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Coexpression cluster:C1910: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.205703,0.500341,0.654974,1.15291,0.653236,1.73914,0.324142,0.321368,0.106358,1.50573,0.778743,0.274093,1.71413,0.453496,1.20439,0.963929,0.395009,0.287891,0.167776,0.500405,0.121147,0.645033,0.44943,1.35492,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.758594,0.417272,0.0526856,0.413782,0.654459,0.388123,0.815792,0.415749,0.580638,0.132849,2.00042,0.0606304,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,1.76707,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,3.71681,3.3636,0.566575,0.330474,0.189341,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,1.20877,0.844289,1.79645,1.41984,1.15413,1.01895,1.71087,0.455791,0.381528,0.28626,1.06255,1.97764,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,1.27602,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,2.07682,0.370186,2.74317,4.66789,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,1.55197,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,2.0258,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,3.43109,0.731946,0.0214572
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.205703,0.500341,0.654974,1.15291,0.653236,1.73914,0.324142,0.321368,0.106358,1.50573,0.778743,0.274093,1.71413,0.453496,1.20439,0.963929,0.395009,0.287891,0.167776,0.500405,0.121147,0.645033,0.44943,1.35492,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.758594,0.417272,0.0526856,0.413782,0.654459,0.388123,0.815792,0.415749,0.580638,0.132849,2.00042,0.0606304,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,1.76707,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,3.71681,3.3636,0.566575,0.330474,0.189341,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,1.20877,0.844289,1.79645,1.41984,1.15413,1.01895,1.71087,0.455791,0.381528,0.28626,1.06255,1.97764,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,1.27602,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,2.07682,0.370186,2.74317,4.66789,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,1.55197,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,2.0258,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,3.43109,0.731946,0.0214572
|tfbs_overrepresentation_jaspar=MA0003.1;0.00991994,MA0004.1;3.75179,MA0006.1;1.14863,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.369468,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;2.9228,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;2.90864,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;1.05691,MA0058.1;3.29768,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;2.48388,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.00220137,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;0.132006,MA0089.1;0,MA0090.1;0.556637,MA0091.1;1.52322,MA0092.1;0.588959,MA0093.1;4.06535,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;1.96988,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;4.48146,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.0118463,MA0138.2;0.837782,MA0002.2;0.83106,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;1.35805,MA0065.2;1.41695,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;0.000396307,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:16, 22 January 2013


Full id: C1910_anaplastic_pineal_temporal_occipital_duodenum_brain_parietal



Phase1 CAGE Peaks

Hg19::chr2:50574926..50574990,-p2@NRXN1
Hg19::chr2:50575000..50575009,-p26@NRXN1
Hg19::chr2:50575014..50575025,-p25@NRXN1
Hg19::chr2:50575032..50575041,-p30@NRXN1
Hg19::chr2:50575145..50575190,-p23@NRXN1


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
regional part of cerebral cortex5.76e-9622
neocortex2.19e-8720
cerebral cortex2.70e-8425
pallium2.70e-8425
regional part of forebrain1.50e-8241
forebrain1.50e-8241
anterior neural tube1.50e-8241
future forebrain1.50e-8241
telencephalon2.38e-7934
cerebral hemisphere5.76e-7832
neural tube7.55e-7356
neural rod7.55e-7356
future spinal cord7.55e-7356
neural keel7.55e-7356
regional part of nervous system3.25e-7253
regional part of brain3.25e-7253
regional part of telencephalon2.26e-7132
brain grey matter5.51e-6734
gray matter5.51e-6734
central nervous system1.41e-6681
brain1.38e-6268
future brain1.38e-6268
nervous system2.42e-5989
pre-chordal neural plate7.16e-5461
neural plate6.79e-4882
presumptive neural plate6.79e-4882
neurectoderm2.23e-4586
ecto-epithelium2.00e-36104
adult organism1.04e-30114
structure with developmental contribution from neural crest2.31e-29132
gyrus2.30e-286
ectoderm-derived structure7.37e-28171
ectoderm7.37e-28171
presumptive ectoderm7.37e-28171
temporal lobe1.82e-246
occipital lobe3.23e-245
organ system subdivision4.28e-24223
parietal lobe9.21e-245
limbic system4.55e-235
tube4.49e-18192
frontal cortex2.43e-153
anatomical conduit4.42e-13240
anatomical cluster2.34e-11373
pineal body8.78e-112
regional part of epithalamus8.78e-112
secretory circumventricular organ8.78e-112
circumventricular organ8.78e-112
epithalamus8.78e-112
middle frontal gyrus1.01e-102
amygdala1.12e-102
middle temporal gyrus1.49e-102
Ammon's horn4.42e-102
lobe parts of cerebral cortex4.42e-102
hippocampal formation4.42e-102
limbic lobe4.42e-102
organ part1.15e-09218
epithelium8.82e-09306
cell layer1.25e-08309
multi-tissue structure7.14e-08342


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)
MA0003.10.00991994
MA0004.13.75179
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.369468
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
MA0038.12.9228
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.12.90864
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.11.05691
MA0058.13.29768
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.12.48388
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.11.52322
MA0092.10.588959
MA0093.14.06535
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.11.96988
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
MA0143.14.48146
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.21.35805
MA0065.21.41695
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
MA0079.20.000396307
MA0102.21.66336
MA0258.10.345771
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
EP300#203356.77394172622327.00901578206049e-050.00110928110208004



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:C1910&oldid=2570421"