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Coexpression cluster:C2356: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!3.27e-53!57;UBERON:0005068!3.27e-53!57;UBERON:0006241!3.27e-53!57;UBERON:0007135!3.27e-53!57;UBERON:0001017!3.74e-46!82;UBERON:0005743!4.62e-45!86;UBERON:0007023!2.05e-44!115;UBERON:0002616!5.98e-44!59;UBERON:0000955!6.86e-44!69;UBERON:0006238!6.86e-44!69;UBERON:0002780!7.76e-43!41;UBERON:0001890!7.76e-43!41;UBERON:0006240!7.76e-43!41;UBERON:0003080!1.69e-41!42;UBERON:0000073!1.96e-40!94;UBERON:0001016!1.96e-40!94;UBERON:0003075!2.75e-38!86;UBERON:0007284!2.75e-38!86;UBERON:0002346!1.02e-35!90;UBERON:0002020!7.09e-34!34;UBERON:0003528!7.09e-34!34;UBERON:0001893!2.19e-33!34;UBERON:0002791!3.34e-32!33;UBERON:0001869!3.75e-31!32;UBERON:0003056!2.82e-29!61;UBERON:0002619!1.83e-27!22;UBERON:0000956!2.79e-25!25;UBERON:0000203!2.79e-25!25;UBERON:0001950!6.30e-25!20;UBERON:0000033!7.09e-25!123;UBERON:0000153!8.47e-24!129;UBERON:0007811!8.47e-24!129;UBERON:0004121!2.18e-22!169;UBERON:0000924!2.27e-21!173;UBERON:0006601!2.27e-21!173;UBERON:0000025!1.93e-17!194;UBERON:0004111!9.50e-16!241;UBERON:0003076!1.68e-12!15;UBERON:0003057!1.68e-12!15;UBERON:0000477!3.08e-12!286;UBERON:0000064!4.86e-12!219;UBERON:0001894!5.78e-11!7;UBERON:0006222!5.78e-11!7;UBERON:0002308!5.86e-10!9;UBERON:0000125!5.86e-10!9;UBERON:0002420!1.35e-09!9;UBERON:0007245!1.35e-09!9;UBERON:0010009!1.35e-09!9;UBERON:0010011!1.35e-09!9;UBERON:0000454!1.35e-09!9;UBERON:0004733!3.06e-09!12;UBERON:0002028!3.06e-09!12;UBERON:0007277!3.06e-09!12;UBERON:0000062!3.65e-09!511;UBERON:0000200!4.20e-09!6;UBERON:0000483!5.29e-09!309;UBERON:0000119!1.02e-08!312;UBERON:0001871!1.21e-08!7;UBERON:0004732!2.43e-08!13;UBERON:0001872!5.12e-08!5;UBERON:0002680!6.24e-08!9;UBERON:0001895!6.24e-08!9;UBERON:0010092!6.24e-08!9;UBERON:0002021!8.49e-08!5;UBERON:0000349!1.34e-07!5;UBERON:0009663!2.51e-07!7;UBERON:0000475!3.11e-07!365;UBERON:0000481!3.25e-07!347;UBERON:0003296!4.73e-07!4;UBERON:0010133!4.73e-07!4;UBERON:0002298!9.32e-07!8
|ontology_enrichment_uberon=UBERON:0001049!3.27e-53!57;UBERON:0005068!3.27e-53!57;UBERON:0006241!3.27e-53!57;UBERON:0007135!3.27e-53!57;UBERON:0001017!3.74e-46!82;UBERON:0005743!4.62e-45!86;UBERON:0007023!2.05e-44!115;UBERON:0002616!5.98e-44!59;UBERON:0000955!6.86e-44!69;UBERON:0006238!6.86e-44!69;UBERON:0002780!7.76e-43!41;UBERON:0001890!7.76e-43!41;UBERON:0006240!7.76e-43!41;UBERON:0003080!1.69e-41!42;UBERON:0000073!1.96e-40!94;UBERON:0001016!1.96e-40!94;UBERON:0003075!2.75e-38!86;UBERON:0007284!2.75e-38!86;UBERON:0002346!1.02e-35!90;UBERON:0002020!7.09e-34!34;UBERON:0003528!7.09e-34!34;UBERON:0001893!2.19e-33!34;UBERON:0002791!3.34e-32!33;UBERON:0001869!3.75e-31!32;UBERON:0003056!2.82e-29!61;UBERON:0002619!1.83e-27!22;UBERON:0000956!2.79e-25!25;UBERON:0000203!2.79e-25!25;UBERON:0001950!6.30e-25!20;UBERON:0000033!7.09e-25!123;UBERON:0000153!8.47e-24!129;UBERON:0007811!8.47e-24!129;UBERON:0004121!2.18e-22!169;UBERON:0000924!2.27e-21!173;UBERON:0006601!2.27e-21!173;UBERON:0000025!1.93e-17!194;UBERON:0004111!9.50e-16!241;UBERON:0003076!1.68e-12!15;UBERON:0003057!1.68e-12!15;UBERON:0000477!3.08e-12!286;UBERON:0000064!4.86e-12!219;UBERON:0001894!5.78e-11!7;UBERON:0006222!5.78e-11!7;UBERON:0002308!5.86e-10!9;UBERON:0000125!5.86e-10!9;UBERON:0002420!1.35e-09!9;UBERON:0007245!1.35e-09!9;UBERON:0010009!1.35e-09!9;UBERON:0010011!1.35e-09!9;UBERON:0000454!1.35e-09!9;UBERON:0004733!3.06e-09!12;UBERON:0002028!3.06e-09!12;UBERON:0007277!3.06e-09!12;UBERON:0000062!3.65e-09!511;UBERON:0000200!4.20e-09!6;UBERON:0000483!5.29e-09!309;UBERON:0000119!1.02e-08!312;UBERON:0001871!1.21e-08!7;UBERON:0004732!2.43e-08!13;UBERON:0001872!5.12e-08!5;UBERON:0002680!6.24e-08!9;UBERON:0001895!6.24e-08!9;UBERON:0010092!6.24e-08!9;UBERON:0002021!8.49e-08!5;UBERON:0000349!1.34e-07!5;UBERON:0009663!2.51e-07!7;UBERON:0000475!3.11e-07!365;UBERON:0000481!3.25e-07!347;UBERON:0003296!4.73e-07!4;UBERON:0010133!4.73e-07!4;UBERON:0002298!9.32e-07!8
