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Coexpression cluster:C1024: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.920816,0.898711,0.341646,0.481684,0.301904,0.480078,0.554663,0.19223,1.05889,0.637689,0.450635,0.597407,2.79721,0.543352,0.300614,0.322799,0.774423,0.250594,0.163559,0.264925,0.341703,0.405031,0.472508,0.29709,0.385586,0.619829,0.135503,0.470396,0.304828,0.122648,0.429397,0.810962,2.58859,0.154814,0.269459,9.00659,1.35136,0.481208,0.244807,6.55597,0.268162,0.413601,0.0547276,0.809926,2.19248,1.72504,0.555735,0.440085,0.0498256,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,1.03556,0.197328,0.63188,1.03748,1.43212,1.36791,0.127753,0.730167,0.797419,0.379656,0.50159,0.745864,0.575394,0.567311,0.986227,0.730725,0.55584,0.378318,1.58596,1.59442,1.22073,0.959334,0.827657,0.227232,0.817658,0.239285,0.162291,0.87,0.664183,3.718,0.246049,0.822041,0.864454,0.778061,0.701386,1.13403,0.762347,0.539961,2.66369,3.03278,0.92894,0.861701,0.336372,0.459808,1.17281,0.265019,1.62816,0.428232,0.710479,0.650514,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,1.1925,4.82541,1.60406,0.960402,1.03091,0.557588,1.36372,0.643609,1.433,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,0.664626
|tfbs_overrepresentation_for_novel_motifs=0.920816,0.898711,0.341646,0.481684,0.301904,0.480078,0.554663,0.19223,1.05889,0.637689,0.450635,0.597407,2.79721,0.543352,0.300614,0.322799,0.774423,0.250594,0.163559,0.264925,0.341703,0.405031,0.472508,0.29709,0.385586,0.619829,0.135503,0.470396,0.304828,0.122648,0.429397,0.810962,2.58859,0.154814,0.269459,9.00659,1.35136,0.481208,0.244807,6.55597,0.268162,0.413601,0.0547276,0.809926,2.19248,1.72504,0.555735,0.440085,0.0498256,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,1.03556,0.197328,0.63188,1.03748,1.43212,1.36791,0.127753,0.730167,0.797419,0.379656,0.50159,0.745864,0.575394,0.567311,0.986227,0.730725,0.55584,0.378318,1.58596,1.59442,1.22073,0.959334,0.827657,0.227232,0.817658,0.239285,0.162291,0.87,0.664183,3.718,0.246049,0.822041,0.864454,0.778061,0.701386,1.13403,0.762347,0.539961,2.66369,3.03278,0.92894,0.861701,0.336372,0.459808,1.17281,0.265019,1.62816,0.428232,0.710479,0.650514,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,1.1925,4.82541,1.60406,0.960402,1.03091,0.557588,1.36372,0.643609,1.433,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,0.664626
|tfbs_overrepresentation_jaspar=MA0003.1;1.34332,MA0004.1;0.455723,MA0006.1;0.812175,MA0007.1;1.1148,MA0009.1;0.918715,MA0014.1;2.6969,MA0017.1;0.896777,MA0019.1;0.602411,MA0024.1;1.90464,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;1.60389,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;3.22913,MA0056.1;0,MA0057.1;6.69229,MA0058.1;0.362328,MA0059.1;1.69011,MA0060.1;0.190336,MA0061.1;0.165998,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.415214,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;6.51901,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.770971,MA0089.1;0,MA0090.1;0.391903,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;0.0818021,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;1.84219,MA0113.1;1.49247,MA0114.1;0.655057,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.155155,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;0.830366,MA0146.1;3.51017,MA0147.1;1.26392,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.485915,MA0035.2;0.515566,MA0039.2;0.881644,MA0138.2;0.653421,MA0002.2;0.531206,MA0137.2;0.321796,MA0104.2;1.66814,MA0047.2;0.586412,MA0112.2;0.458158,MA0065.2;0.226158,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.0799828,MA0155.1;0.197713,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.682702,MA0160.1;0.495355,MA0161.1;0,MA0162.1;4.37832,MA0163.1;5.02939,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;27.7181,MA0102.2;1.46209,MA0258.1;0.603127,MA0259.1;0.699589,MA0442.1;0
}}
}}

