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Coexpression cluster:C2267: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.87e-47!115;UBERON:0000073!1.64e-41!94;UBERON:0001016!1.64e-41!94;UBERON:0005743!1.68e-40!86;UBERON:0001017!6.30e-39!82;UBERON:0001049!8.63e-39!57;UBERON:0005068!8.63e-39!57;UBERON:0006241!8.63e-39!57;UBERON:0007135!8.63e-39!57;UBERON:0002346!2.36e-37!90;UBERON:0003075!1.55e-34!86;UBERON:0007284!1.55e-34!86;UBERON:0002616!1.10e-33!59;UBERON:0000955!2.92e-32!69;UBERON:0006238!2.92e-32!69;UBERON:0003080!2.60e-29!42;UBERON:0002780!7.14e-29!41;UBERON:0001890!7.14e-29!41;UBERON:0006240!7.14e-29!41;UBERON:0000924!8.48e-27!173;UBERON:0006601!8.48e-27!173;UBERON:0002020!3.53e-25!34;UBERON:0003528!3.53e-25!34;UBERON:0001893!3.61e-25!34;UBERON:0004121!1.44e-24!169;UBERON:0002791!2.00e-24!33;UBERON:0001869!9.97e-24!32;UBERON:0003056!1.05e-23!61;UBERON:0000025!4.13e-23!194;UBERON:0000153!1.37e-19!129;UBERON:0007811!1.37e-19!129;UBERON:0000033!3.44e-19!123;UBERON:0000956!1.37e-18!25;UBERON:0000203!1.37e-18!25;UBERON:0002619!9.60e-18!22;UBERON:0004111!4.49e-17!241;UBERON:0000483!2.05e-16!309;UBERON:0000119!2.56e-16!312;UBERON:0001950!3.34e-16!20;UBERON:0000477!2.74e-14!286;UBERON:0000468!1.47e-13!659;UBERON:0000922!3.40e-12!612;UBERON:0000475!7.16e-12!365;UBERON:0000467!3.06e-11!625;UBERON:0000480!4.46e-11!626;UBERON:0000481!4.65e-11!347;UBERON:0003076!1.99e-10!15;UBERON:0003057!1.99e-10!15;UBERON:0000064!2.66e-10!219;UBERON:0002050!3.18e-10!605;UBERON:0005423!3.18e-10!605;UBERON:0000923!6.61e-10!604;UBERON:0005291!6.61e-10!604;UBERON:0006598!6.61e-10!604;UBERON:0002532!6.61e-10!604;UBERON:0004732!6.01e-09!13;UBERON:0004733!2.02e-08!12;UBERON:0002028!2.02e-08!12;UBERON:0007277!2.02e-08!12;UBERON:0002420!3.41e-08!9;UBERON:0007245!3.41e-08!9;UBERON:0010009!3.41e-08!9;UBERON:0010011!3.41e-08!9;UBERON:0000454!3.41e-08!9;UBERON:0002308!4.94e-08!9;UBERON:0000125!4.94e-08!9;UBERON:0000062!8.55e-08!511;UBERON:0001871!3.73e-07!7
|ontology_enrichment_uberon=UBERON:0007023!2.87e-47!115;UBERON:0000073!1.64e-41!94;UBERON:0001016!1.64e-41!94;UBERON:0005743!1.68e-40!86;UBERON:0001017!6.30e-39!82;UBERON:0001049!8.63e-39!57;UBERON:0005068!8.63e-39!57;UBERON:0006241!8.63e-39!57;UBERON:0007135!8.63e-39!57;UBERON:0002346!2.36e-37!90;UBERON:0003075!1.55e-34!86;UBERON:0007284!1.55e-34!86;UBERON:0002616!1.10e-33!59;UBERON:0000955!2.92e-32!69;UBERON:0006238!2.92e-32!69;UBERON:0003080!2.60e-29!42;UBERON:0002780!7.14e-29!41;UBERON:0001890!7.14e-29!41;UBERON:0006240!7.14e-29!41;UBERON:0000924!8.48e-27!173;UBERON:0006601!8.48e-27!173;UBERON:0002020!3.53e-25!34;UBERON:0003528!3.53e-25!34;UBERON:0001893!3.61e-25!34;UBERON:0004121!1.44e-24!169;UBERON:0002791!2.00e-24!33;UBERON:0001869!9.97e-24!32;UBERON:0003056!1.05e-23!61;UBERON:0000025!4.13e-23!194;UBERON:0000153!1.37e-19!129;UBERON:0007811!1.37e-19!129;UBERON:0000033!3.44e-19!123;UBERON:0000956!1.37e-18!25;UBERON:0000203!1.37e-18!25;UBERON:0002619!9.60e-18!22;UBERON:0004111!4.49e-17!241;UBERON:0000483!2.05e-16!309;UBERON:0000119!2.56e-16!312;UBERON:0001950!3.34e-16!20;UBERON:0000477!2.74e-14!286;UBERON:0000468!1.47e-13!659;UBERON:0000922!3.40e-12!612;UBERON:0000475!7.16e-12!365;UBERON:0000467!3.06e-11!625;UBERON:0000480!4.46e-11!626;UBERON:0000481!4.65e-11!347;UBERON:0003076!1.99e-10!15;UBERON:0003057!1.99e-10!15;UBERON:0000064!2.66e-10!219;UBERON:0002050!3.18e-10!605;UBERON:0005423!3.18e-10!605;UBERON:0000923!6.61e-10!604;UBERON:0005291!6.61e-10!604;UBERON:0006598!6.61e-10!604;UBERON:0002532!6.61e-10!604;UBERON:0004732!6.01e-09!13;UBERON:0004733!2.02e-08!12;UBERON:0002028!2.02e-08!12;UBERON:0007277!2.02e-08!12;UBERON:0002420!3.41e-08!9;UBERON:0007245!3.41e-08!9;UBERON:0010009!3.41e-08!9;UBERON:0010011!3.41e-08!9;UBERON:0000454!3.41e-08!9;UBERON:0002308!4.94e-08!9;UBERON:0000125!4.94e-08!9;UBERON:0000062!8.55e-08!511;UBERON:0001871!3.73e-07!7
