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Difference between revisions of "Coexpression cluster:C3443"

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|full_id=C3443_amygdala_putamen_caudate_Dendritic_medulloblastoma_occipital_medial
 
|full_id=C3443_amygdala_putamen_caudate_Dendritic_medulloblastoma_occipital_medial
 
|id=C3443
 
|id=C3443
|ontology_enrichment_celltype=CL:0002319!2.85e-07!25
+
|ontology_enrichment_celltype=CL:0002319!2.05e-07!25
 
|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!6.77e-30!82;UBERON:0005743!3.09e-28!86;UBERON:0000073!2.83e-27!94;UBERON:0001016!2.83e-27!94;UBERON:0000955!3.22e-25!69;UBERON:0006238!3.22e-25!69;UBERON:0003080!1.71e-23!42;UBERON:0002780!2.66e-23!41;UBERON:0001890!2.66e-23!41;UBERON:0006240!2.66e-23!41;UBERON:0001049!1.89e-22!57;UBERON:0005068!1.89e-22!57;UBERON:0006241!1.89e-22!57;UBERON:0007135!1.89e-22!57;UBERON:0001869!1.13e-21!32;UBERON:0002616!1.37e-21!59;UBERON:0001893!8.15e-21!34;UBERON:0002020!1.19e-20!34;UBERON:0003528!1.19e-20!34;UBERON:0002791!3.44e-20!33;UBERON:0002346!4.59e-19!90;UBERON:0003056!7.27e-19!61;UBERON:0003075!1.34e-18!86;UBERON:0007284!1.34e-18!86;UBERON:0000956!5.35e-17!25;UBERON:0000203!5.35e-17!25;UBERON:0002619!1.01e-15!22;UBERON:0001950!2.13e-14!20;UBERON:0007023!2.39e-14!115;UBERON:0000924!4.37e-12!173;UBERON:0006601!4.37e-12!173;UBERON:0000033!4.84e-12!123;UBERON:0000153!5.98e-12!129;UBERON:0007811!5.98e-12!129;UBERON:0004121!1.37e-11!169
+
|ontology_enrichment_uberon=UBERON:0001017!4.79e-31!81;UBERON:0001016!2.32e-29!89;UBERON:0000955!1.60e-25!68;UBERON:0006238!1.60e-25!68;UBERON:0001869!1.45e-24!32;UBERON:0002780!2.51e-24!41;UBERON:0001890!2.51e-24!41;UBERON:0003080!2.51e-24!41;UBERON:0006240!2.51e-24!41;UBERON:0001893!3.35e-23!34;UBERON:0003528!9.04e-23!34;UBERON:0002020!9.04e-23!34;UBERON:0002791!1.49e-22!32;UBERON:0000073!4.16e-21!53;UBERON:0002616!4.16e-21!53;UBERON:0001049!9.25e-21!56;UBERON:0005068!9.25e-21!56;UBERON:0006241!9.25e-21!56;UBERON:0007135!9.25e-21!56;UBERON:0000956!5.19e-19!25;UBERON:0000203!5.19e-19!25;UBERON:0011216!2.16e-18!223;UBERON:0003056!3.68e-18!61;UBERON:0002619!1.86e-17!22;UBERON:0002346!4.67e-16!86;UBERON:0001950!7.08e-16!20;UBERON:0003075!3.34e-15!82;UBERON:0007284!3.34e-15!82;UBERON:0007023!3.33e-13!114;UBERON:0004121!1.21e-12!171;UBERON:0000924!1.21e-12!171;UBERON:0006601!1.21e-12!171;UBERON:0010371!9.02e-10!104;UBERON:0000477!5.98e-08!373;UBERON:0010314!6.92e-08!132;UBERON:0002420!9.87e-07!9;UBERON:0007245!9.87e-07!9;UBERON:0010009!9.87e-07!9;UBERON:0010011!9.87e-07!9;UBERON:0000454!9.87e-07!9
 
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278903905005649!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324396787327582!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321294816262196!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00913733321700373!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00245317856806913!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136397439685163!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139851655469118
 
