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Coexpression cluster:C2734: Difference between revisions

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|full_id=C2734_occipital_locus_brain_amygdala_cerebellum_temporal_postcentral
|full_id=C2734_occipital_locus_brain_amygdala_cerebellum_temporal_postcentral
|id=C2734
|id=C2734
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0000066!4.68e-07!253
|ontology_enrichment_disease=DOID:0050687!5.24e-14!143;DOID:305!1.28e-12!106;DOID:14566!1.84e-12!239;DOID:162!9.31e-12!235
|ontology_enrichment_disease=DOID:0050687!1.10e-14!143;DOID:305!1.97e-13!106;DOID:14566!6.72e-13!239;DOID:162!3.47e-12!235
|ontology_enrichment_uberon=UBERON:0005743!3.21e-32!86;UBERON:0000073!4.20e-32!94;UBERON:0001016!4.20e-32!94;UBERON:0001017!8.22e-32!82;UBERON:0001049!3.00e-27!57;UBERON:0005068!3.00e-27!57;UBERON:0006241!3.00e-27!57;UBERON:0007135!3.00e-27!57;UBERON:0000955!5.76e-26!69;UBERON:0006238!5.76e-26!69;UBERON:0002616!1.27e-22!59;UBERON:0003075!5.38e-22!86;UBERON:0007284!5.38e-22!86;UBERON:0002780!1.08e-21!41;UBERON:0001890!1.08e-21!41;UBERON:0006240!1.08e-21!41;UBERON:0002346!1.36e-20!90;UBERON:0003080!1.84e-20!42;UBERON:0002020!1.06e-19!34;UBERON:0003528!1.06e-19!34;UBERON:0001893!2.21e-19!34;UBERON:0002791!9.35e-19!33;UBERON:0001869!1.61e-18!32;UBERON:0004121!2.48e-18!169;UBERON:0000924!1.28e-17!173;UBERON:0006601!1.28e-17!173;UBERON:0003056!7.59e-17!61;UBERON:0000033!2.12e-16!123;UBERON:0002619!2.68e-15!22;UBERON:0000956!1.35e-14!25;UBERON:0000203!1.35e-14!25;UBERON:0000153!1.71e-14!129;UBERON:0007811!1.71e-14!129;UBERON:0001950!3.88e-14!20;UBERON:0000025!4.71e-13!194;UBERON:0000475!5.08e-11!365;UBERON:0000483!2.69e-10!309;UBERON:0000481!2.97e-10!347;UBERON:0000119!3.43e-10!312;UBERON:0000477!1.27e-09!286;UBERON:0004111!2.51e-09!241;UBERON:0000064!1.29e-08!219;UBERON:0003076!6.14e-08!15;UBERON:0003057!6.14e-08!15;UBERON:0000922!8.94e-07!612
|ontology_enrichment_uberon=UBERON:0001017!1.20e-31!81;UBERON:0001016!2.70e-31!89;UBERON:0001049!7.42e-27!56;UBERON:0005068!7.42e-27!56;UBERON:0006241!7.42e-27!56;UBERON:0007135!7.42e-27!56;UBERON:0000955!1.35e-25!68;UBERON:0006238!1.35e-25!68;UBERON:0000073!5.24e-25!53;UBERON:0002616!5.24e-25!53;UBERON:0003075!3.24e-21!82;UBERON:0007284!3.24e-21!82;UBERON:0002780!7.31e-21!41;UBERON:0001890!7.31e-21!41;UBERON:0003080!7.31e-21!41;UBERON:0006240!7.31e-21!41;UBERON:0003528!4.90e-20!34;UBERON:0002020!4.90e-20!34;UBERON:0002346!7.00e-20!86;UBERON:0001893!1.19e-19!34;UBERON:0001869!8.41e-19!32;UBERON:0002791!1.27e-18!32;UBERON:0003056!1.06e-17!61;UBERON:0010371!2.65e-17!104;UBERON:0004121!3.85e-16!171;UBERON:0000924!3.85e-16!171;UBERON:0006601!3.85e-16!171;UBERON:0011216!4.53e-16!223;UBERON:0002619!1.33e-15!22;UBERON:0010314!2.96e-15!132;UBERON:0000956!8.08e-15!25;UBERON:0000203!8.08e-15!25;UBERON:0001950!2.15e-14!20;UBERON:0000477!9.61e-13!373;UBERON:0000025!9.98e-12!192;UBERON:0000481!5.37e-10!342;UBERON:0000483!3.86e-09!306;UBERON:0000119!5.04e-09!309;UBERON:0004111!2.98e-08!240;UBERON:0000064!1.05e-07!218;UBERON:0003076!3.33e-07!15;UBERON:0003057!3.33e-07!15
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106661436514725!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00998225516906899!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378740067051757!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387067816863868!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485973178329987!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.0014260801369505!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088876577155719!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157323865573548!SMARCC1#6599;3:32.7475194897236:4.71941722862287e-05:0.000825060622598165!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508616213716392!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000682321244070956