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916,0.0149794,0.28498,0.0103095,0.0695559,0.00641248,0.224626,0.183585,0.271662,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.357807,0.621787,0.0170294,0.019419,0.0866228,0.271849,0.282657,0.00576196,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.00357445,0.064656,0.226143,4.52659e-05,0.0438521,0.435508,0.0439557,0.0522771,0.0787278,0.0372041,0.159873,0.142462,0.143935,0.332403,0.0379537,0.287316,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.0429523,0.0328172,0.170848,0.144756,0.051371,0.0757292,0.100188,0.223102,0.107653,0.235857,0.103852,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.0210393,0.0465855,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.00103527,0.0102393,0.000675831,0.278645,0.365775,0.155708,0.248017,0.22995,0.00463504,0.0760151,0.0629459,0.486024,0.0803251,0.0278785,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.00605585,0.499775,0.265324,0.279778,0.141699,0.0887743,0.0106427,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.00516485,0.199201,0.049937,4.63863e-05,0.0595495,0.071232,0.000625037,0.121978,0.22302,0.137423,0.284016,0.00292377,0.299492,0.100006,0.362866,0.197817,0.0345492,0.0434358,0.133127,0.0988568,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.00128049,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.0475113,0.320355,0.364334,0.15547,7.06917e-06,0.0173373,0.14794,0.0114255,0.0316373,0.0277041,0.124417,0.335582,0.317428,0.182843,1.43735e-05,0.327768,0.135777,0.011511,0.0339286,0.217363,0.119015,3.17987e-05,0.21618,0.0323312,0.107021,0.238657,0.0220967,0.392453,0.0164195,0.0780061,0.000635017,0.230477,0.279823,0.295555,0.502112,0.0103352,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.163504,0.0245723,0.189333,0.502211,0.296013,0.282366,0.00120864,0.127256,0.0392766,0.548059,0.25423,0.490559,0.00332016,0.500698,0.00420596,0.322168,0.0133357,0.000134583,7.41116e-05,6.08382e-06,0.224887,0.0671621,0.541914,0.0181844,0.14959,0.00709718,0.290703,0.622694,1.20073e-07,0.0284983,0.00116273,0.0153629,1.76436e-09,8.58786e-05,0.0768516,0.212703,0.56318,0.364079,0.107716,0.215551,0.421038,0.0108102,0.328518,0.00132729,0.310552,8.41878e-06,0.142433,0.000503744,0.000195845,0.209437,4.13196e-06,0.0514874,0.232518,1.54435e-05,0.12974,1.04219e-05,0.579004,0.00506481,2.24964e-05,0.137711,0.261575,0.257956,0.264245,0.000137974,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.158557,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,5.02151e-05,0.721266,0.00575146,0.620526,1.73524e-05,0.416164,0.0187136,0.0018862,0.479581,0.62689,0.172925,0.00410246,0.284496,1.04991e-05,0.162017,0.563206,0.260945,0.684899,0.263302,0.192292,0.180735,0.439629,0.216102,0.254659,0.109605,0.397869,0.582542,0.02784,0.102502,0.463987,0.0782409,0.503881,0.0237654,0.639483,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.0124698,0.385425,0.000569773,0.461541,0.386339,0.0131065,0.598787,0.478745,0.000445343,0.319747,0.0277333,2.13482e-07,0.608127,0.00475194,0.000452027,0.2536,0.246827,0.0103145,0.00849832,0.0136122,0.050476,0.0738474,0.100705,0.00187124,0.0317703,0.346636,0.00360135,0.348802,0.476541,0.0118751,0.000375425,0.42505,0.00339873,6.6811e-06,0.479347,0.0175608,0.0806585,0.378333,0.152547,0.264038,0.22798,0.102495,0.00976647,0.263896,0.0446972,0.24452,0.329284,0.0029143,0.0947248,0.336551,0.210656,0.246234,0.211271,0.0439036,0.0394002,0.118257,0.125087,0.215123,0.321224,0.133173,0.0597961,0.000301162,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.0433305,0.25563,0.000193312,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.00521493,0.353147,0.112422,0.000953659,0.267687,0.315656,0.284866,0.0887542,0.000306974,0.338547,2.4045e-05,0.189388,3.87439e-09,0.210125,0.292967,0.218414,0.00132289,0.00391269,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.000232671,0.162089,0.330223,0.0016375,8.83169e-06,0.207281,0.327401,0.195748,0.00454462,0.000801851,0.000182735,0.239139,0.095257,0.328852,0.00080978,0.0377937,0.274403,0.00394881,0.184534,0.00314989,0.00699456,0.15156,0.287598,0.0554083,0.223773,0.25788,0.181895,0.253768,0.30702,0.00164332,0.170837,0.327002,0.28543,0.222656,0.00239762,0.127111,0.259989,0.390754,0.355805,0.0433915,0.108118,0.259901,0.139723,0.0708274,6.31328e-05,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.000182136,0.0149493,0.142846,0.0583767,0.088258,9.25675e-06,0.00120515,0.175784,0.038024,0.0805224,0.362662,0.111581,0.184359,0.000828779,0.00761927,0.25747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}}
}}

