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Coexpression cluster:C2668: Difference between revisions

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|full_id=C2668_kidney_choriocarcinoma_thyroid_mesothelioma_optic_substantia_colon
|full_id=C2668_kidney_choriocarcinoma_thyroid_mesothelioma_optic_substantia_colon
|id=C2668
|id=C2668
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0002322!4.55e-08!5
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.59e-48!57;UBERON:0005068!2.59e-48!57;UBERON:0006241!2.59e-48!57;UBERON:0007135!2.59e-48!57;UBERON:0003075!8.34e-46!86;UBERON:0007284!8.34e-46!86;UBERON:0002346!4.36e-44!90;UBERON:0002616!1.54e-41!59;UBERON:0007023!2.54e-41!115;UBERON:0005743!9.08e-41!86;UBERON:0001017!9.54e-39!82;UBERON:0000955!3.66e-37!69;UBERON:0006238!3.66e-37!69;UBERON:0003080!8.08e-37!42;UBERON:0000073!1.33e-36!94;UBERON:0001016!1.33e-36!94;UBERON:0002780!1.07e-35!41;UBERON:0001890!1.07e-35!41;UBERON:0006240!1.07e-35!41;UBERON:0003056!2.08e-35!61;UBERON:0001893!6.15e-33!34;UBERON:0002020!6.51e-33!34;UBERON:0003528!6.51e-33!34;UBERON:0002791!8.36e-32!33;UBERON:0001869!2.54e-30!32;UBERON:0000153!1.29e-24!129;UBERON:0007811!1.29e-24!129;UBERON:0000956!7.73e-23!25;UBERON:0000203!7.73e-23!25;UBERON:0000033!8.31e-23!123;UBERON:0002619!1.78e-20!22;UBERON:0004121!2.74e-19!169;UBERON:0000924!5.50e-19!173;UBERON:0006601!5.50e-19!173;UBERON:0001950!1.87e-18!20;UBERON:0000064!2.45e-14!219;UBERON:0004732!2.14e-12!13;UBERON:0003076!2.80e-12!15;UBERON:0003057!2.80e-12!15;UBERON:0000025!4.25e-12!194;UBERON:0002308!1.36e-11!9;UBERON:0000125!1.36e-11!9;UBERON:0002298!2.96e-11!8;UBERON:0002420!3.65e-11!9;UBERON:0007245!3.65e-11!9;UBERON:0010009!3.65e-11!9;UBERON:0010011!3.65e-11!9;UBERON:0000454!3.65e-11!9;UBERON:0004733!3.81e-11!12;UBERON:0002028!3.81e-11!12;UBERON:0007277!3.81e-11!12;UBERON:0000477!9.30e-11!286;UBERON:0000483!5.90e-10!309;UBERON:0000062!1.20e-09!511;UBERON:0000119!1.24e-09!312;UBERON:0000481!1.90e-09!347;UBERON:0009663!3.13e-09!7;UBERON:0000063!1.92e-08!97;UBERON:0001737!2.19e-08!9;UBERON:0000200!6.29e-08!6;UBERON:0002680!1.11e-07!9;UBERON:0001895!1.11e-07!9;UBERON:0010092!1.11e-07!9;UBERON:0001871!2.15e-07!7;UBERON:0000922!2.50e-07!612;UBERON:0004111!3.69e-07!241;UBERON:0001872!8.56e-07!5
|ontology_enrichment_uberon=UBERON:0007023!4.97e-43!114;UBERON:0001049!5.30e-42!56;UBERON:0005068!5.30e-42!56;UBERON:0006241!5.30e-42!56;UBERON:0007135!5.30e-42!56;UBERON:0000073!5.09e-40!53;UBERON:0002616!5.09e-40!53;UBERON:0003075!1.62e-38!82;UBERON:0007284!1.62e-38!82;UBERON:0002346!5.05e-36!86;UBERON:0003056!4.98e-33!61;UBERON:0002780!1.53e-32!41;UBERON:0001890!1.53e-32!41;UBERON:0003080!1.53e-32!41;UBERON:0006240!1.53e-32!41;UBERON:0001893!4.03e-32!34;UBERON:0003528!5.40e-32!34;UBERON:0002020!5.40e-32!34;UBERON:0000955!1.07e-31!68;UBERON:0006238!1.07e-31!68;UBERON:0001017!6.33e-31!81;UBERON:0002791!5.79e-29!32;UBERON:0001869!9.44e-29!32;UBERON:0010371!9.49e-29!104;UBERON:0001016!3.51e-28!89;UBERON:0010314!2.98e-24!132;UBERON:0000956!3.38e-19!25;UBERON:0000203!3.38e-19!25;UBERON:0002619!3.74e-18!22;UBERON:0001950!7.71e-18!20;UBERON:0011216!2.22e-17!223;UBERON:0004121!1.74e-15!171;UBERON:0000924!1.74e-15!171;UBERON:0006601!1.74e-15!171;UBERON:0000125!2.83e-15!9;UBERON:0002308!2.83e-15!9;UBERON:0002420!1.29e-14!9;UBERON:0007245!1.29e-14!9;UBERON:0010009!1.29e-14!9;UBERON:0010011!1.29e-14!9;UBERON:0000454!1.29e-14!9;UBERON:0000064!2.23e-12!218;UBERON:0000477!2.58e-12!373;UBERON:0009663!4.22e-12!7;UBERON:0000481!6.85e-12!342;UBERON:0002298!1.59e-11!6;UBERON:0003076!1.95e-10!15;UBERON:0003057!1.95e-10!15;UBERON:0004732!4.30e-10!13;UBERON:0000025!1.69e-09!192;UBERON:0000062!6.20e-09!503;UBERON:0004733!1.31e-08!12;UBERON:0002028!1.31e-08!12;UBERON:0007277!1.31e-08!12;UBERON:0001871!3.13e-08!6;UBERON:0000483!7.24e-08!306;UBERON:0000119!1.22e-07!309;UBERON:0000200!1.85e-07!6;UBERON:0000922!2.65e-07!592;UBERON:0000369!6.72e-07!4;UBERON:0002435!6.72e-07!4;UBERON:0000204!6.72e-07!4;UBERON:0010082!6.72e-07!4
|tf_chipseq_enrich=HNF4A#3172;3:17.3492177722153:0.000312564155748275:0.0032155129887898!HNF4G#3174;3:21.5650668948351:0.000163803242129261:0.00203684329143206!SUZ12#23512;3:37.5868356832972:3.12785741999833e-05:0.000631857448911422
|tf_chipseq_enrich=HNF4A#3172;3:17.3492177722153:0.000312564155748275:0.0032155129887898!HNF4G#3174;3:21.5650668948351:0.000163803242129261:0.00203684329143206!SUZ12#23512;3:37.5868356832972:3.12785741999833e-05:0.000631857448911422
