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Coexpression cluster:C1034: Difference between revisions

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5012,0.320667,0.456504,0.240369,0.5938,2.5325e-05,0.00833795,0.00964119,0.187049,0.448658,8.21738e-05,0.243993,0.0445425,0.000208928,0.223701,0.000208708,0.055434,0.373141,0.024718,0.447066,0.594101,0.512982,0.000758682,0.0434152,0.481032,0.00067154,0.278645,0.114833,0.110579,4.17782e-06,0.223113,0.535591,0.0128959,0.491941,0.00246592,0.0913688,0.000701222,0.462673,0.0302547,0.0245036,0.000645385,1.03294e-06,0.369527,0.0539394,0.178571,0.000241005,0.00308973,0.48895,0.403105,0.366377,0.0281133,0.00822966,0.00366282,0.0334302
|tfbs_overrepresentation_for_novel_motifs=0.348717,0.360433,0.905112,0.481684,0.301904,0.480078,0.554663,0.19223,1.05889,0.994235,0.450635,0.597407,0.907465,0.543352,0.300614,0.863056,0.774423,0.250594,1.51831,0.0766963,0.341703,0.715078,0.472508,0.29709,0.385586,0.619829,0.135503,1.18607,0.822672,0.122648,0.429397,0.810962,0.220667,0.154814,0.742281,0.570077,1.35136,0.481208,0.244807,0.518171,0.268162,1.06332,0.444349,0.299183,0.949078,0.371118,0.555735,1.12076,0.416595,0.822946,0.63387,0.567337,0.0927889,0.887323,1.03948,1.34776,0.308962,0.514077,0.122557,1.27736,1.98297,0.558065,0.556977,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,2.77815,1.03748,2.05941,0.429044,0.401476,1.73257,0.797419,0.379656,0.167664,0.745864,0.575394,0.19474,0.986227,0.450611,0.0757344,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,4.08104,0.239285,0.488357,0.87,0.664183,0.106284,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,1.77423,0.782066,0.92894,0.861701,0.893372,2.02714,1.17281,0.265019,0.518187,1.0951,0.710479,0.650514,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.364369,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.637373,0.999704,3.32906,0.960402,0.183004,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.611402,2.33631,0.926865
|tfbs_overrepresentation_for_novel_motifs=0.348717,0.360433,0.905112,0.481684,0.301904,0.480078,0.554663,0.19223,1.05889,0.994235,0.450635,0.597407,0.907465,0.543352,0.300614,0.863056,0.774423,0.250594,1.51831,0.0766963,0.341703,0.715078,0.472508,0.29709,0.385586,0.619829,0.135503,1.18607,0.822672,0.122648,0.429397,0.810962,0.220667,0.154814,0.742281,0.570077,1.35136,0.481208,0.244807,0.518171,0.268162,1.06332,0.444349,0.299183,0.949078,0.371118,0.555735,1.12076,0.416595,0.822946,0.63387,0.567337,0.0927889,0.887323,1.03948,1.34776,0.308962,0.514077,0.122557,1.27736,1.98297,0.558065,0.556977,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,2.77815,1.03748,2.05941,0.429044,0.401476,1.73257,0.797419,0.379656,0.167664,0.745864,0.575394,0.19474,0.986227,0.450611,0.0757344,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,4.08104,0.239285,0.488357,0.87,0.664183,0.106284,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,1.77423,0.782066,0.92894,0.861701,0.893372,2.02714,1.17281,0.265019,0.518187,1.0951,0.710479,0.650514,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.364369,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.637373,0.999704,3.32906,0.960402,0.183004,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.611402,2.33631,0.926865
|tfbs_overrepresentation_jaspar=MA0003.1;0.06829,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.473479,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,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;2.65641,MA0056.1;0,MA0057.1;0.305162,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.497495,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.133123,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;1.87644,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;0.818737,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;0.586268,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.231781,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;0.470675,MA0140.1;1.28413,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;1.7555,MA0146.1;0.418694,MA0147.1;0.681318,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;0.284736,MA0138.2;0.653421,MA0002.2;0.531206,MA0137.2;0.321796,MA0104.2;0.55506,MA0047.2;0.586412,MA0112.2;0.458158,MA0065.2;0.490252,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.274121,MA0155.1;1.16939,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.378102,MA0163.1;0.75401,MA0164.1;0.627336,MA0080.2;1.48508,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;1.29044,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.699589,MA0442.1;0
}}
}}

Revision as of 19:38, 22 January 2013


Full id: C1034_pituitary_olfactory_amygdala_insula_temporal_hippocampus_frontal



Phase1 CAGE Peaks

Hg19::chr14:62584201..62584208,+p1@ENST00000334389
Hg19::chr16:1383632..1383652,+p1@BAIAP3
Hg19::chr1:204320105..204320146,-p@chr1:204320105..204320146
-
Hg19::chr2:220379118..220379131,+p1@ACCN4
Hg19::chr6:69942915..69942931,+p@chr6:69942915..69942931
+
Hg19::chr6:69942947..69942963,+p@chr6:69942947..69942963
+
Hg19::chr6:69942992..69943002,+p@chr6:69942992..69943002
+
Hg19::chrX:101397536..101397555,+p@chrX:101397536..101397555
+


