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Coexpression cluster:C2230: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.87e-71!57;UBERON:0005068!2.87e-71!57;UBERON:0006241!2.87e-71!57;UBERON:0007135!2.87e-71!57;UBERON:0001017!1.85e-63!82;UBERON:0000073!4.13e-63!94;UBERON:0001016!4.13e-63!94;UBERON:0005743!1.25e-62!86;UBERON:0002616!1.06e-61!59;UBERON:0000955!8.34e-56!69;UBERON:0006238!8.34e-56!69;UBERON:0003075!1.11e-52!86;UBERON:0007284!1.11e-52!86;UBERON:0002780!5.78e-50!41;UBERON:0001890!5.78e-50!41;UBERON:0006240!5.78e-50!41;UBERON:0002346!9.04e-50!90;UBERON:0003080!1.39e-48!42;UBERON:0002020!2.71e-46!34;UBERON:0003528!2.71e-46!34;UBERON:0001893!3.59e-46!34;UBERON:0001869!7.58e-46!32;UBERON:0002619!1.06e-44!22;UBERON:0002791!8.54e-44!33;UBERON:0001950!2.66e-40!20;UBERON:0000956!8.39e-39!25;UBERON:0000203!8.39e-39!25;UBERON:0007023!3.40e-38!115;UBERON:0003056!2.50e-35!61;UBERON:0004121!5.23e-32!169;UBERON:0000924!6.15e-31!173;UBERON:0006601!6.15e-31!173;UBERON:0000033!2.00e-29!123;UBERON:0000153!6.87e-29!129;UBERON:0007811!6.87e-29!129;UBERON:0003076!4.20e-23!15;UBERON:0003057!4.20e-23!15;UBERON:0004733!9.47e-21!12;UBERON:0002028!9.47e-21!12;UBERON:0007277!9.47e-21!12;UBERON:0004732!5.77e-19!13;UBERON:0000025!3.06e-17!194;UBERON:0000200!1.00e-15!6;UBERON:0002680!6.81e-14!9;UBERON:0001895!6.81e-14!9;UBERON:0010092!6.81e-14!9;UBERON:0001872!2.15e-13!5;UBERON:0002021!5.17e-13!5;UBERON:0000064!5.46e-12!219;UBERON:0002298!8.96e-12!8;UBERON:0000483!9.29e-12!309;UBERON:0000477!1.63e-11!286;UBERON:0000119!1.64e-11!312;UBERON:0004111!1.73e-11!241;UBERON:0001871!8.37e-11!7;UBERON:0002308!3.02e-09!9;UBERON:0000125!3.02e-09!9;UBERON:0000475!6.89e-09!365;UBERON:0001896!7.30e-09!3;UBERON:0005290!7.30e-09!3;UBERON:0010096!7.30e-09!3;UBERON:0000988!7.89e-09!3;UBERON:0000349!2.77e-08!5;UBERON:0002771!3.07e-08!3;UBERON:0002037!2.30e-07!6;UBERON:0006215!2.30e-07!6
|ontology_enrichment_uberon=UBERON:0001049!6.14e-54!56;UBERON:0005068!6.14e-54!56;UBERON:0006241!6.14e-54!56;UBERON:0007135!6.14e-54!56;UBERON:0000073!1.34e-52!53;UBERON:0002616!1.34e-52!53;UBERON:0001017!4.44e-45!81;UBERON:0001016!3.59e-43!89;UBERON:0000955!5.72e-43!68;UBERON:0006238!5.72e-43!68;UBERON:0001950!7.13e-41!20;UBERON:0003075!2.25e-38!82;UBERON:0007284!2.25e-38!82;UBERON:0002619!4.41e-37!22;UBERON:0002346!2.37e-36!86;UBERON:0003528!7.73e-36!34;UBERON:0002020!7.73e-36!34;UBERON:0001893!8.71e-36!34;UBERON:0001869!1.33e-33!32;UBERON:0000956!1.73e-32!25;UBERON:0000203!1.73e-32!25;UBERON:0010371!1.09e-31!104;UBERON:0002780!3.11e-29!41;UBERON:0001890!3.11e-29!41;UBERON:0003080!3.11e-29!41;UBERON:0006240!3.11e-29!41;UBERON:0002791!4.85e-29!32;UBERON:0007023!9.32e-29!114;UBERON:0004733!2.50e-28!12;UBERON:0002028!2.50e-28!12;UBERON:0007277!2.50e-28!12;UBERON:0003076!3.86e-28!15;UBERON:0003057!3.86e-28!15;UBERON:0004732!4.69e-26!13;UBERON:0010314!8.76e-24!132;UBERON:0004121!2.29e-23!171;UBERON:0000924!2.29e-23!171;UBERON:0006601!2.29e-23!171;UBERON:0000200!1.08e-22!6;UBERON:0002298!1.29e-22!6;UBERON:0002680!8.55e-22!9;UBERON:0001895!8.55e-22!9;UBERON:0010092!8.55e-22!9;UBERON:0003056!3.60e-21!61;UBERON:0011216!7.82e-18!223;UBERON:0001872!9.54e-18!5;UBERON:0000988!4.69e-17!3;UBERON:0001870!9.96e-17!3;UBERON:0000025!1.24e-14!192;UBERON:0000064!3.32e-12!218;UBERON:0002148!1.18e-11!2;UBERON:0006331!1.18e-11!2;UBERON:0009662!1.18e-11!2;UBERON:0002702!1.24e-11!2;UBERON:0004111!1.44e-10!240;UBERON:0002037!4.43e-09!6;UBERON:0006215!4.43e-09!6;UBERON:0000477!6.18e-09!373;UBERON:0000483!1.11e-08!306;UBERON:0000119!1.54e-08!309;UBERON:0001896!3.31e-08!3;UBERON:0005290!3.31e-08!3;UBERON:0010096!3.31e-08!3;UBERON:0001871!1.78e-07!6;UBERON:0002902!5.13e-07!1;UBERON:0009899!5.13e-07!1;UBERON:0002581!5.43e-07!1;UBERON:0007190!5.75e-07!1;UBERON:0002022!7.19e-07!1
|tf_chipseq_enrich=SUZ12#23512;3:37.5868356832972:3.12785741999833e-05:0.000631491013120443!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279624854944839
