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Coexpression cluster:C1567: Difference between revisions

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|full_id=C1567_Neural_pituitary_caudate_spinal_Neurons_parietal_putamen
|full_id=C1567_Neural_pituitary_caudate_spinal_Neurons_parietal_putamen
|id=C1567
|id=C1567
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0000047!6.06e-10!8;CL:0002605!1.06e-08!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.89e-79!57;UBERON:0005068!2.89e-79!57;UBERON:0006241!2.89e-79!57;UBERON:0007135!2.89e-79!57;UBERON:0001017!5.34e-76!82;UBERON:0005743!6.65e-74!86;UBERON:0000073!1.52e-73!94;UBERON:0001016!1.52e-73!94;UBERON:0002616!3.13e-66!59;UBERON:0002780!2.51e-64!41;UBERON:0001890!2.51e-64!41;UBERON:0006240!2.51e-64!41;UBERON:0000955!4.76e-63!69;UBERON:0006238!4.76e-63!69;UBERON:0003080!1.75e-62!42;UBERON:0003075!1.17e-56!86;UBERON:0007284!1.17e-56!86;UBERON:0007023!1.25e-53!115;UBERON:0002346!2.69e-53!90;UBERON:0002020!5.27e-53!34;UBERON:0003528!5.27e-53!34;UBERON:0001893!5.45e-53!34;UBERON:0002791!2.30e-51!33;UBERON:0001869!5.19e-50!32;UBERON:0003056!4.56e-45!61;UBERON:0004121!3.83e-40!169;UBERON:0000924!1.07e-38!173;UBERON:0006601!1.07e-38!173;UBERON:0000956!2.16e-38!25;UBERON:0000203!2.16e-38!25;UBERON:0000033!2.98e-37!123;UBERON:0000153!4.99e-36!129;UBERON:0007811!4.99e-36!129;UBERON:0002619!3.48e-34!22;UBERON:0001950!5.32e-31!20;UBERON:0003076!3.34e-17!15;UBERON:0003057!3.34e-17!15;UBERON:0000025!4.05e-17!194;UBERON:0002308!8.41e-16!9;UBERON:0000125!8.41e-16!9;UBERON:0002420!1.16e-15!9;UBERON:0007245!1.16e-15!9;UBERON:0010009!1.16e-15!9;UBERON:0010011!1.16e-15!9;UBERON:0000454!1.16e-15!9;UBERON:0004111!7.01e-15!241;UBERON:0004732!9.74e-14!13;UBERON:0009663!8.69e-13!7;UBERON:0004733!1.92e-12!12;UBERON:0002028!1.92e-12!12;UBERON:0007277!1.92e-12!12;UBERON:0001894!2.01e-12!7;UBERON:0006222!2.01e-12!7;UBERON:0000477!7.94e-12!286;UBERON:0000064!2.14e-11!219;UBERON:0000200!5.61e-11!6;UBERON:0000475!3.11e-10!365;UBERON:0002298!3.22e-10!8;UBERON:0001871!3.77e-10!7;UBERON:0001872!7.95e-10!5;UBERON:0002021!1.52e-09!5;UBERON:0000349!2.45e-09!5;UBERON:0000483!4.36e-09!309;UBERON:0000062!6.25e-09!511;UBERON:0000119!7.82e-09!312;UBERON:0000369!1.85e-08!4;UBERON:0002435!1.85e-08!4;UBERON:0000204!1.85e-08!4;UBERON:0010082!1.85e-08!4;UBERON:0002680!2.82e-08!9;UBERON:0001895!2.82e-08!9;UBERON:0010092!2.82e-08!9;UBERON:0000922!5.20e-08!612;UBERON:0000481!6.98e-08!347;UBERON:0003296!1.01e-07!4;UBERON:0010133!1.01e-07!4;UBERON:0000923!4.08e-07!604;UBERON:0005291!4.08e-07!604;UBERON:0006598!4.08e-07!604;UBERON:0002532!4.08e-07!604;UBERON:0002050!4.64e-07!605;UBERON:0005423!4.64e-07!605;UBERON:0000467!8.45e-07!625;UBERON:0005383!8.57e-07!3;UBERON:0005382!8.57e-07!3;UBERON:0000480!9.57e-07!626
