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Coexpression cluster:C402: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0005905!coated pit!0.0316437065818909!9026$GO:0030136!clathrin-coated vesicle!0.0358138074492719!9026$GO:0030135!coated vesicle!0.0358138074492719!9026$GO:0005543!phospholipid binding!0.0358138074492719!9026$GO:0016023!cytoplasmic membrane-bound vesicle!0.0358138074492719!9026$GO:0031988!membrane-bound vesicle!0.0358138074492719!9026$GO:0031410!cytoplasmic vesicle!0.0358138074492719!9026$GO:0031982!vesicle!0.0358138074492719!9026$GO:0003779!actin binding!0.0358138074492719!9026$GO:0008289!lipid binding!0.0403407083908673!9026$GO:0008092!cytoskeletal protein binding!0.0403407083908673!9026
|gostat_on_coexpression_clusters=GO:0005905!coated pit!0.0316437065818909!9026$GO:0030136!clathrin-coated vesicle!0.0358138074492719!9026$GO:0030135!coated vesicle!0.0358138074492719!9026$GO:0005543!phospholipid binding!0.0358138074492719!9026$GO:0016023!cytoplasmic membrane-bound vesicle!0.0358138074492719!9026$GO:0031988!membrane-bound vesicle!0.0358138074492719!9026$GO:0031410!cytoplasmic vesicle!0.0358138074492719!9026$GO:0031982!vesicle!0.0358138074492719!9026$GO:0003779!actin binding!0.0358138074492719!9026$GO:0008289!lipid binding!0.0403407083908673!9026$GO:0008092!cytoskeletal protein binding!0.0403407083908673!9026
|id=C402
|id=C402
|ontology_enrichment_celltype=CL:0002319!6.90e-07!25
|ontology_enrichment_celltype=CL:0000047!3.24e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.96e-35!82;UBERON:0000073!3.40e-35!94;UBERON:0001016!3.40e-35!94;UBERON:0001049!1.20e-33!57;UBERON:0005068!1.20e-33!57;UBERON:0006241!1.20e-33!57;UBERON:0007135!1.20e-33!57;UBERON:0005743!1.56e-33!86;UBERON:0007023!7.83e-29!115;UBERON:0000955!1.15e-28!69;UBERON:0006238!1.15e-28!69;UBERON:0002346!1.36e-27!90;UBERON:0002616!1.00e-26!59;UBERON:0002780!1.03e-26!41;UBERON:0001890!1.03e-26!41;UBERON:0006240!1.03e-26!41;UBERON:0003080!2.37e-26!42;UBERON:0003075!5.69e-26!86;UBERON:0007284!5.69e-26!86;UBERON:0002020!1.01e-22!34;UBERON:0003528!1.01e-22!34;UBERON:0001893!1.14e-22!34;UBERON:0002791!4.32e-22!33;UBERON:0000924!1.66e-21!173;UBERON:0006601!1.66e-21!173;UBERON:0001869!2.45e-21!32;UBERON:0004121!4.14e-20!169;UBERON:0003056!2.13e-17!61;UBERON:0000956!5.36e-17!25;UBERON:0000203!5.36e-17!25;UBERON:0000153!1.31e-16!129;UBERON:0007811!1.31e-16!129;UBERON:0000033!2.43e-16!123;UBERON:0002619!1.13e-15!22;UBERON:0001950!2.14e-14!20;UBERON:0003076!2.05e-08!15;UBERON:0003057!2.05e-08!15;UBERON:0004732!2.95e-07!13;UBERON:0002308!3.56e-07!9;UBERON:0000125!3.56e-07!9;UBERON:0002420!3.68e-07!9;UBERON:0007245!3.68e-07!9;UBERON:0010009!3.68e-07!9;UBERON:0010011!3.68e-07!9;UBERON:0000454!3.68e-07!9
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1717,0.480884,0.578932,0.35239,0.496246,0.981868,0.252841,0.717414,0.88333,0.048426,0.413157,0.848698,0.312783,0.263868,0.635839,0.927666,0.0267922,0.992094,0.741609,0.290643,0.54757,0.387699,0.154131,0.465395,0.880067,0.545078,0.343791,0.807843,0.415977,0.33744,0.496516,0.806195,0.523055,0.255632,0.970884,0.402999,0.733369,0.795332,0.731097,0.554007,0.959672,0.561642,0.0669867,0.0570561,0.99397,0.350249,0.502686,0.26502,0.334713,0.705188,0.93575,0.587456,0.369553,0.0640722,0.359095,0.106723,0.0318082,0.210084,0.154149,0.0369306,0.0303637,0.939921,0.944898,0.321669,0.626278,0.94817,0.667184,0.843198,0.506272,0.998971,0.0944443,0.344655,0.805917,0.103916,0.235031,0.8151,0.473376,0.888806,0.572733,0.269487,0.112648,0.0276369,0.997227,0.999997,0.865221,0.628866,0.26174,0.453527,0.631301,0.355403,0.582406,0.864154,0.493945,0.333013,0.268677,0.468216,0.650802,0.764005,0.283212,0.349292,0.32906,0.381418,0.650542,0.570678,0.806062,0.617451,0.886008,0.399614,0.0853568,0.495