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106661436514725!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00998225516906899!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378740067051757!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387067816863868!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485973178329987!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.0014260801369505!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088876577155719!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157323865573548!SMARCC1#6599;3:32.7475194897236:4.71941722862287e-05:0.000825060622598165!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508616213716392!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000682321244070956
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615,0.161213,0.118999,0.0737069,0.357807,0.00325259,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,5.56672e-05,0.220368,0.258624,0.064656,0.226143,2.05103e-08,0.0438521,0.435508,0.0439557,0.0522771,0.0787278,0.164404,0.159873,0.142462,0.143935,0.332403,0.0379537,1.57854e-05,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.0303627,0.00598877,0.363016,0.100188,0.223102,0.107653,0.235857,0.000253229,0.191914,0.184022,0.216557,0.182956,0.116818,0.00167639,0.0757944,0.0625685,0.124464,0.00856472,0.173134,0.101893,0.142875,0.167635,0.171311,5.44444e-06,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,7.77569e-09,0.415079,0.278645,0.365775,0.155708,0.248017,0.22995,1.86392e-07,0.0760151,0.0629459,0.0300882,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,2.64248e-17,2.49943e-09,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.0109294,0.197817,0.251078,0.0434358,0.133127,0.016612,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,6.5975e-07,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.00213517,0.24948,0.178639,0.291976,0.320355,0.0763252,0.15547,0.110256,0.00226167,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.000120794,0.243266,0.107021,0.238657,0.20272,0.392453,0.61565,0.0780061,0.00683871,0.028874,0.279823,0.295555,0.502112,1.0409e-11,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.000106434,0.1267,0.54832,0.502211,0.296013,0.00447273,0.537932,0.459994,0.523209,0.0465928,0.25423,0.490559,0.45013,0.0334811,0.135135,0.322168,0.747471,0.174869,0.000399183,0.483077,4.12862e-05,0.0671621,0.0446875,0.627201,1.12963e-09,3.86613e-16,0.290703,0.254935,0.138899,0.000570481,0.360199,0.0153629,0.00485804,0.519564,0.365494,0.212703,0.201391,0.364079,0.0287777,0.00199999,0.421038,0.206595,0.328518,0.545608,0.310552,4.70505e-05,0.142433,0.000503744,4.93713e-06,0.209437,0.0404917,0.0134757,0.0141441,8.0873e-05,0.12974,5.69321e-05,0.579004,2.61836e-07,1.43675e-13,1.1769e-06,0.0376583,0.257956,0.264245,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.0146433,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,1.50107e-06,0.721266,0.50338,0.620526,0.404625,0.416164,0.424691,9.80995e-08,0.479581,0.62689,1.42009e-09,0.642173,0.284496,0.512545,0.512178,0.201413,5.18139e-08,0.00663196,0.263302,0.552023,0.180735,0.000163899,0.216102,0.254659,0.109605,0.397869,0.0585759,0.226491,0.0175854,0.129731,0.627953,0.503881,0.454761,0.271678,0.0295677,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,8.43794e-05,0.385425,0.307816,0.128211,0.0866806,0.382854,0.0650585,0.478745,0.24434,0.319747,0.475047,0.557967,0.608127,0.282281,0.00293082,0.2536,0.246827,0.564333,0.12664,0.387134,0.559969,0.358813,0.303004,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.579645,0.447581,0.42505,0.254628,4.88736e-05,0.479347,0.416962,0.264955,0.378333,0.387805,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.0138731,0.23235,0.00521493,0.353147,0.112422,0.170886,0.267687,0.0560879,0.284866,0.00406065,0.00400315,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.04166,0.266687,0.184534,0.0338675,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.000372103,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.0206568,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.00417718,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.0163014,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746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}}
}}