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69,0.357807,0.0173365,0.178782,0.019419,0.0866228,0.0408454,0.044355,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.0593965,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.112715,0.281453,0.0522771,0.0787278,0.164404,0.159873,0.142462,0.143935,0.332403,0.0379537,0.0230803,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.017951,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.186295,0.173134,0.101893,0.142875,0.167635,0.171311,0.458838,0.0465855,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.107849,0.0560157,0.278645,0.0769795,0.000712178,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.22476,0.165788,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.0213072,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.0448074,0.0754883,0.299492,0.100006,0.0756617,0.197817,0.251078,0.279874,0.133127,0.0988568,0.223717,0.107609,0.196838,0.0826805,0.246601,0.193021,0.000422824,0.202165,0.0946865,0.120618,0.079499,0.18762,0.0205193,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.0127656,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.0639386,0.0567624,0.182843,0.130771,0.00777449,0.135777,0.147842,0.0339286,0.217363,0.119015,0.32805,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.248134,0.0780061,0.315336,0.230477,0.279823,0.295555,0.154895,0.0420826,0.0478217,0.158752,0.170854,0.0575231,0.174063,0.163504,0.1267,0.54832,0.0338476,0.296013,0.0221603,0.537932,0.459994,0.523209,0.0465928,0.25423,0.490559,0.121268,0.153911,0.135135,0.322168,0.160788,0.529642,0.0301009,0.14198,0.590496,0.23695,0.00835925,0.627201,0.526336,0.514482,0.290703,0.0757071,0.138899,0.139104,0.360199,0.241059,0.0937029,0.0323345,0.365494,0.212703,0.56318,0.364079,0.315494,0.0575699,0.104625,0.569409,0.0610883,0.187186,0.310552,0.00110665,0.142433,0.00961647,0.00493585,0.209437,0.11765,0.401218,0.0651244,0.0221843,0.0255132,0.00127982,0.214786,0.0565519,0.0112416,0.137711,0.0376583,0.257956,0.264245,0.379063,0.326516,0.16985,0.436016,0.475063,0.202522,0.183837,0.158557,0.126097,0.0912229,0.116739,0.212239,0.294954,0.156999,0.0742603,0.667777,0.00179415,0.234254,0.357409,0.000254095,0.365184,0.00575146,0.252827,0.404625,0.759068,0.424691,0.0388817,0.479581,0.259048,0.172925,0.00410246,0.00487493,0.16228,0.512178,0.201413,0.00957951,0.110875,0.263302,0.552023,0.180735,0.439629,0.0252414,0.0355932,0.109605,0.0924199,0.0585759,0.226491,0.0175854,0.129731,0.260097,0.0342559,0.0237654,0.0840572,0.00471559,0.122467,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.0485429,0.0134085,0.0531591,0.461541,0.386339,0.0849889,0.0141241,0.478745,0.07062,0.319747,0.475047,0.197104,0.241014,0.282281,0.0159965,0.2536,0.246827,0.202347,0.12664,0.387134,0.050476,0.358813,0.000992912,0.574252,0.493455,0.00937114,0.00360135,0.348802,0.476541,0.0574793,0.022473,0.00252179,0.254628,0.000319058,0.0286377,0.416962,0.632833,0.378333,0.0473484,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.0613938,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.0582227,0.133173,0.325254,0.266651,0.0460393,0.231754,0.249415,0.283107,0.285648,0.10809,0.391071,0.0433305,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.0293669,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.0651578,0.147872,0.0191872,0.0480552,0.210125,0.0478543,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.042497,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.0078603,0.0627948,0.262022,0.00433276,0.0392261,0.184534,0.248707,0.31749,0.15156,0.287598,0.0554083,0.223773,0.00354126,0.181895,0.035332,0.30702,0.202977,0.170837,0.0604859,0.28543,0.0268645,0.00239762,0.127111,0.259989,0.390754,0.355805,0.0433915,0.108118,0.0371525,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.0944985,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.0634867,0.325785,0.257476,0.291176,0.376537,0.322827,0.0286371,0.0739466,0.335984,0.171704,0.208256,0.265058,0.256405,0.0756763,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.0729297,0.0104945,0.318525,0.213257,0.287217,0.122782,0.0991993,0.0465068,0.266974,0.00825997,0.112897,0.0926658,0.222091,0.205977,0.34423,0.0936726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}}
}}