853,0.790156,0.76134,0.8473,0.881654,0.604897,0.26196,0.807189,0.487635,0.172526,0.429331,0.549117,0.751913,0.997728,0.0616965,0.137465,0.204015,0.416343,0.740918,0.413309,0.223113,0.76775,0.801693,0.556346,0.365773,0.656098,0.918748,0.564383,0.666576,0.532024,0.0644884,0.646772,0.645061,0.534287,0.810784,0.57837,0.74352,0.45163,0.145776,0.597864,0.119972,0.612681,0.278914,0.200976,0.21485,0.561172,0.1494,0.469639,0.836645,0.520853,0.00967613,0.432953,0.6282,0.98558,0.0987824,0.446501,0.817845,0.62897,0.663865,0.989251,0.920323,0.272775,0.989998,0.343807,0.319607,0.711493,0.94787,0.761056,0.58815,0.474387,0.0815989,0.966083,0.562709,0.0514399,0.858821,0.757025,0.298088,0.932825,0.349192,0.82805,0.596766,0.869927,0.88096,0.956164,0.863115,0.427455,0.522225,0.154557,0.745281,0.766511,0.91143,0.999615,0.00216293,0.447431,0.72602,0.924148,0.168692,0.726825,0.165255,0.933629,0.567085,0.788699,0.904152,0.563788,0.609199,0.919731,0.0694013,0.638868,0.730434,0.40634,0.0980274,0.901095,0.622441,0.711661,0.412289,0.198104,0.544716,0.672522,0.843248,0.818495,0.381624,0.914214,0.918955,0.912171,0.838959,0.940463,0.860687,0.856189,0.592525,0.374583,0.257354,0.952682,0.317176,0.921333,0.770295,0.380395,0.674519,0.218788,0.0189115,0.892411,0.787889,0.896864,0.304672,0.553626,0.92633,0.634858,0.823579,0.781323,0.842123,0.835031,0.831918,0.60097,0.654566,0.952939,0.15499,0.909564,0.795681,0.987792,0.998251,0.795775,0.370841,0.499946,0.325612,0.62411,0.809017,0.622748,0.862791,0.597157,0.141912,0.987145,0.469429,0.56921,0.529796,0.841076,0.922034,0.2347,0.27619,0.223267,0.768024,0.478511,0.555207,0.649768,0.802195,0.979983,0.903004,0.586295,0.522868,0.387624,0.963666,0.722548,0.767421,0.871149,0.612608,0.428035,0.910149,0.10247,0.820432,0.544021,0.79433,0.417486,0.457313,0.602538,0.437642,0.85659,0.365438,0.420312,0.566594,0.841578,0.626801,0.404934,0.216271,0.900936,0.551445,0.974256,0.3219,0.817331,0.93712,0.211463,0.305421,0.411616,0.335017,0.897399,0.293098,0.851944,0.563717,0.612393,0.464827,0.988847,0.596621,0.766483,0.86368,0.237991,0.504847,0.770522,0.591688,0.257123,0.543857,0.122035,0.835967,0.0279967,0.27864,0.200648,0.840766,0.0711106,0.883163,0.329051,0.197712,0.580462,0.466786,0.716481,0.916835,0.724245,0.145751,0.753682,0.510995,0.286804,0.885065,0.373656,0.489712,0.831949,0.358799,0.853233,0.267269,0.680401,0.574196,0.249619,0.572138,0.682686,0.247732,0.652681,0.538054,0.539381,0.704205,0.600735,0.705531,0.640369,0.123262,0.868159,0.282947,0.646588,0.744562,0.895517,0.784162,0.39157,0.798465,0.288382,0.119495,0.371627,0.332393,0.75361,0.134195,0.514057,0.767537,0.670381,0.593577,0.630276,0.412697,0.622496,0.440628,0.634794,0.847755,0.319041,0.265146,0.827479,0.822061,0.445471,0.728326,0.41367,0.356117,0.68227,0.103255,0.263089,0.478308,0.731062,0.927923,0.587175,0.15852,0.598358,0.382349,0.55441,0.451783,0.656413,0.378422,0.442873,0.807279,0.306707,0.144033,0.567011,0.688039,0.184822,0.34376,0.72757,0.641631,0.084019,0.814749,0.221543,0.135218,0.402145,0.77868,0.359251,0.171144,0.582041,0.624035,0.379665,0.38062,0.758291,0.505383,0.302549,0.380404,0.648822,0.927907,0.872233,0.537759,0.405572,0.54354,0.520393,0.225684,0.437044,0.675914,0.435608,0.616173,0.448313,0.497122,0.6971,0.632816,0.0591485,0.451511,0.196118,0.277082,0.357724,0.589,0.58548,0.560476,0.713553,0.734084,0.493219,0.922876,0.30575,0.65435,0.592533,0.719586,0.505277,0.783982,0.744254,0.125869,0.780819,0.323801,0.303217,0.173175,0.208469,0.443451,0.0929872,0.628474,0.0720653,0.654072,0.56046,0.548047,0.546559,0.327213,0.917315,0.789664,0.645615,0.573225,0.667931,0.649672,0.867176,0.582512,0.183558,0.641086,0.225061,0.441899,0.0602211,0.472341,0.935084,0.235931,0.640943,0.23673,0.186893,0.621858,0.247913,0.322961,0.349151
}}
}}