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1436,0.05892,0.0691994,0.00402689,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.0104244,0.0173365,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,5.56672e-05,0.220368,0.258624,0.064656,0.226143,0.12751,0.0438521,0.435508,2.63477e-09,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.0626466,0.0379537,0.6545,0.187953,0.00134733,0.114868,0.0726892,0.18732,0.32305,0.0429523,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.00222156,0.107653,0.235857,0.00237223,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.0109594,0.0625685,0.124464,0.544477,0.173134,0.101893,6.38482e-07,0.167635,0.171311,0.0721023,0.00136699,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.00252788,0.758305,0.278645,0.365775,0.155708,0.248017,0.22995,0.285695,0.0760151,0.0629459,0.00483066,0.0803251,0.226641,0.379174,0.0939463,0.00500232,0.367925,0.0471607,0.163865,0.226359,0.00188396,0.000439133,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.0385301,0.0994829,0.0604041,0.0109338,0.0925862,0.289561,0.199201,0.049937,0.0158721,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.00120288,0.197817,0.0032479,0.0434358,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.0153391,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.0170013,0.291976,0.320355,0.0763252,0.15547,0.110256,0.101581,0.14794,0.147307,0.240761,0.00231398,0.00808241,0.0639386,0.317428,0.182843,0.130771,0.06079,0.135777,0.147842,0.0339286,0.0255494,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.0142611,7.81872e-07,0.0780061,0.315336,0.028874,0.279823,0.0487563,0.000772604,8.58791e-06,0.0478217,0.0351792,0.170854,0.0575231,0.174063,0.000900882,0.459091,0.54832,0.0338476,0.296013,0.0895871,0.537932,0.459994,0.523209,0.548059,0.25423,0.490559,0.0229254,0.0334811,0.472542,0.685908,0.747471,0.529642,1.24344e-05,0.483077,0.590496,0.0671621,0.0446875,0.627201,0.304145,0.00013331,0.0470729,0.017476,0.0413786,0.139104,0.360199,0.0690757,0.657141,0.0021436,0.0768516,0.212703,0.201391,0.364079,0.107716,0.0575699,0.421038,0.569409,0.328518,0.545608,0.0065017,0.00110665,0.483764,9.68504e-05,4.93713e-06,0.209437,0.000136886,0.00298496,0.0651244,0.000386547,0.464001,0.00127982,0.0572388,0.0181398,0.000125145,7.26844e-06,0.261575,0.257956,0.264245,0.379063,0.00767615,0.522925,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.0146433,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,3.28381e-08,0.00995016,0.15578,0.0746831,1.73524e-05,0.000684584,0.424691,0.715362,0.00452282,0.259048,0.884725,0.642173,0.284496,0.512545,0.512178,0.201413,0.00957951,0.00663196,0.263302,0.552023,0.180735,0.189249,0.216102,0.254659,0.109605,0.0149457,0.217863,0.226491,0.417131,0.463987,0.260097,0.503881,0.0237654,0.271678,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.0458396,0.438176,0.349112,0.741477,0.385425,0.307816,0.128211,0.386339,0.382854,0.598787,0.478745,0.611661,0.319747,0.475047,0.557967,0.608127,0.282281,0.0710918,0.2536,0.00307371,0.564333,0.70712,0.387134,0.559969,0.358813,0.668972,0.574252,0.493455,0.346636,0.00360135,0.348802,0.476541,0.579645,0.447581,0.42505,0.254628,0.131374,0.479347,0.416962,0.00368966,0.378333,0.738545,0.264038,0.22798,0.102495,0.00976647,0.0038162,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.0331645,0.211271,0.281295,0.00397584,0.118257,0.125087,0.0250035,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.00479755,0.285648,0.427316,0.391071,0.00037101,0.25563,0.240967,0.160955,0.036192,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.00489571,0.0887542,0.267811,0.338547,0.147872,0.0191872,0.0480552,0.210125,0.000456832,0.00207568,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.0207461,0.201057,0.15696,0.129351,0.0105865,0.0786166,0.276997,0.205513,0.282389,0.251421,0.0139099,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.000767461,0.00817635,0.262022,0.274403,0.266687,0.184534,0.248707,0.00699456,0.15156,0.00505104,0.313858,0.223773,0.25788,0.0176484,1.40447e-05,0.30702,0.00164332,0.170837,0.00771419,0.00492748,6.85234e-06,0.228479,0.000378293,0.259989,0.0140513,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.000477314,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.00104239,0.262778,0.373453,0.362662,0.111581,0.184359,0.334474,0.00761927,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.0233701,0.0387226,0.000253547,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696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}}
}}