|ontology_enrichment_uberon=UBERON:0001049!5.56e-125!56;UBERON:0005068!5.56e-125!56;UBERON:0006241!5.56e-125!56;UBERON:0007135!5.56e-125!56;UBERON:0001017!5.02e-118!81;UBERON:0000073!3.78e-116!53;UBERON:0002616!3.78e-116!53;UBERON:0002780!9.97e-111!41;UBERON:0001890!9.97e-111!41;UBERON:0003080!9.97e-111!41;UBERON:0006240!9.97e-111!41;UBERON:0001016!3.99e-105!89;UBERON:0000955!4.16e-99!68;UBERON:0006238!4.16e-99!68;UBERON:0001893!1.16e-90!34;UBERON:0003528!1.64e-90!34;UBERON:0002020!1.64e-90!34;UBERON:0001869!2.12e-85!32;UBERON:0002791!3.27e-85!32;UBERON:0003075!4.05e-85!82;UBERON:0007284!4.05e-85!82;UBERON:0002346!1.31e-80!86;UBERON:0003056!6.05e-75!61;UBERON:0000956!1.54e-65!25;UBERON:0000203!1.54e-65!25;UBERON:0010371!1.46e-64!104;UBERON:0002619!2.55e-58!22;UBERON:0007023!5.84e-58!114;UBERON:0001950!1.69e-52!20;UBERON:0004121!6.86e-51!171;UBERON:0000924!6.86e-51!171;UBERON:0006601!6.86e-51!171;UBERON:0010314!1.79e-50!132;UBERON:0011216!6.55e-39!223;UBERON:0000025!3.00e-29!192;UBERON:0000125!1.07e-25!9;UBERON:0002308!1.07e-25!9;UBERON:0002420!1.32e-25!9;UBERON:0007245!1.32e-25!9;UBERON:0010009!1.32e-25!9;UBERON:0010011!1.32e-25!9;UBERON:0000454!1.32e-25!9;UBERON:0004111!4.55e-23!240;UBERON:0000477!1.96e-22!373;UBERON:0009663!1.15e-20!7;UBERON:0001894!1.22e-20!7;UBERON:0006222!1.22e-20!7;UBERON:0000200!1.65e-17!6;UBERON:0003076!2.44e-17!15;UBERON:0003057!2.44e-17!15;UBERON:0002298!1.24e-16!6;UBERON:0001872!7.16e-16!5;UBERON:0002021!1.82e-15!5;UBERON:0000349!2.68e-15!5;UBERON:0000483!1.78e-14!306;UBERON:0000119!3.27e-14!309;UBERON:0001871!5.51e-14!6;UBERON:0000481!1.10e-13!342;UBERON:0000369!6.53e-13!4;UBERON:0002435!6.53e-13!4;UBERON:0000204!6.53e-13!4;UBERON:0010082!6.53e-13!4;UBERON:0003296!2.50e-12!4;UBERON:0010133!2.50e-12!4;UBERON:0000064!3.48e-12!218;UBERON:0002784!9.51e-12!4;UBERON:0004733!1.44e-10!12;UBERON:0002028!1.44e-10!12;UBERON:0007277!1.44e-10!12;UBERON:0005383!5.53e-10!3;UBERON:0005382!5.53e-10!3;UBERON:0002240!5.87e-10!3;UBERON:0005174!5.87e-10!3;UBERON:0001137!5.87e-10!3;UBERON:0001870!9.76e-10!3;UBERON:0004732!1.12e-09!13;UBERON:0000922!2.61e-09!592;UBERON:0001896!2.97e-09!3;UBERON:0005290!2.97e-09!3;UBERON:0010096!2.97e-09!3;UBERON:0005423!3.98e-09!581;UBERON:0000062!4.43e-09!503;UBERON:0000988!4.44e-09!3;UBERON:0000923!9.31e-09!560;UBERON:0010316!9.31e-09!560;UBERON:0005291!9.31e-09!560;UBERON:0006598!9.31e-09!560;UBERON:0010317!9.31e-09!560;UBERON:0002532!9.31e-09!560;UBERON:0002050!1.37e-08!564;UBERON:0000467!4.63e-08!624;UBERON:0000480!5.04e-08!625;UBERON:0000007!8.88e-08!2;UBERON:0001954!2.01e-07!2;UBERON:0003022!2.01e-07!2;UBERON:0002421!2.01e-07!2;UBERON:0002600!2.01e-07!2;UBERON:0001873!3.50e-07!2;UBERON:0010122!3.50e-07!2;UBERON:0001897!3.72e-07!2;UBERON:0010225!3.72e-07!2;UBERON:0001875!4.87e-07!2;UBERON:0006514!4.87e-07!2;UBERON:0002702!5.18e-07!2;UBERON:0000468!6.30e-07!656
|tf_chipseq_enrich=RAD21#5885;3:6.2130203372738:0.00775105506881164:0.0318818652408971!SRF#6722;3:8.27830695730069:0.00340484607377615:0.0173538977648288
