atypical epithelium3.28e-094
corpus striatum3.90e-094
striatum3.90e-094
ventral part of telencephalon3.90e-094
future corpus striatum3.90e-094
developing anatomical structure5.03e-09581
embryo5.32e-09592
multi-cellular organism9.92e-09656
frontal cortex7.48e-083
pons8.57e-083
diencephalon8.88e-087
future diencephalon8.88e-087
ciliary epithelium9.60e-083
ciliary body9.60e-083
medulla oblongata3.92e-073
caudate-putamen3.92e-073
myelencephalon3.92e-073
dorsal striatum3.92e-073
future myelencephalon3.92e-073
spinal cord6.66e-073
dorsal region element6.66e-073


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)
MA0003.10.737422
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
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
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.16.52915
MA0056.10
MA0057.12.36624
MA0058.10.523638
MA0059.10.522232
MA0060.12.35759
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0469445
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.92154
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
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.13.1147
MA0114.10.372523
MA0115.11.35895
MA0116.12.64838
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
MA0140.11.65391
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.13.47082
MA0145.10.442008
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.311551
MA0138.20.837782
MA0002.20.30855
MA0137.22.08722
MA0104.20.320919
MA0047.20.767096
MA0112.21.96224
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.11.66846
MA0153.11.21379
MA0154.10.172764
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.23503
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.15891
MA0102.21.66336
MA0258.11.63655
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

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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