Revision as of 12:13, 19 October 2012


Full id: C2230_pons_cerebellum_merkel_occipital_paracentral_medulla_postcentral



Phase1 CAGE Peaks

Hg19::chr12:65218487..65218501,+p7@TBC1D30
Hg19::chr21:31312141..31312150,-p9@GRIK1
Hg19::chr3:56809691..56809715,-p12@ARHGEF3
Hg19::chr9:135457981..135458003,+p1@BARHL1


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:0051966regulation of synaptic transmission, glutamatergic0.0211920527965079
GO:0035249synaptic transmission, glutamatergic0.0211920527965079
GO:0015277kainate selective glutamate receptor activity0.0278006519143408
GO:0007399nervous system development0.0278006519143408
GO:0050804regulation of synaptic transmission0.0278006519143408
GO:0051969regulation of transmission of nerve impulse0.0278006519143408
GO:0007270nerve-nerve synaptic transmission0.0278006519143408
GO:0007215glutamate signaling pathway0.0278006519143408
GO:0031644regulation of neurological process0.0294152147210372
GO:0001764neuron migration0.0344016163843688
GO:0004970ionotropic glutamate receptor activity0.0344016163843688
GO:0005234extracellular-glutamate-gated ion channel activity0.0344016163843688
GO:0050877neurological system process0.0376508935600235
GO:0050789regulation of biological process0.0457532010981795
GO:0003008system process0.0457532010981795
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0457532010981795
GO:0048731system development0.0457532010981795



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 tube6.14e-5456
neural rod6.14e-5456
future spinal cord6.14e-5456
neural keel6.14e-5456
regional part of nervous system1.34e-5253
regional part of brain1.34e-5253
central nervous system4.44e-4581
nervous system3.59e-4389
brain5.72e-4368
future brain5.72e-4368
neocortex7.13e-4120
neural plate2.25e-3882
presumptive neural plate2.25e-3882
regional part of cerebral cortex4.41e-3722
neurectoderm2.37e-3686
brain grey matter7.73e-3634
gray matter7.73e-3634
telencephalon8.71e-3634
cerebral hemisphere1.33e-3332
cerebral cortex1.73e-3225
pallium1.73e-3225
ecto-epithelium1.09e-31104
regional part of forebrain3.11e-2941
forebrain3.11e-2941
anterior neural tube3.11e-2941
future forebrain3.11e-2941
regional part of telencephalon4.85e-2932
adult organism9.32e-29114
segmental subdivision of hindbrain2.50e-2812
hindbrain2.50e-2812
presumptive hindbrain2.50e-2812
posterior neural tube3.86e-2815
chordal neural plate3.86e-2815
segmental subdivision of nervous system4.69e-2613
structure with developmental contribution from neural crest8.76e-24132
ectoderm-derived structure2.29e-23171
ectoderm2.29e-23171
presumptive ectoderm2.29e-23171
gyrus1.08e-226
brainstem1.29e-226
regional part of metencephalon8.55e-229
metencephalon8.55e-229
future metencephalon8.55e-229
pre-chordal neural plate3.60e-2161
organ system subdivision7.82e-18223
parietal lobe9.54e-185
pons4.69e-173
frontal cortex9.96e-173
tube1.24e-14192
organ part3.32e-12218
locus ceruleus1.18e-112
brainstem nucleus1.18e-112
hindbrain nucleus1.18e-112
middle frontal gyrus1.24e-112
anatomical conduit1.44e-10240
cerebellum4.43e-096
rhombic lip4.43e-096
anatomical cluster6.18e-09373
epithelium1.11e-08306
cell layer1.54e-08309
medulla oblongata3.31e-083
myelencephalon3.31e-083
future myelencephalon3.31e-083
temporal lobe1.78e-076
occipital pole5.13e-071
pole of cerebral hemisphere5.13e-071
postcentral gyrus5.43e-071
paracentral gyrus5.75e-071
insula7.19e-071


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
SUZ12#23512337.58683568329723.12785741999833e-050.000631491013120443
ZNF263#1012736.166381227758010.006539814347975980.0279624854944839



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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