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916,0.294266,0.0790025,0.0541661,0.0119441,0.203728,0.00438696,0.288155,0.265827,0.0105597,0.153627,0.0186891,0.342497,0.171961,0.415228,0.00800917,0.00423094,0.223952,0.327153,0.0496113,0.0236593,0.0730994,0.0857377,0.323267,4.96389e-07,0.00876055,3.09658e-05,0.252398,0.197279,1.91359e-08,0.0912686,0.425114,0.7034,0.218241,0.0242146,0.000222469,0.327369,0.339826,0.00883919,1.11711e-05,0.254847,0.300809,0.0898207,0.000373087,0.0918749,0.0686325,0.0569043,0.0639461,0.387306,0.267408,0.312064,0.080156,0.274185,0.53753,0.0545112,0.510703,0.33844,0.0649137,0.0974216,0.000355178,0.195675,0.0162521,0.176557,0.396547,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.385962,0.000833826,0.296227,0.208788,0.203834,0.36304,0.430936,0.123626,0.00414123,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.223204,0.143824,0.460679,0.431098,4.14418e-12,0.153079,0.0771804,0.0018736,0.00036542,0.0163476,0.204954,0.209341,0.855975,0.261552,0.00371012,0.160115,2.08471e-06,0.10091,0.122658,0.151161,0.000153186,0.056055,0.120552,0.41771,0.893893,0.104741,0.00837769,0.434016,0.190688,0.000505851,0.278645,0.0454186,0.000149394,0.0780533,0.564811,0.00511013,0.00435162,0.448923,0.00700685,0.344528,0.113233,0.0585992,0.20045,0.000341918,0.911136,0.989834,0.00716652,0.336512,0.173868,0.000239769,0.00102033,0.0809806,0.154589,0.00709017,0.122767,7.42739e-05,0.176858,0.114361,0.0690296,0.242462,0.0620267,0.00186222,0.0738743,0.0882327,0.183058,2.5585e-05,0.00413644,0.16872,0.0663381,0.000146263,0.359135,0.123404,2.18978e-06,0.000192813,0.0515122,0.000853249,0.163542,0.483244,0.00417724,0.154031,0.0313367,0.00541645,0.29809,0.0301117,0.689826,0.245965,0.116923,0.148426,0.0983658,4.07922e-10,0.0309424,0.156976,0.00299259,0.267391,0.00589379,0.21807,0.350528,0.0850129,0.432408,0.190404,0.135865,0.0307173,0.18137,0.00113534,0.00526616,0.273972,0.000674445,7.33669e-08,0.0127293,0.0269689,0.0136652,0.391307,0.166736,0.181253,0.0422294,0.263877,0.146486,0.183121,0.262486,0.294204,0.131936,0.288826,0.246621,0.000466905,0.697373,0.0965376,0.377203,0.279263,0.336564,0.35463,0.581771,0.800557,0.0594155,0.587524,4.83299e-06,0.0713793,0.212621,0.000348645,0.53612,0.0791056,0.21728,0.0722318,0.145569,0.619037,0.0432366,0.236988,0.261576,0.0528459,0.569605,0.526495,0.215897,0.00906483,0.0162156,0.820986,0.610475,0.881697,0.561689,0.306829,0.321844,0.255366,0.349408,0.96913,0.967174,0.0695904,0.00823428,0.798758,0.0494957,0.00260019,0.00132826,0.737642,0.886619,0.0201302,0.258394,0.00423004,0.432123,0.416657,0.661773,0.494975,0.651196,0.392155,0.077743,0.0797325,0.457109,0.562417,0.890566,0.85279,0.254547,0.901563,0.821811,0.0063379,0.746881,0.00126065,0.47213,0.660884,0.723387,0.898765,0.705225,0.315485,0.00655278,0.318577,0.0226885,0.389888,0.603509,0.0361061,0.553178,0.246387,0.224252,0.587237,0.155054,0.131605,0.518234,0.00353982,0.353942,0.192234,2.58839e-05,0.747776,0.466967,0.283682,0.424668,0.7175,0.797471,0.583101,0.