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019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.00814638,0.0379537,0.0230803,6.6314e-05,0.051459,0.00686557,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.0883765,0.36316,0.0625685,0.124464,0.0454742,0.173134,0.101893,0.142875,0.167635,0.171311,0.787798,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.535567,0.415079,0.278645,0.0769795,0.155708,0.000219214,0.22995,0.00463504,0.0760151,0.0629459,0.0300882,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.0114526,0.0471607,0.163865,0.226359,0.960445,0.00459675,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,1.7643e-05,0.0994829,0.0604041,0.144185,0.0925862,0.0466818,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.00776177,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.0988568,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.240896,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.06079,0.135777,0.147842,0.0339286,0.217363,0.119015,0.32805,0.21618,0.243266,0.107021,0.0310605,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.0338237,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.0161134,0.514243,0.459091,0.54832,0.502211,0.296013,0.649813,0.0434876,0.459994,0.523209,0.548059,0.25423,0.490559,0.121268,0.500698,0.472542,0.685908,0.747471,0.174869,0.244786,0.483077,0.224887,0.00264315,0.184287,0.0778742,0.304145,0.142078,0.290703,0.622694,0.366999,0.478691,0.360199,0.608176,0.657141,0.824761,0.365494,0.212703,0.0515679,0.364079,0.680099,0.0575699,0.421038,0.569409,0.328518,0.545608,0.310552,0.865054,0.483764,0.528161,0.19941,0.209437,0.284058,0.161672,0.598945,0.630688,0.464001,0.871271,0.0019793,0.870272,0.839946,0.860705,0.261575,0.257956,0.264245,0.379063,0.00767615,0.0391986,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,0.599068,0.0408829,0.50338,0.620526,0.404625,0.759068,0.424691,0.357704,0.479581,0.259048,0.36666,0.642173,0.284496,0.512545,0.512178,0.563206,0.527709,0.684899,0.263302,0.552023,0.180735,0.775168,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.503881,0.454761,0.271678,0.483658,0.452129,0.301581,0.0376831,0.00938391,0.466529,0.545655,0.438176,0.0696091,0.391754,0.385425,0.307816,0.128211,0.386339,0.382854,0.598787,0.478745,0.24434,0.319747,0.475047,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.70712,0.387134,0.559969,0.358813,0.303004,0.574252,0.493455,0.346636,0.457747,0.348802,0.137708,0.579645,0.119749,0.42505,0.254628,0.713293,0.479347,0.416962,0.0806585,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.00728552,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.00871319,0.231754,0.0340704,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.0469743,0.353147,0.112422,0.170886,0.00399713,0.315656,0.00489571,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.0478543,0.00207568,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.0311922,0.095257,0.328852,0.332769,0.0377937,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.0102294,0.279739,0.108118,0.259901,0.139723,1.14424e-06,0.0710478,0.196248,0.00545806,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.000497863,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.00593844,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.00917587,0.285122,0.22741,0.203996,0.276721,0.000697427,0.264707,0.450113
}}
}}

