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Coexpression cluster:C1711: Difference between revisions

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0.253154,0.319519,0.309489,0.430805,0.00119205,0.480785,6.26696e-05,0.336314,0.0676318,0.184651,0.303359,0.0494743,0.018596,0.107309,0.00150414,3.32563e-08,0.345068,0.151046,0.0296322,0.347171,0.00730933,0.15463,1.85896e-05,0.0267252,0.000315243,0.250466,0.409882,0.115686,9.10492e-08,0.162633,0.342661,0.27567,0.248127,0.000812213,0.384731,1.75815e-07,0.526476
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,2.66447,0.454983,0.653236,0.733342,0.324142,0.321368,0.106358,0.621241,1.83296,0.274093,0.721271,1.14971,0.478935,0.963929,1.80748,0.287891,0.969147,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.758594,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.132849,0.451846,0.0606304,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.709554,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.873042,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,2.68381,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,3.85379,0.767198,1.48307,2.12036,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,3.82358,1.38998,2.25246,1.84906,1.35224,0.728494,2.4059,2.06113,0.680988,0.87256,2.09294,0.577088,0.363423,1.00998,0.126633,1.15522,2.31232,0.736459,1.56426,0.827475,0.439798,1.35505,0.518696,1.35101,2.56291,0.98692,1.29666,0.906429,0.754576,0.35004,0.731946,0.0214572
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,2.66447,0.454983,0.653236,0.733342,0.324142,0.321368,0.106358,0.621241,1.83296,0.274093,0.721271,1.14971,0.478935,0.963929,1.80748,0.287891,0.969147,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.758594,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.132849,0.451846,0.0606304,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.709554,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.873042,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,2.68381,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,3.85379,0.767198,1.48307,2.12036,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,3.82358,1.38998,2.25246,1.84906,1.35224,0.728494,2.4059,2.06113,0.680988,0.87256,2.09294,0.577088,0.363423,1.00998,0.126633,1.15522,2.31232,0.736459,1.56426,0.827475,0.439798,1.35505,0.518696,1.35101,2.56291,0.98692,1.29666,0.906429,0.754576,0.35004,0.731946,0.0214572
|tfbs_overrepresentation_jaspar=MA0003.1;0.00991994,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;1.47524,MA0009.1;2.51467,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;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;1.48918,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;1.05691,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;4.00811,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.111822,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;1.95181,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;0.629594,MA0092.1;1.43794,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;2.64674,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;0.759606,MA0140.1;2.78334,MA0141.1;0.520334,MA0142.1;2.10746,MA0143.1;0.797437,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;1.65235,MA0039.2;0.0118463,MA0138.2;0.837782,MA0002.2;3.17169,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,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;1.60707,MA0161.1;0,MA0162.1;0.0592265,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;1.83842,MA0099.2;1.66926,MA0079.2;3.83292e-05,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:07, 22 January 2013


Full id: C1711_astrocytoma_Astrocyte_Neural_Wilms_acute_Ciliary_Lens



Phase1 CAGE Peaks

Hg19::chr13:99349888..99349893,+p@chr13:99349888..99349893
+
Hg19::chr6:151042225..151042241,+p5@PLEKHG1
Hg19::chr6:151042248..151042293,+p2@PLEKHG1
Hg19::chr6:151042296..151042316,+p8@PLEKHG1
Hg19::chr6:151042333..151042356,+p9@PLEKHG1


