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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!7.65e-46!94;UBERON:0001016!7.65e-46!94;UBERON:0001017!1.40e-44!82;UBERON:0001049!1.83e-44!57;UBERON:0005068!1.83e-44!57;UBERON:0006241!1.83e-44!57;UBERON:0007135!1.83e-44!57;UBERON:0005743!2.93e-44!86;UBERON:0000955!1.82e-37!69;UBERON:0006238!1.82e-37!69;UBERON:0002616!2.33e-36!59;UBERON:0002780!2.67e-36!41;UBERON:0001890!2.67e-36!41;UBERON:0006240!2.67e-36!41;UBERON:0003075!6.02e-36!86;UBERON:0007284!6.02e-36!86;UBERON:0002346!1.13e-35!90;UBERON:0003080!4.62e-35!42;UBERON:0007023!1.55e-34!115;UBERON:0001893!3.28e-30!34;UBERON:0002020!4.18e-30!34;UBERON:0003528!4.18e-30!34;UBERON:0002791!4.73e-29!33;UBERON:0001869!2.09e-28!32;UBERON:0003056!6.99e-27!61;UBERON:0002619!5.74e-26!22;UBERON:0000924!1.50e-24!173;UBERON:0006601!1.50e-24!173;UBERON:0004121!2.83e-24!169;UBERON:0001950!7.80e-24!20;UBERON:0000956!8.11e-22!25;UBERON:0000203!8.11e-22!25;UBERON:0000153!1.60e-20!129;UBERON:0007811!1.60e-20!129;UBERON:0000033!5.24e-20!123;UBERON:0003076!2.18e-10!15;UBERON:0003057!2.18e-10!15;UBERON:0002420!6.01e-10!9;UBERON:0007245!6.01e-10!9;UBERON:0010009!6.01e-10!9;UBERON:0010011!6.01e-10!9;UBERON:0000454!6.01e-10!9;UBERON:0001871!6.14e-10!7;UBERON:0002308!1.03e-09!9;UBERON:0000125!1.03e-09!9;UBERON:0004732!1.02e-08!13;UBERON:0000483!1.18e-08!309;UBERON:0000025!2.23e-08!194;UBERON:0000200!2.33e-08!6;UBERON:0000119!2.52e-08!312;UBERON:0009663!8.91e-08!7;UBERON:0004733!8.97e-08!12;UBERON:0002028!8.97e-08!12;UBERON:0007277!8.97e-08!12;UBERON:0000475!1.61e-07!365;UBERON:0001894!1.97e-07!7;UBERON:0006222!1.97e-07!7;UBERON:0001872!4.92e-07!5;UBERON:0002298!5.66e-07!8;UBERON:0000349!6.00e-07!5
|ontology_enrichment_uberon=UBERON:0000073!7.65e-46!94;UBERON:0001016!7.65e-46!94;UBERON:0001017!1.40e-44!82;UBERON:0001049!1.83e-44!57;UBERON:0005068!1.83e-44!57;UBERON:0006241!1.83e-44!57;UBERON:0007135!1.83e-44!57;UBERON:0005743!2.93e-44!86;UBERON:0000955!1.82e-37!69;UBERON:0006238!1.82e-37!69;UBERON:0002616!2.33e-36!59;UBERON:0002780!2.67e-36!41;UBERON:0001890!2.67e-36!41;UBERON:0006240!2.67e-36!41;UBERON:0003075!6.02e-36!86;UBERON:0007284!6.02e-36!86;UBERON:0002346!1.13e-35!90;UBERON:0003080!4.62e-35!42;UBERON:0007023!1.55e-34!115;UBERON:0001893!3.28e-30!34;UBERON:0002020!4.18e-30!34;UBERON:0003528!4.18e-30!34;UBERON:0002791!4.73e-29!33;UBERON:0001869!2.09e-28!32;UBERON:0003056!6.99e-27!61;UBERON:0002619!5.74e-26!22;UBERON:0000924!1.50e-24!173;UBERON:0006601!1.50e-24!173;UBERON:0004121!2.83e-24!169;UBERON:0001950!7.80e-24!20;UBERON:0000956!8.11e-22!25;UBERON:0000203!8.11e-22!25;UBERON:0000153!1.60e-20!129;UBERON:0007811!1.60e-20!129;UBERON:0000033!5.24e-20!123;UBERON:0003076!2.18e-10!15;UBERON:0003057!2.18e-10!15;UBERON:0002420!6.01e-10!9;UBERON:0007245!6.01e-10!9;UBERON:0010009!6.01e-10!9;UBERON:0010011!6.01e-10!9;UBERON:0000454!6.01e-10!9;UBERON:0001871!6.14e-10!7;UBERON:0002308!1.03e-09!9;UBERON:0000125!1.03e-09!9;UBERON:0004732!1.02e-08!13;UBERON:0000483!1.18e-08!309;UBERON:0000025!2.23e-08!194;UBERON:0000200!2.33e-08!6;UBERON:0000119!2.52e-08!312;UBERON:0009663!8.91e-08!7;UBERON:0004733!8.97e-08!12;UBERON:0002028!8.97e-08!12;UBERON:0007277!8.97e-08!12;UBERON:0000475!1.61e-07!365;UBERON:0001894!1.97e-07!7;UBERON:0006222!1.97e-07!7;UBERON:0001872!4.92e-07!5;UBERON:0002298!5.66e-07!8;UBERON:0000349!6.00e-07!5
|tf_chipseq_enrich=GATA3#2625;3:20.4273872679045:0.000192441557625832:0.00232083185183421!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157303311109794!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322882269301217!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244755930353214