Revision as of 12:24, 5 September 2012


Full id: C2267_neuroblastoma_spleen_amygdala_neuroectodermal_lung_occipital_parietal



Phase1 CAGE Peaks

Hg19::chr13:58204232..58204248,+p@chr13:58204232..58204248
+
Hg19::chr13:58205869..58205900,+p2@PCDH17
Hg19::chr13:58205930..58205965,+p1@PCDH17
Hg19::chr13:58206234..58206253,+p5@PCDH17


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
adult organism2.87e-47115
regional part of nervous system1.64e-4194
nervous system1.64e-4194
central nervous system6.30e-3982
neural tube8.63e-3957
neural rod8.63e-3957
future spinal cord8.63e-3957
neural keel8.63e-3957
neurectoderm2.36e-3790
neural plate1.55e-3486
presumptive neural plate1.55e-3486
regional part of brain1.10e-3359
brain2.92e-3269
future brain2.92e-3269
anterior neural tube2.60e-2942
regional part of forebrain7.14e-2941
forebrain7.14e-2941
future forebrain7.14e-2941
ectoderm8.48e-27173
presumptive ectoderm8.48e-27173
gray matter3.53e-2534
brain grey matter3.53e-2534
telencephalon3.61e-2534
ectoderm-derived structure1.44e-24169
regional part of telencephalon2.00e-2433
cerebral hemisphere9.97e-2432
pre-chordal neural plate1.05e-2361
tube4.13e-23194
anterior region of body1.37e-19129
craniocervical region1.37e-19129
head3.44e-19123
cerebral cortex1.37e-1825
pallium1.37e-1825
regional part of cerebral cortex9.60e-1822
anatomical conduit4.49e-17241
epithelium2.05e-16309
cell layer2.56e-16312
neocortex3.34e-1620
anatomical cluster2.74e-14286
multi-cellular organism1.47e-13659
embryo3.40e-12612
organism subdivision7.16e-12365
anatomical system3.06e-11625
anatomical group4.46e-11626
multi-tissue structure4.65e-11347
posterior neural tube1.99e-1015
chordal neural plate1.99e-1015
organ part2.66e-10219
embryonic structure3.18e-10605
developing anatomical structure3.18e-10605
germ layer6.61e-10604
embryonic tissue6.61e-10604
presumptive structure6.61e-10604
epiblast (generic)6.61e-10604
segmental subdivision of nervous system6.01e-0913
segmental subdivision of hindbrain2.02e-0812
hindbrain2.02e-0812
presumptive hindbrain2.02e-0812
basal ganglion3.41e-089
nuclear complex of neuraxis3.41e-089
aggregate regional part of brain3.41e-089
collection of basal ganglia3.41e-089
cerebral subcortex3.41e-089
nucleus of brain4.94e-089
neural nucleus4.94e-089
organ8.55e-08511
temporal lobe3.73e-077


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
GATA2#2624412.7449317335543.78864877853583e-050.000720339868526313
GATA3#2625320.42738726790450.0001924415576258320.00231922499848652



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.