702164,4.35381e-07,4.09699e-07,0.498956,0.792095,0.00972298,0.127604,0.932831,0.723248,0.34194,0.592696,4.71237e-06,0.00423131,0.89036,0.177129,0.317485,1.16004e-06,0.0263405,0.0121843,0.262394,0.000566838,0.135076,3.69697e-07,0.00527383,2.17654e-05,0.147074,0.183857,0.128394,0.00208999,0.531474,0.000360372,0.200667,0.528646,0.361524,0.31558,0.412744,0.54408,0.0777665,0.0367094,0.415367,0.815658,0.45585,0.36864,0.0437303,0.456862,0.453004,0.680686,0.557093,0.693441,0.382214,0.048225,0.271769,0.00132738,0.0655077,0.694478,0.306231,2.03054e-06,0.646049,0.453817,2.83874e-07,9.74974e-05,0.10749,0.162155,0.656093,0.209347,0.412586,0.534679,0.41502,0.000195803,0.66153,0.523749,0.152974,0.0530156,0.790204,0.196912,0.00505635,0.714189,0.119992,0.813041,0.318338,0.276338,0.00835262,0.0176264,0.000661155,0.0555558,0.00553063,9.92708e-07,0.00540731,0.00712443,1.63206e-05,0.255983,0.00565432,0.256708,4.8361e-06,0.00733321,0.145568,0.000685682,0.261242,0.0132275,0.54721,0.0137717,0.0582761,0.0182544,0.280757,0.301366,0.340343,0.343265,8.78068e-05,0.0251441,0.000849,0.308589,0.0473553,0.19697,0.309816,0.0537285,0.15063,0.198077,2.49868e-05,0.348739,0.0179916,0.138495,0.00179898,0.32256,0.082459,0.0667472,3.09183e-09,0.322704,7.96462e-08,0.181288,0.230841,0.352328,0.255358,0.0707105,0.265112,0.0633313,0.10772,0.0854747,7.37741e-05,0.0968383,0.000613083,0.0365105,0.244656,0.0197801,0.158985,0.174153,0.0972854,0.333309,0.00319971,0.339517,0.303699,0.198326,1.43258e-05,0.458518,0.282501,0.00328682,0.390891,0.00274742,0.334983,0.197875,0.287909,0.046623,0.117618,0.392533,1.08084e-06,0.316002,0.330317,0.00728437,0.225079,0.00583612,0.379651,0.00123984,0.00926916,0.375521,0.271405,0.311201,0.221943,0.306427,0.367733,0.246925,0.00179736,0.0140126,0.343014,1.98499e-05,0.276922,3.03413e-05,0.313647,0.461742,2.39768e-05,0.00848325,0.000438215,0.313545,0.17149,0.0877361,0.000121621,0.238969,0.00037373,0.0669467,0.0879453,0.474066,0.396935,0.00769678,0.00536078,0.358198,0.00552168,0.131776,0.158116,0.104606,0.0203447,0.104167,4.13679e-0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}}
}}

Revision as of 11:26, 19 October 2012


Full id: C1567_Neural_pituitary_caudate_spinal_Neurons_parietal_putamen



Phase1 CAGE Peaks

Hg19::chr10:123951927..123951952,+p17@TACC2
Hg19::chr10:123951957..123951980,+p18@TACC2
Hg19::chr17:61194527..61194561,+p@chr17:61194527..61194561
+
Hg19::chr17:61194578..61194599,+p@chr17:61194578..61194599
+
Hg19::chr17:61194620..61194635,+p@chr17:61194620..61194635
+


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>

Cell Type
Ontology termp-valuen
neuronal stem cell6.06e-108
astrocyte of the cerebral cortex1.06e-083
Uber Anatomy
Ontology termp-valuen
neural tube5.56e-12556
neural rod5.56e-12556
future spinal cord5.56e-12556
neural keel5.56e-12556
central nervous system5.02e-11881
regional part of nervous system3.78e-11653
regional part of brain3.78e-11653