Revision as of 15:36, 19 October 2012


Full id: C402_parietal_occipital_temporal_thalamus_optic_globus_brain



Phase1 CAGE Peaks

Hg19::chr12:123319068..123319080,+p6@HIP1R
Hg19::chr14:32799950..32799951,+p@chr14:32799950..32799951
+
Hg19::chr19:11562361..11562386,-p@chr19:11562361..11562386
-
Hg19::chr19:13134043..13134054,+p@chr19:13134043..13134054
+
Hg19::chr19:47142400..47142423,-p1@uc002pez.1
Hg19::chr19:55946892..55946910,-p@chr19:55946892..55946910
-
Hg19::chr1:172051480..172051484,+p@chr1:172051480..172051484
+
Hg19::chr20:58279639..58279642,+p@chr20:58279639..58279642
+
Hg19::chr21:41551108..41551112,-p@chr21:41551108..41551112
-
Hg19::chr22:18503369..18503380,-p@chr22:18503369..18503380
-
Hg19::chr3:181442608..181442615,+p@chr3:181442608..181442615
+
Hg19::chr4:113994134..113994138,+p@chr4:113994134..113994138
+
Hg19::chr4:114286837..114286840,+p@chr4:114286837..114286840
+
Hg19::chr4:164928140..164928142,-p@chr4:164928140..164928142
-
Hg19::chr4:164948511..164948515,-p@chr4:164948511..164948515
-
Hg19::chr4:165244747..165244750,-p@chr4:165244747..165244750
-
Hg19::chr5:146146606..146146609,-p@chr5:146146606..146146609
-
Hg19::chr5:146243956..146243960,-p@chr5:146243956..146243960
-
Hg19::chr7:86415034..86415036,+p@chr7:86415034..86415036
+
Hg19::chr9:103281957..103281962,+p@chr9:103281957..103281962
+
Hg19::chr9:8463305..8463309,-p@chr9:8463305..8463309
-
Hg19::chr9:8491655..8491659,-p@chr9:8491655..8491659
-
Hg19::chr9:8500547..8500558,-p@chr9:8500547..8500558
-
Hg19::chr9:8576629..8576632,-p@chr9:8576629..8576632
-
Hg19::chr9:8858623..8858638,-p@chr9:8858623..8858638
-
Hg19::chrX:13904834..13904839,-p@chrX:13904834..13904839
-