Revision as of 19:38, 22 January 2013


Full id: C1024_Pericytes_cerebellum_neuroblastoma_HES3GFP_iPS_extraskeletal_teratocarcinoma



Phase1 CAGE Peaks

Hg19::chr13:100623360..100623373,-p2@ZIC5
Hg19::chr13:100623375..100623425,-p1@ZIC5
Hg19::chr13:100633445..100633468,+p1@AK298232
Hg19::chr13:100633480..100633490,+p3@AK298232
Hg19::chr13:100634031..100634045,+p1@ZIC2
Hg19::chr13:100634809..100634826,+p11@ZIC2
Hg19::chr13:100638100..100638115,+p4@ZIC2
Hg19::chr13:100638124..100638136,+p7@ZIC2


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>disease_data<br>

Cell Type
Ontology termp-valuen
neural cell6.09e-1125
neurectodermal cell9.34e-0859
neuron3.95e-076
neuroblast3.95e-076
electrically signaling cell3.95e-076
embryonic stem cell5.80e-075
neuronal stem cell7.64e-078
Uber Anatomy
Ontology termp-valuen
central nervous system2.38e-4381
nervous system1.30e-4189
brain1.17e-3368
future brain1.17e-3368
neural tube7.80e-3256
neural rod7.80e-3256
future spinal cord7.80e-3256
neural keel7.80e-3256
neurectoderm4.56e-3086
regional part of nervous system8.79e-3053
regional part of brain8.79e-3053
neural plate1.38e-2682
presumptive neural plate1.38e-2682
ectoderm-derived structure1.83e-23171
ectoderm1.83e-23171
presumptive ectoderm1.83e-23171
regional part of forebrain7.44e-2041
forebrain7.44e-2041
anterior neural tube7.44e-2041
future forebrain7.44e-2041
telencephalon9.01e-2034
brain grey matter2.72e-1934
gray matter2.72e-1934
pre-chordal neural plate3.48e-1961
cerebral hemisphere2.52e-1832
ecto-epithelium2.62e-18104
regional part of telencephalon2.81e-1832
cerebral cortex1.12e-1725
pallium1.12e-1725
organ system subdivision1.64e-16223
regional part of cerebral cortex1.67e-1522
neocortex7.97e-1420
posterior neural tube1.25e-1315
chordal neural plate1.25e-1315
structure with developmental contribution from neural crest1.96e-12132
segmental subdivision of hindbrain1.01e-1112
hindbrain1.01e-1112
presumptive hindbrain1.01e-1112
segmental subdivision of nervous system1.66e-1013
regional part of metencephalon1.48e-099
metencephalon1.48e-099
future metencephalon1.48e-099
cerebellum5.48e-086
rhombic lip5.48e-086
Disease
Ontology termp-valuen
cell type cancer8.40e-22143
cancer1.33e-20235
disease of cellular proliferation1.77e-19239
carcinoma1.56e-15106
germ cell and embryonal cancer2.50e-0822
germ cell cancer2.50e-0822
adenocarcinoma1.07e-0725
organ system cancer7.90e-07137


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)
MA0003.11.34332
MA0004.10.455723
MA0006.10.812175
MA0007.11.1148
MA0009.10.918715
MA0014.12.6969
MA0017.10.896777
MA0019.10.602411
MA0024.11.90464
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.11.60389
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.13.22913
MA0056.10
MA0057.16.69229
MA0058.10.362328
MA0059.11.69011
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.415214
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.16.51901
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.770971
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.11.84219
MA0113.11.49247
MA0114.10.655057
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.830366
MA0146.13.51017
MA0147.11.26392
MA0148.10.480298
MA0149.10.506665
MA0062.20.485915
MA0035.20.515566
MA0039.20.881644
MA0138.20.653421
MA0002.20.531206
MA0137.20.321796
MA0104.21.66814
MA0047.20.586412
MA0112.20.458158
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.197713
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.14.37832
MA0163.15.02939
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.227.7181
MA0102.21.46209
MA0258.10.603127
MA0259.10.699589
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
E2F6#187653.135722332310870.01024880501420960.0381472948743376
EGR1#195853.117611934256340.01051390990388360.0389204351345726
ZNF263#1012755.138651023131670.001082531249033560.00763805439250206



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:C1024&oldid=2569535"