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737069,0.00112766,6.0891e-10,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.000447146,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.00648069,0.159873,0.142462,0.143935,0.332403,0.0379537,0.000812168,0.187953,0.051459,0.114868,0.0726892,0.18732,0.00740893,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.0139335,0.36316,0.0625685,0.124464,0.186295,0.173134,0.101893,0.142875,0.167635,0.171311,0.20386,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.0705088,0.267945,0.0150607,0.278645,0.365775,0.155708,0.248017,0.22995,1.53275e-05,0.0760151,0.0629459,0.00483066,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.014226,0.226359,0.626334,1.37583e-08,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,7.93081e-06,8.2505e-05,0.251078,0.000372899,0.00043676,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.0689994,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.00631475,0.000238291,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.32805,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,3.17817e-18,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.0161134,0.514243,0.459091,0.54832,0.502211,0.296013,0.649813,0.537932,0.0247432,0.523209,0.00885937,0.25423,0.490559,0.45013,0.500698,0.0272171,0.0302459,0.0510811,1.42941e-05,0.0943307,0.483077,0.590496,0.603763,0.541914,0.627201,0.765905,0.00207528,0.290703,0.622694,0.0413786,0.00448166,0.360199,0.608176,0.657141,0.099511,0.365494,0.212703,0.56318,0.364079,0.315494,0.579886,0.421038,0.569409,0.328518,0.545608,0.310552,0.143396,0.483764,0.00961647,0.453065,0.209437,0.11765,0.161672,0.0141441,0.169076,0.12974,0.336867,0.579004,0.150592,0.546688,0.315519,0.261575,0.257956,0.264245,0.379063,0.326516,0.16985,0.436016,0.136753,0.202522,0.183837,0.507324,0.126097,1.47028e-05,0.442469,0.212239,0.00548706,0.156999,0.35974,0.025886,0.39549,0.234254,0.357409,0.146291,0.721266,0.50338,0.620526,0.404625,0.759068,0.424691,0.715362,0.479581,0.62689,0.0682871,0.642173,0.284496,0.512545,0.512178,0.563206,0.103692,0.684899,0.263302,0.552023,0.180735,0.189249,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.102502,0.463987,0.627953,0.503881,0.454761,0.639483,0.0295677,0.452129,0.301581,0.261657,0.346776,0.466529,0.187223,0.438176,0.349112,0.741477,0.385425,0.307816,0.461541,0.386339,0.382854,0.0650585,0.478745,0.611661,0.319747,0.475047,0.197104,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.347466,0.387134,0.559969,0.358813,0.303004,0.574252,0.0317703,0.346636,0.457747,0.348802,0.476541,0.579645,0.447581,0.42505,0.254628,0.00183295,0.139532,0.416962,0.0806585,0.378333,0.152547,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.00871319,0.231754,0.249415,0.283107,0.0453548,0.427316,0.391071,0.00037101,0.25563,0.240967,0.160955,0.256687,0.0432189,0.00782177,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.0450921,0.0887542,0.267811,0.338547,0.147872,0.0191872,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,7.46256e-05,0.259328,0.437467,0.201057,0.0130187,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.000782065,0.387837,0.233244,0.207281,0.327401,0.195748,0.0429696,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.0725176,0.279739,0.108118,0.000269064,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.000809519,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.0571822,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.000944652,0.0936726,0.343425,0.132374,0.2851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}}
}}