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
central nervous system2.41e-4581
neural tube1.58e-4456
neural rod1.58e-4456
future spinal cord1.58e-4456
neural keel1.58e-4456
regional part of nervous system1.77e-4253
regional part of brain1.77e-4253
nervous system1.69e-3989
neural plate1.99e-3882
presumptive neural plate1.99e-3882
brain2.87e-3668
future brain2.87e-3668
neurectoderm4.84e-3686
regional part of forebrain3.96e-3341
forebrain3.96e-3341
anterior neural tube3.96e-3341
future forebrain3.96e-3341
pre-chordal neural plate3.61e-3161
brain grey matter4.87e-3034
gray matter4.87e-3034
telencephalon6.98e-3034
ecto-epithelium1.36e-27104
cerebral hemisphere8.48e-2732
regional part of telencephalon9.31e-2732
structure with developmental contribution from neural crest9.42e-24132
ectoderm-derived structure1.36e-22171
ectoderm1.36e-22171
presumptive ectoderm1.36e-22171
adult organism2.06e-21114
organ system subdivision8.69e-20223
cerebral cortex1.10e-1825
pallium1.10e-1825
regional part of cerebral cortex1.42e-1322
neural nucleus1.68e-139
nucleus of brain1.68e-139
neocortex7.73e-1320
brainstem1.18e-126
posterior neural tube3.15e-1215
chordal neural plate3.15e-1215
anatomical cluster4.36e-11373
segmental subdivision of hindbrain2.37e-1012
hindbrain2.37e-1012
presumptive hindbrain2.37e-1012
basal ganglion5.03e-109
nuclear complex of neuraxis5.03e-109
aggregate regional part of brain5.03e-109
collection of basal ganglia5.03e-109
cerebral subcortex5.03e-109
telencephalic nucleus5.61e-107
segmental subdivision of nervous system1.97e-0913
tube3.00e-09192
organ part7.58e-09218
corpus striatum1.04e-084
striatum1.04e-084
ventral part of telencephalon1.04e-084
future corpus striatum1.04e-084
ciliary epithelium5.18e-083
ciliary body5.18e-083
gyrus7.28e-086
anatomical conduit2.46e-07240
medulla oblongata2.56e-073
myelencephalon2.56e-073
future myelencephalon2.56e-073
caudate-putamen3.52e-073
dorsal striatum3.52e-073
multi-tissue structure3.86e-07342
pons5.45e-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)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.11.47524
MA0009.12.51467
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
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.11.48918
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.11.05691
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
MA0070.14.00811
MA0071.10.695094
MA0072.11.0812
MA0073.10.111822
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.11.95181
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.11.43794
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
MA0122.12.64674
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.12.78334
MA0141.10.520334
MA0142.12.10746
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.21.65235
MA0039.20.0118463
MA0138.20.837782
MA0002.23.17169
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
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
MA0160.11.60707
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.21.83842
MA0099.21.66926
MA0079.23.83292e-05
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
BATF#10538419.48624143384291.37275300118359e-050.000332026286916658
BCL11A#53335422.69556408288567.49488101632307e-060.000214278094296131
BCLAF1#9774417.32211808809752.18923511079637e-050.000481451938800721
CTCF#1066444.288205098460020.005152015588243280.0239291717522254
E2F1#186943.925911371903460.007214984547106360.0298733654898209
EBF1#187947.12517347725520.0007230531046774210.00576978477990565
EP300#203345.419153380978560.00209386927943890.0121146536854091
ESR1#2099424.61488263692365.42856809638808e-060.000165582425063865
IRF4#3662417.53161014939532.08739444052064e-050.000460801919200031
JUN#3725410.01026335386910.0001908531347801070.00230486939677377
JUND#372745.595731153496820.001849593301755460.0109320698835336
MAFF#23764445.05228519195614.89188569148035e-072.30033160617972e-05
MAFK#7975421.68058651026398.98818656648185e-060.000242062201345229
MEF2A#4205414.99458472771523.876195075647e-050.000727973273701666
MEF2C#4208433.04908359409921.68127439756556e-066.36197886983151e-05
NFKB1#479044.390450739355070.004707732692524960.0221993360427404
NR3C1#2908411.97841866493849.4122920812787e-050.00136529218427315
PAX5#507945.335652424942260.002223389586187790.0127769662700488
POU2F2#545247.284899246194020.0006631223288743860.00542374758440849
SP1#666744.558705102512720.00407573565781680.0194803787637512
SPI1#668846.563458806818180.0009957429636454020.00714149151079262
TRIM28#10155414.872420036214.00368496902357e-050.000734611480112179



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:C1711&oldid=2570222"