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278903905005649!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324396787327582!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321294816262196!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00913733321700373!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00245317856806913!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136397439685163!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139851655469118
 
|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.00687964,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.0175714,0.111283,0.00766099,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.00190755,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.00989266,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.00327964,0.064341,0.209032,0.241734,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0594776,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.00862108,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.0249033,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.0641358,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.12972,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.0859236,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.0585224,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.355018,0.00485874,0.635872,0.563047,0.252249,0.000314554,0.335423,0.0790073,0.261553,0.446302,0.0120704,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.615744,0.271958,0.292154,0.405773,0.39729,0.0582602,0.0643874,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.0821552,0.463191,0.647576,0.528324,0.520763,0.370782,0.0173702,0.484505,0.253571,0.276829,0.00591608,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.21363,0.291709,0.448095,0.576651,0.416816,0.292835,0.137839,0.439556,0.373868,0.57762,0.608919,0.18237,0.126021,0.00847576,0.747852,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.0367769,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.230427,0.762864,0.217247,0.1002,0.671377,0.546839,0.191921,0.448039,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.229003,0.0222308,0.589326,0.000772974,0.294698,0.34331,0.0282052,0.289204,0.327108,0.109738,0.278044,0.490301,0.428671,0.228096,0.336314,0.19763,0.15631,0.20495,0.421464,0.48267,0.104399,0.516462,1.62855e-07,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.0247309,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.464871,0.166672,0.206222,0.171685,0.651524,0.437176,0.040018,0.339277,0.552319,0.281425,0.141758,0.0238793,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.630264,0.00689935,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.0842821,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.016022,0.127758,0.175785,0.184486,0.169234,0.00395801,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.055805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0.205954,0.361435
 
}}
 
}}

Revision as of 06:07, 19 October 2012


Full id: C3443_amygdala_putamen_caudate_Dendritic_medulloblastoma_occipital_medial



Phase1 CAGE Peaks

Hg19::chr14:64932162..64932175,+p4@AKAP5
Hg19::chr14:64932186..64932205,+p2@AKAP5
Hg19::chr14:64932210..64932226,+p1@AKAP5


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
neural cell2.05e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system4.79e-3181
nervous system2.32e-2989
brain1.60e-2568
future brain1.60e-2568
cerebral hemisphere1.45e-2432
regional part of forebrain2.51e-2441
forebrain2.51e-2441
anterior neural tube2.51e-2441
future forebrain2.51e-2441
telencephalon3.35e-2334
brain grey matter9.04e-2334
gray matter9.04e-2334
regional part of telencephalon1.49e-2232
regional part of nervous system4.16e-2153
regional part of brain4.16e-2153
neural tube9.25e-2156
neural rod9.25e-2156
future spinal cord9.25e-2156
neural keel9.25e-2156
cerebral cortex5.19e-1925
pallium5.19e-1925
organ system subdivision2.16e-18223
pre-chordal neural plate3.68e-1861
regional part of cerebral cortex1.86e-1722
neurectoderm4.67e-1686
neocortex7.08e-1620
neural plate3.34e-1582
presumptive neural plate3.34e-1582
adult organism3.33e-13114
ectoderm-derived structure1.21e-12171
ectoderm1.21e-12171
presumptive ectoderm1.21e-12171
ecto-epithelium9.02e-10104
anatomical cluster5.98e-08373
structure with developmental contribution from neural crest6.92e-08132
basal ganglion9.87e-079
nuclear complex of neuraxis9.87e-079
aggregate regional part of brain9.87e-079
collection of basal ganglia9.87e-079
cerebral subcortex9.87e-079


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
CTCF#1066435.360256373075030.0064925092527670.0278903905005649
E2F1#186934.907389214879320.008460985347239390.0324396787327582
E2F6#187635.017155731697390.00791769806886330.0321294816262196
EBF1#187938.9064668465690.00141523283560980.00913733321700373
NFYB#4801316.75979325353650.0002123649923296180.00245317856806913
PBX3#5090321.91451268674419.49854535978121e-050.00136397439685163
ZBTB7A#5134137.35190930787590.002516255860282270.0139851655469118



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.