Revision as of 12:51, 5 September 2012


Full id: C2356_cerebellum_pineal_small_pons_medial_globus_brain



Phase1 CAGE Peaks

Hg19::chr15:91643424..91643440,+p11@SV2B
Hg19::chr6:166253676..166253680,-p@chr6:166253676..166253680
-
Hg19::chr7:26415791..26415799,-p2@ENST00000451368
Hg19::chr7:26415806..26415813,-p3@ENST00000451368


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:0001669acrosome0.0219003885552808
GO:0008021synaptic vesicle0.0237254209348875
GO:0006836neurotransmitter transport0.0237254209348875
GO:0030136clathrin-coated vesicle0.0262348404568468
GO:0030135coated vesicle0.0263326100486115
GO:0005764lysosome0.0263326100486115
GO:0000323lytic vacuole0.0263326100486115
GO:0005773vacuole0.0265770340280231
GO:0016023cytoplasmic membrane-bound vesicle0.0303236149226965
GO:0031988membrane-bound vesicle0.0303236149226965
GO:0031410cytoplasmic vesicle0.0303236149226965
GO:0030054cell junction0.0303236149226965
GO:0031982vesicle0.0303236149226965



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 tube3.27e-5357
neural rod3.27e-5357
future spinal cord3.27e-5357
neural keel3.27e-5357
central nervous system3.74e-4682
adult organism2.05e-44115
regional part of brain5.98e-4459
brain6.86e-4469
future brain6.86e-4469
regional part of forebrain7.76e-4341
forebrain7.76e-4341
future forebrain7.76e-4341
anterior neural tube1.69e-4142
regional part of nervous system1.96e-4094
nervous system1.96e-4094
neural plate2.75e-3886
presumptive neural plate2.75e-3886
neurectoderm1.02e-3590
gray matter7.09e-3434
brain grey matter7.09e-3434
telencephalon2.19e-3334
regional part of telencephalon3.34e-3233
cerebral hemisphere3.75e-3132
pre-chordal neural plate2.82e-2961
regional part of cerebral cortex1.83e-2722
cerebral cortex2.79e-2525
pallium2.79e-2525
neocortex6.30e-2520
head7.09e-25123
anterior region of body8.47e-24129
craniocervical region8.47e-24129
ectoderm-derived structure2.18e-22169
ectoderm2.27e-21173
presumptive ectoderm2.27e-21173
tube1.93e-17194
anatomical conduit9.50e-16241
posterior neural tube1.68e-1215
chordal neural plate1.68e-1215
anatomical cluster3.08e-12286
organ part4.86e-12219
diencephalon5.78e-117
future diencephalon5.78e-117
nucleus of brain5.86e-109
neural nucleus5.86e-109
basal ganglion1.35e-099
nuclear complex of neuraxis1.35e-099
aggregate regional part of brain1.35e-099
collection of basal ganglia1.35e-099
cerebral subcortex1.35e-099
segmental subdivision of hindbrain3.06e-0912
hindbrain3.06e-0912
presumptive hindbrain3.06e-0912
organ3.65e-09511
gyrus4.20e-096
epithelium5.29e-09309
cell layer1.02e-08312
temporal lobe1.21e-087
segmental subdivision of nervous system2.43e-0813
parietal lobe5.12e-085
regional part of metencephalon6.24e-089
metencephalon6.24e-089
future metencephalon6.24e-089
occipital lobe8.49e-085
limbic system1.34e-075
telencephalic nucleus2.51e-077
organism subdivision3.11e-07365
multi-tissue structure3.25e-07347
gland of diencephalon4.73e-074
neuroendocrine gland4.73e-074
brainstem9.32e-078


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
ESR1#2099215.38430164807720.006065572629693510.026835649405768
SREBF1#6720223.50292472024410.002638454900768240.0145828530578606



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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