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

GO IDGO nameFDR corrected p-value
GO:0015081sodium ion transmembrane transporter activity0.0170718784065629
GO:0007269neurotransmitter secretion0.0380050197822336
GO:0045055regulated secretory pathway0.0380050197822336
GO:0005272sodium channel activity0.0380050197822336
GO:0003001generation of a signal involved in cell-cell signaling0.0380050197822336
GO:0008022protein C-terminus binding0.0380050197822336
GO:0001505regulation of neurotransmitter levels0.0380050197822336
GO:0031402sodium ion binding0.0409176272807585



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
neural tube1.57e-9356
neural rod1.57e-9356
future spinal cord1.57e-9356
neural keel1.57e-9356
nervous system6.21e-9289
central nervous system2.72e-8981
regional part of nervous system3.02e-8653
regional part of brain3.02e-8653
regional part of forebrain2.27e-7941
forebrain2.27e-7941
anterior neural tube2.27e-7941
future forebrain2.27e-7941
brain6.65e-7868
future brain6.65e-7868
telencephalon1.89e-7034
brain grey matter2.42e-7034
gray matter2.42e-7034
neural plate7.25e-6982
presumptive neural plate7.25e-6982
cerebral hemisphere5.16e-6632
regional part of telencephalon1.61e-6532
neurectoderm4.39e-6586
pre-chordal neural plate1.97e-5961
ecto-epithelium2.66e-56104
regional part of cerebral cortex2.98e-5622
adult organism1.70e-52114
neocortex2.69e-5120
cerebral cortex5.46e-4925
pallium5.46e-4925
ectoderm-derived structure1.03e-46171
ectoderm1.03e-46171
presumptive ectoderm1.03e-46171
structure with developmental contribution from neural crest9.99e-42132
organ system subdivision6.29e-38223
basal ganglion7.86e-239
nuclear complex of neuraxis7.86e-239
aggregate regional part of brain7.86e-239
collection of basal ganglia7.86e-239
cerebral subcortex7.86e-239
neural nucleus1.73e-229
nucleus of brain1.73e-229
tube8.33e-20192
telencephalic nucleus7.79e-187
anatomical cluster2.02e-17373
gyrus2.31e-176
posterior neural tube1.00e-1515
chordal neural plate1.00e-1515
occipital lobe3.90e-155
temporal lobe9.90e-156
parietal lobe1.20e-145
limbic system4.98e-145
organ part1.32e-13218
anatomical conduit1.87e-13240
segmental subdivision of nervous system1.09e-1113
corpus striatum1.96e-114
striatum1.96e-114
ventral part of telencephalon1.96e-114
future corpus striatum1.96e-114
epithelium2.85e-11306
cell layer4.86e-11309
brainstem6.15e-116
diencephalon2.29e-107
future diencephalon2.29e-107
segmental subdivision of hindbrain7.09e-1012
hindbrain7.09e-1012
presumptive hindbrain7.09e-1012
multi-tissue structure2.62e-09342
frontal cortex2.64e-093
germ layer4.05e-09560
germ layer / neural crest4.05e-09560
embryonic tissue4.05e-09560
presumptive structure4.05e-09560
germ layer / neural crest derived structure4.05e-09560
epiblast (generic)4.05e-09560
caudate-putamen6.01e-093
dorsal striatum6.01e-093
embryonic structure6.14e-09564
spinal cord1.14e-083
dorsal region element1.14e-083
dorsum1.14e-083
pons1.27e-083
embryo2.43e-08592
organ3.14e-08503
developing anatomical structure3.37e-08581
pituitary gland2.72e-072
regional part of metencephalon3.88e-079
metencephalon3.88e-079
future metencephalon3.88e-079
anatomical system4.59e-07624
anatomical group5.01e-07625
middle temporal gyrus5.95e-072
middle frontal gyrus9.10e-072


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)
MA0003.10.06829
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.473479
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
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
MA0055.12.65641
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.11.87644
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
MA0093.10.818737
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.586268
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
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
MA0139.10.470675
MA0140.11.28413
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.11.7555
MA0146.10.418694
MA0147.10.681318
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.284736
MA0138.20.653421
MA0002.20.531206
MA0137.20.321796
MA0104.20.55506
MA0047.20.586412
MA0112.20.458158
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.11.16939
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.378102
MA0163.10.75401
MA0164.10.627336
MA0080.21.48508
MA0018.20.599912
MA0099.20.523145
MA0079.21.29044
MA0102.21.46209
MA0258.10.209744
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#187653.135722332310870.01024880501420960.0381500141454552
GATA2#262446.3724658667770.002048740757051450.0118950653727872
GATA3#2625310.21369363395230.002410870126189130.0135896408197898
HDAC2#306658.384762647891410.000106287309381870.00148086183358233
MAX#414964.839416631755340.0002917504313705360.00309750160637465
MXI1#460144.980785814379650.005094415320429170.0236964165879972
RAD21#588545.177516947728160.004420594525976950.0209408296683679
REST#597844.825014358064010.005720735398269540.0257851574925499
SIN3A#2594253.380552954259460.007342226961170280.0303628921638354
SUZ12#23512425.05789045553151.03898994633546e-050.000270129626600273
ZNF263#1012744.110920818505340.01019992782316260.0379910935065365



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:C1034&oldid=2569545"