Revision as of 14:17, 19 October 2012


Full id: C2668_kidney_choriocarcinoma_thyroid_mesothelioma_optic_substantia_colon



Phase1 CAGE Peaks

Hg19::chr2:169984040..169984044,-p@chr2:169984040..169984044
-
Hg19::chr2:170219007..170219018,-p2@LRP2
Hg19::chr2:170219037..170219050,-p1@LRP2
Hg19::chr2:170219079..170219084,-p3@LRP2


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><br>


Cell Type
Ontology termp-valuen
embryonic stem cell4.55e-085
Uber Anatomy
Ontology termp-valuen
adult organism4.97e-43114
neural tube5.30e-4256
neural rod5.30e-4256
future spinal cord5.30e-4256
neural keel5.30e-4256
regional part of nervous system5.09e-4053
regional part of brain5.09e-4053
neural plate1.62e-3882
presumptive neural plate1.62e-3882
neurectoderm5.05e-3686
pre-chordal neural plate4.98e-3361
regional part of forebrain1.53e-3241
forebrain1.53e-3241
anterior neural tube1.53e-3241
future forebrain1.53e-3241
telencephalon4.03e-3234
brain grey matter5.40e-3234
gray matter5.40e-3234
brain1.07e-3168
future brain1.07e-3168
central nervous system6.33e-3181
regional part of telencephalon5.79e-2932
cerebral hemisphere9.44e-2932
ecto-epithelium9.49e-29104
nervous system3.51e-2889
structure with developmental contribution from neural crest2.98e-24132
cerebral cortex3.38e-1925
pallium3.38e-1925
regional part of cerebral cortex3.74e-1822
neocortex7.71e-1820
organ system subdivision2.22e-17223
ectoderm-derived structure1.74e-15171
ectoderm1.74e-15171
presumptive ectoderm1.74e-15171
neural nucleus2.83e-159
nucleus of brain2.83e-159
basal ganglion1.29e-149
nuclear complex of neuraxis1.29e-149
aggregate regional part of brain1.29e-149
collection of basal ganglia1.29e-149
cerebral subcortex1.29e-149
organ part2.23e-12218
anatomical cluster2.58e-12373
telencephalic nucleus4.22e-127
multi-tissue structure6.85e-12342
brainstem1.59e-116
posterior neural tube1.95e-1015
chordal neural plate1.95e-1015
segmental subdivision of nervous system4.30e-1013
tube1.69e-09192
organ6.20e-09503
segmental subdivision of hindbrain1.31e-0812
hindbrain1.31e-0812
presumptive hindbrain1.31e-0812
temporal lobe3.13e-086
epithelium7.24e-08306
cell layer1.22e-07309
gyrus1.85e-076
embryo2.65e-07592
corpus striatum6.72e-074
striatum6.72e-074
ventral part of telencephalon6.72e-074
future corpus striatum6.72e-074


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
HNF4A#3172317.34921777221530.0003125641557482750.0032155129887898
HNF4G#3174321.56506689483510.0001638032421292610.00203684329143206
SUZ12#23512337.58683568329723.12785741999833e-050.000631857448911422



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.