Revision as of 14:22, 19 October 2012


Full id: C2734_occipital_locus_brain_amygdala_cerebellum_temporal_postcentral



Phase1 CAGE Peaks

Hg19::chr3:183979256..183979300,-p2@CAMK2N2
Hg19::chr3:183979335..183979351,-p4@CAMK2N2
Hg19::chr3:183979353..183979390,-p3@CAMK2N2
Hg19::chr3:183979460..183979484,-p5@CAMK2N2


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell4.68e-07253
Uber Anatomy
Ontology termp-valuen
central nervous system1.20e-3181
nervous system2.70e-3189
neural tube7.42e-2756
neural rod7.42e-2756
future spinal cord7.42e-2756
neural keel7.42e-2756
brain1.35e-2568
future brain1.35e-2568
regional part of nervous system5.24e-2553
regional part of brain5.24e-2553
neural plate3.24e-2182
presumptive neural plate3.24e-2182
regional part of forebrain7.31e-2141
forebrain7.31e-2141
anterior neural tube7.31e-2141
future forebrain7.31e-2141
brain grey matter4.90e-2034
gray matter4.90e-2034
neurectoderm7.00e-2086
telencephalon1.19e-1934
cerebral hemisphere8.41e-1932
regional part of telencephalon1.27e-1832
pre-chordal neural plate1.06e-1761
ecto-epithelium2.65e-17104
ectoderm-derived structure3.85e-16171
ectoderm3.85e-16171
presumptive ectoderm3.85e-16171
organ system subdivision4.53e-16223
regional part of cerebral cortex1.33e-1522
structure with developmental contribution from neural crest2.96e-15132
cerebral cortex8.08e-1525
pallium8.08e-1525
neocortex2.15e-1420
anatomical cluster9.61e-13373
tube9.98e-12192
multi-tissue structure5.37e-10342
epithelium3.86e-09306
cell layer5.04e-09309
anatomical conduit2.98e-08240
organ part1.05e-07218
posterior neural tube3.33e-0715
chordal neural plate3.33e-0715
Disease
Ontology termp-valuen
cell type cancer1.10e-14143
carcinoma1.97e-13106
disease of cellular proliferation6.72e-13239
cancer3.47e-12235


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
E2F1#186944.907389214879320.001724022357361790.0106661436514725
E2F6#187645.017155731697390.00157802193473060.00998225516906899
GABPB1#255335.300762877136630.01012678824234270.0378740067051757
JUND#372735.245997956403270.01043432751748420.0387067816863868
MAX#414946.452555509007120.0005767613195645490.00485973178329987
MXI1#460149.96157162875930.0001015224754950450.0014260801369505
MYC#460945.22228187160940.001344309395272740.0088876577155719
REST#597849.650028716128020.0001152825614219170.00157323865573548
SMARCC1#6599332.74751948972364.71941722862287e-050.000825060622598165
USF1#739146.361499277207960.0006105011399140830.00508616213716392
USF2#7392412.99219738506963.50833029870167e-050.000682321244070956



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.