Revision as of 14:21, 5 September 2012


Full id: C2733_small_medial_medulloblastoma_paracentral_frontal_parietal_smallcell



Phase1 CAGE Peaks

Hg19::chr3:179754706..179754732,-p4@PEX5L
Hg19::chr3:179754733..179754773,-p3@PEX5L
Hg19::chr3:179754789..179754804,-p6@PEX5L
Hg19::chr3:179754806..179754872,-p2@PEX5L


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system7.65e-4694
nervous system7.65e-4694
central nervous system1.40e-4482
neural tube1.83e-4457
neural rod1.83e-4457
future spinal cord1.83e-4457
neural keel1.83e-4457
brain1.82e-3769
future brain1.82e-3769
regional part of brain2.33e-3659
regional part of forebrain2.67e-3641
forebrain2.67e-3641
future forebrain2.67e-3641
neural plate6.02e-3686
presumptive neural plate6.02e-3686
neurectoderm1.13e-3590
anterior neural tube4.62e-3542
adult organism1.55e-34115
telencephalon3.28e-3034
gray matter4.18e-3034
brain grey matter4.18e-3034
regional part of telencephalon4.73e-2933
cerebral hemisphere2.09e-2832
pre-chordal neural plate6.99e-2761
regional part of cerebral cortex5.74e-2622
ectoderm1.50e-24173
presumptive ectoderm1.50e-24173
ectoderm-derived structure2.83e-24169
neocortex7.80e-2420
cerebral cortex8.11e-2225
pallium8.11e-2225
anterior region of body1.60e-20129
craniocervical region1.60e-20129
head5.24e-20123
posterior neural tube2.18e-1015
chordal neural plate2.18e-1015
basal ganglion6.01e-109
nuclear complex of neuraxis6.01e-109
aggregate regional part of brain6.01e-109
collection of basal ganglia6.01e-109
cerebral subcortex6.01e-109
temporal lobe6.14e-107
nucleus of brain1.03e-099
neural nucleus1.03e-099
segmental subdivision of nervous system1.02e-0813
epithelium1.18e-08309
tube2.23e-08194
gyrus2.33e-086
cell layer2.52e-08312
telencephalic nucleus8.91e-087
segmental subdivision of hindbrain8.97e-0812
hindbrain8.97e-0812
presumptive hindbrain8.97e-0812
organism subdivision1.61e-07365
diencephalon1.97e-077
future diencephalon1.97e-077
parietal lobe4.92e-075
brainstem5.66e-078
limbic system6.00e-075


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
GATA3#2625320.42738726790450.0001924415576258320.00232083185183421
REST#597849.650028716128020.0001152825614219170.00157303311109794
TAF1#687243.343046285745290.008005664898701650.0322882269301217
TBP#690843.706770687096390.005296377814784350.0244755930353214



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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