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:0005905coated pit0.0316437065818909
GO:0030136clathrin-coated vesicle0.0358138074492719
GO:0030135coated vesicle0.0358138074492719
GO:0005543phospholipid binding0.0358138074492719
GO:0016023cytoplasmic membrane-bound vesicle0.0358138074492719
GO:0031988membrane-bound vesicle0.0358138074492719
GO:0031410cytoplasmic vesicle0.0358138074492719
GO:0031982vesicle0.0358138074492719
GO:0003779actin binding0.0358138074492719
GO:0008289lipid binding0.0403407083908673
GO:0008092cytoskeletal protein binding0.0403407083908673



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>

Cell Type
Ontology termp-valuen
neuronal stem cell3.24e-078
Uber Anatomy
Ontology termp-valuen
central nervous system3.92e-9281
neural tube2.07e-9156
neural rod2.07e-9156
future spinal cord2.07e-9156
neural keel2.07e-9156
nervous system4.70e-8889
regional part of nervous system4.10e-8453
regional part of brain4.10e-8453
brain5.55e-7568
future brain5.55e-7568
regional part of forebrain4.78e-7341
forebrain4.78e-7341
anterior neural tube4.78e-7341
future forebrain4.78e-7341
neural plate1.04e-7282
presumptive neural plate1.04e-7282
neurectoderm1.60e-7186
brain grey matter4.41e-7034
gray matter4.41e-7034
telencephalon7.23e-7034
regional part of telencephalon3.97e-6532
cerebral hemisphere7.82e-6532
pre-chordal neural plate1.78e-5761
ecto-epithelium1.98e-54104
regional part of cerebral cortex4.35e-5122
adult organism3.66e-50114
cerebral cortex2.12e-4825
pallium2.12e-4825
ectoderm-derived structure3.00e-47171
ectoderm3.00e-47171
presumptive ectoderm3.00e-47171
neocortex2.71e-4620
structure with developmental contribution from neural crest2.21e-45132
organ system subdivision1.16e-32223
tube7.15e-23192
neural nucleus7.18e-239
nucleus of brain7.18e-239
basal ganglion8.80e-239
nuclear complex of neuraxis8.80e-239
aggregate regional part of brain8.80e-239
collection of basal ganglia8.80e-239
cerebral subcortex8.80e-239
posterior neural tube7.93e-1915
chordal neural plate7.93e-1915
anatomical cluster1.59e-18373
telencephalic nucleus4.50e-187
anatomical conduit1.32e-15240
gyrus2.20e-156
brainstem3.36e-156
segmental subdivision of nervous system9.40e-1513
organ part2.18e-14218
occipital lobe1.34e-135
parietal lobe1.52e-135
temporal lobe2.23e-136
limbic system2.73e-135
segmental subdivision of hindbrain1.45e-1212
hindbrain1.45e-1212
presumptive hindbrain1.45e-1212
epithelium3.94e-12306
cell layer7.01e-12309
corpus striatum1.37e-104
striatum1.37e-104
ventral part of telencephalon1.37e-104
future corpus striatum1.37e-104
multi-tissue structure2.41e-09342
embryo4.40e-09592
spinal cord1.00e-083
dorsal region element1.00e-083
dorsum1.00e-083
pons1.06e-083
frontal cortex1.06e-083
caudate-putamen2.10e-083
dorsal striatum2.10e-083
germ layer2.82e-08560
germ layer / neural crest2.82e-08560
embryonic tissue2.82e-08560
presumptive structure2.82e-08560
germ layer / neural crest derived structure2.82e-08560
epiblast (generic)2.82e-08560
medulla oblongata3.47e-083
myelencephalon3.47e-083
future myelencephalon3.47e-083
embryonic structure4.28e-08564
developing anatomical structure7.18e-08581
regional part of metencephalon4.26e-079
metencephalon4.26e-079
future metencephalon4.26e-079
dorsal plus ventral thalamus8.22e-072
thalamic complex8.22e-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)

{{{tfbs_overrepresentation_jaspar}}}



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

No analysis results for this cluster

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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