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Coexpression cluster:C1668: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.787587,0.500341,0.654974,2.01096,0.653236,0.733342,0.324142,0.321368,0.345702,1.50573,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,1.42981,0.167776,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,1.88355,1.1597,2.79716,0.654459,0.388123,0.301779,0.415749,0.580638,0.821929,0.451846,0.218848,1.32072,1.74151,2.51915,1.28013,0.458489,0.817229,1.76707,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,1.64682,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,1.66643,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.914416,12.8454,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,3.3304,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,3.41206,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,2.12036,0.72668,1.02407,1.2687,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,0.177807,1.87689,1.15522,1.51895,0.736459,1.56426,0.827475,0.439798,0.54968,1.2893,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.923751,0.731946,4.10331
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.787587,0.500341,0.654974,2.01096,0.653236,0.733342,0.324142,0.321368,0.345702,1.50573,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,1.42981,0.167776,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,1.88355,1.1597,2.79716,0.654459,0.388123,0.301779,0.415749,0.580638,0.821929,0.451846,0.218848,1.32072,1.74151,2.51915,1.28013,0.458489,0.817229,1.76707,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,1.64682,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,1.66643,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.914416,12.8454,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,3.3304,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,3.41206,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,2.12036,0.72668,1.02407,1.2687,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,0.177807,1.87689,1.15522,1.51895,0.736459,1.56426,0.827475,0.439798,0.54968,1.2893,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.923751,0.731946,4.10331
|tfbs_overrepresentation_jaspar=MA0003.1;0.280184,MA0004.1;3.75179,MA0006.1;4.0459,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;1.9468,MA0017.1;0.496101,MA0019.1;1.84387,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;5.81246,MA0058.1;2.23895,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;1.28241,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;6.69924,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;1.3271,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;4.06535,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,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;0.973423,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;1.39016,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,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;1.12758,MA0138.2;0.837782,MA0002.2;0.83106,MA0137.2;0.47779,MA0104.2;2.35335,MA0047.2;0.767096,MA0112.2;1.35805,MA0065.2;0.880827,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;4.22787,MA0163.1;1.49262,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;13.6951,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;2.71109,MA0442.1;0
}}
}}

Revision as of 20:05, 22 January 2013


Full id: C1668_spinal_thalamus_substantia_pineal_lymphangiectasia_globus_renal



Phase1 CAGE Peaks

Hg19::chr12:26276068..26276086,-p1@AK311258
Hg19::chr12:26277798..26277809,-p5@BHLHE41
Hg19::chr12:26277817..26277863,-p2@BHLHE41
Hg19::chr12:26277929..26277955,-p3@BHLHE41
Hg19::chr12:26277956..26277980,-p1@BHLHE41


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
adult organism4.16e-38114
neural tube3.85e-2656
neural rod3.85e-2656
future spinal cord3.85e-2656
neural keel3.85e-2656
neural plate1.80e-2582
presumptive neural plate1.80e-2582
neurectoderm2.56e-2486
regional part of nervous system3.18e-2453
regional part of brain3.18e-2453
central nervous system1.40e-2181
brain1.61e-2168
future brain1.61e-2168
nervous system3.61e-2089
structure with developmental contribution from neural crest2.05e-19132
ecto-epithelium7.75e-19104
regional part of forebrain3.08e-1841
forebrain3.08e-1841
anterior neural tube3.08e-1841
future forebrain3.08e-1841
pre-chordal neural plate4.07e-1861
brain grey matter2.13e-1434
gray matter2.13e-1434
telencephalon2.22e-1434
regional part of telencephalon3.39e-1332
cerebral hemisphere4.35e-1332
ectoderm-derived structure4.80e-13171
ectoderm4.80e-13171
presumptive ectoderm4.80e-13171
organ9.21e-12503
tube5.82e-11192
regional part of cerebral cortex3.83e-1022
multi-cellular organism4.38e-10656
anatomical conduit5.57e-10240
anatomical cluster9.05e-10373
multi-tissue structure1.02e-09342
cerebral cortex2.59e-0925
pallium2.59e-0925
posterior neural tube3.84e-0915
chordal neural plate3.84e-0915
neocortex5.64e-0920
anatomical group1.39e-08625
epithelium1.56e-08306
cell layer1.67e-08309
anatomical system2.98e-08624
segmental subdivision of nervous system5.65e-0813
organ system subdivision6.22e-08223
embryo9.65e-08592
segmental subdivision of hindbrain2.71e-0712
hindbrain2.71e-0712
presumptive hindbrain2.71e-0712
neural nucleus6.49e-079
nucleus of brain6.49e-079
basal ganglion9.28e-079
nuclear complex of neuraxis9.28e-079
aggregate regional part of brain9.28e-079
collection of basal ganglia9.28e-079
cerebral subcortex9.28e-079


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)
MA0003.10.280184
MA0004.13.75179
MA0006.14.0459
MA0007.10.606704
MA0009.11.11255
MA0014.11.9468
MA0017.10.496101
MA0019.11.84387
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
MA0057.15.81246
MA0058.12.23895
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.11.28241
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.16.69924
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.14.06535
MA0095.10
MA0098.10
MA0100.10.750974
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
MA0114.10.973423
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
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.143081
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.21.12758
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.22.35335
MA0047.20.767096
MA0112.21.35805
MA0065.20.880827
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
MA0162.14.22787
MA0163.11.49262
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.213.6951
MA0102.21.66336
MA0258.10.345771
MA0259.12.71109
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
JUND#372745.595731153496820.001849593301755460.0109308326642168
MAX#414956.452555509007128.93743970843928e-050.00130602667652118
SUZ12#23512550.11578091106293.15480790456198e-092.61288646109872e-07
TRIM28#10155414.872420036214.00368496902357e-050.000734482442437822
USF1#739156.361499277207969.59569864925045e-050.0013675834760222



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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