regional part of forebrain9.97e-11141
forebrain9.97e-11141
anterior neural tube9.97e-11141
future forebrain9.97e-11141
nervous system3.99e-10589
brain4.16e-9968
future brain4.16e-9968
telencephalon1.16e-9034
brain grey matter1.64e-9034
gray matter1.64e-9034
cerebral hemisphere2.12e-8532
regional part of telencephalon3.27e-8532
neural plate4.05e-8582
presumptive neural plate4.05e-8582
neurectoderm1.31e-8086
pre-chordal neural plate6.05e-7561
cerebral cortex1.54e-6525
pallium1.54e-6525
ecto-epithelium1.46e-64104
regional part of cerebral cortex2.55e-5822
adult organism5.84e-58114
neocortex1.69e-5220
ectoderm-derived structure6.86e-51171
ectoderm6.86e-51171
presumptive ectoderm6.86e-51171
structure with developmental contribution from neural crest1.79e-50132
organ system subdivision6.55e-39223
tube3.00e-29192
neural nucleus1.07e-259
nucleus of brain1.07e-259
basal ganglion1.32e-259
nuclear complex of neuraxis1.32e-259
aggregate regional part of brain1.32e-259
collection of basal ganglia1.32e-259
cerebral subcortex1.32e-259
anatomical conduit4.55e-23240
anatomical cluster1.96e-22373
telencephalic nucleus1.15e-207
diencephalon1.22e-207
future diencephalon1.22e-207
gyrus1.65e-176
posterior neural tube2.44e-1715
chordal neural plate2.44e-1715
brainstem1.24e-166
parietal lobe7.16e-165
occipital lobe1.82e-155
limbic system2.68e-155
epithelium1.78e-14306
cell layer3.27e-14309
temporal lobe5.51e-146
multi-tissue structure1.10e-13342
corpus striatum6.53e-134
striatum6.53e-134
ventral part of telencephalon6.53e-134
future corpus striatum6.53e-134
gland of diencephalon2.50e-124
neuroendocrine gland2.50e-124
organ part3.48e-12218
regional part of diencephalon9.51e-124
segmental subdivision of hindbrain1.44e-1012
hindbrain1.44e-1012
presumptive hindbrain1.44e-1012
caudate-putamen5.53e-103
dorsal striatum5.53e-103
spinal cord5.87e-103
dorsal region element5.87e-103
dorsum5.87e-103
frontal cortex9.76e-103
segmental subdivision of nervous system1.12e-0913
embryo2.61e-09592
medulla oblongata2.97e-093
myelencephalon2.97e-093
future myelencephalon2.97e-093
developing anatomical structure3.98e-09581
organ4.43e-09503
pons4.44e-093
germ layer9.31e-09560
germ layer / neural crest9.31e-09560
embryonic tissue9.31e-09560
presumptive structure9.31e-09560
germ layer / neural crest derived structure9.31e-09560
epiblast (generic)9.31e-09560
embryonic structure1.37e-08564
anatomical system4.63e-08624
anatomical group5.04e-08625
pituitary gland8.88e-082
Ammon's horn2.01e-072
lobe parts of cerebral cortex2.01e-072
hippocampal formation2.01e-072
limbic lobe2.01e-072
caudate nucleus3.50e-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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
RAD21#588536.21302033727380.007751055068811640.0318818652408971
SRF#672238.278306957300690.003404846073776150.0173538977648288



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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