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Coexpression cluster:C1958: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.26722,0.0561813,0.500341,0.654974,2.01096,0.653236,1.73914,0.324142,0.321368,1.16078,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.501863,0.500405,0.121147,0.645033,1.14094,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,1.68319,0.758594,0.417272,0.757784,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,1.33238,0.451846,1.74542,1.32072,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.554326,1.23387,0.269111,2.02182,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,1.37242,0.963115,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.780629,1.06255,0.849074,0.211081,2.68381,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,1.11542,4.38731,1.05402,1.23742,3.7711,1.37132,1.05995,1.00558,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,4.35365,1.48307,0.918767,0.72668,1.02407,2.83049,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.526389,0.398598,1.15522,0.840171,1.74559,1.56426,0.827475,0.439798,0.54968,5.64739,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.233587
|tfbs_overrepresentation_for_novel_motifs=1.26722,0.0561813,0.500341,0.654974,2.01096,0.653236,1.73914,0.324142,0.321368,1.16078,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.501863,0.500405,0.121147,0.645033,1.14094,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,1.68319,0.758594,0.417272,0.757784,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,1.33238,0.451846,1.74542,1.32072,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.554326,1.23387,0.269111,2.02182,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,1.37242,0.963115,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.780629,1.06255,0.849074,0.211081,2.68381,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,1.11542,4.38731,1.05402,1.23742,3.7711,1.37132,1.05995,1.00558,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,4.35365,1.48307,0.918767,0.72668,1.02407,2.83049,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.526389,0.398598,1.15522,0.840171,1.74559,1.56426,0.827475,0.439798,0.54968,5.64739,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.233587
|tfbs_overrepresentation_jaspar=MA0003.1;0.280184,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;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;0.731787,MA0052.1;1.03442,MA0055.1;2.69304,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;1.28241,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.362215,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;1.36977,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;0.175503,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;4.96316,MA0143.1;1.87149,MA0144.1;0.938075,MA0145.1;0.143698,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;1.63245,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.801354,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.449243,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;2.57641,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;1.05321,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;3.94612,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:18, 22 January 2013


Full id: C1958_mesodermal_Lens_Smooth_Ciliary_Fibroblast_teratocarcinoma_leiomyoma



Phase1 CAGE Peaks

Hg19::chr5:31193785..31193810,+p2@CDH6
Hg19::chr5:31193820..31193841,+p3@CDH6
Hg19::chr5:31193847..31193887,+p1@CDH6
Hg19::chr5:31193890..31193901,+p4@CDH6
Hg19::chr5:31194106..31194136,+p@chr5:31194106..31194136
+


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
anatomical cluster9.71e-29373
multi-tissue structure7.92e-25342
tube5.58e-22192
structure with developmental contribution from neural crest2.32e-21132
anatomical conduit1.18e-19240
neural plate6.94e-1882
presumptive neural plate6.94e-1882
central nervous system4.50e-1781
nervous system9.23e-1789
brain1.07e-1668
future brain1.07e-1668
neurectoderm2.30e-1686
cell layer5.32e-16309
neural tube6.51e-1656
neural rod6.51e-1656
future spinal cord6.51e-1656
neural keel6.51e-1656
epithelium2.09e-15306
artery3.86e-1542
arterial blood vessel3.86e-1542
arterial system3.86e-1542
regional part of nervous system5.99e-1553
regional part of brain5.99e-1553
systemic artery2.08e-1433
systemic arterial system2.08e-1433
pre-chordal neural plate1.71e-1361
regional part of forebrain5.26e-1341
forebrain5.26e-1341
anterior neural tube5.26e-1341
future forebrain5.26e-1341
splanchnic layer of lateral plate mesoderm1.24e-1183
muscle tissue2.11e-1164
musculature2.11e-1164
musculature of body2.11e-1164
brain grey matter2.79e-1134
gray matter2.79e-1134
epithelial tube3.18e-11117
multi-cellular organism3.30e-11656
telencephalon4.46e-1134
adult organism5.40e-11114
skeletal muscle tissue5.52e-1162
striated muscle tissue5.52e-1162
myotome5.52e-1162
organ system subdivision6.37e-11223
cerebral hemisphere6.72e-1132
ectoderm-derived structure1.13e-10171
ectoderm1.13e-10171
presumptive ectoderm1.13e-10171
regional part of telencephalon1.26e-1032
embryo2.93e-10592
ecto-epithelium2.97e-10104
mesenchyme2.25e-09160
entire embryonic mesenchyme2.25e-09160
vasculature2.26e-0978
vascular system2.26e-0978
epithelial tube open at both ends3.93e-0959
blood vessel3.93e-0959
blood vasculature3.93e-0959
vascular cord3.93e-0959
anatomical system5.90e-09624
anatomical group8.08e-09625
developing anatomical structure8.95e-09581
dense mesenchyme tissue1.08e-0873
cerebral cortex1.16e-0825
pallium1.16e-0825
cardiovascular system1.21e-08109
heart1.72e-0824
primitive heart tube1.72e-0824
primary heart field1.72e-0824
anterior lateral plate mesoderm1.72e-0824
heart tube1.72e-0824
heart primordium1.72e-0824
cardiac mesoderm1.72e-0824
cardiogenic plate1.72e-0824
heart rudiment1.72e-0824
organism subdivision1.95e-08264
circulatory system2.83e-08112
paraxial mesoderm2.96e-0872
presumptive paraxial mesoderm2.96e-0872
compound organ3.41e-0868
somite4.78e-0871
presomitic mesoderm4.78e-0871
presumptive segmental plate4.78e-0871
dermomyotome4.78e-0871
trunk paraxial mesoderm4.78e-0871
epithelial vesicle6.68e-0878
blood vessel smooth muscle8.12e-0810
arterial system smooth muscle8.12e-0810


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
MA0004.10.626788
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
MA0028.10.470679
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
MA0051.10.731787
MA0052.11.03442
MA0055.12.69304
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
MA0068.11.28241
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.362215
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
MA0090.11.36977
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
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
MA0114.10.372523
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
MA0142.14.96316
MA0143.11.87149
MA0144.10.938075
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.11.63245
MA0062.20.284987
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.12.57641
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.14.22787
MA0163.11.05321
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.94612
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
TAF1#687253.343046285745290.002394600090870310.0135542593295975
TBP#690853.706770687096390.001428755106721120.00920188422489191



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:C1958&oldid=2570469"