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Coexpression cluster:C3464: Difference between revisions

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|full_id=C3464_Small_granulosa_Fibroblast_squamous_amygdala_thalamus_epidermoid
|full_id=C3464_Small_granulosa_Fibroblast_squamous_amygdala_thalamus_epidermoid
|id=C3464
|id=C3464
|ontology_enrichment_celltype=CL:0002076!7.06e-07!43
|ontology_enrichment_celltype=CL:0002076!1.08e-07!42
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.12e-20!57;UBERON:0005068!1.12e-20!57;UBERON:0006241!1.12e-20!57;UBERON:0007135!1.12e-20!57;UBERON:0000033!2.56e-18!123;UBERON:0000153!4.67e-18!129;UBERON:0007811!4.67e-18!129;UBERON:0005743!1.44e-17!86;UBERON:0003075!2.36e-17!86;UBERON:0007284!2.36e-17!86;UBERON:0001017!3.96e-17!82;UBERON:0002616!9.90e-17!59;UBERON:0000955!2.16e-16!69;UBERON:0006238!2.16e-16!69;UBERON:0002346!1.79e-15!90;UBERON:0003080!2.06e-15!42;UBERON:0002780!3.79e-15!41;UBERON:0001890!3.79e-15!41;UBERON:0006240!3.79e-15!41;UBERON:0000073!2.15e-14!94;UBERON:0001016!2.15e-14!94;UBERON:0004121!3.34e-14!169;UBERON:0000924!4.15e-13!173;UBERON:0006601!4.15e-13!173;UBERON:0003056!2.76e-12!61;UBERON:0002020!5.20e-12!34;UBERON:0003528!5.20e-12!34;UBERON:0001893!9.79e-12!34;UBERON:0002791!2.81e-11!33;UBERON:0001869!2.82e-11!32;UBERON:0000475!3.57e-11!365;UBERON:0007023!4.47e-11!115;UBERON:0000062!5.48e-10!511;UBERON:0002619!5.49e-10!22;UBERON:0001950!8.43e-09!20;UBERON:0000956!4.96e-08!25;UBERON:0000203!4.96e-08!25
|ontology_enrichment_uberon=UBERON:0001049!1.72e-20!56;UBERON:0005068!1.72e-20!56;UBERON:0006241!1.72e-20!56;UBERON:0007135!1.72e-20!56;UBERON:0000073!3.33e-19!53;UBERON:0002616!3.33e-19!53;UBERON:0010371!3.54e-17!104;UBERON:0001017!5.74e-17!81;UBERON:0000955!2.95e-16!68;UBERON:0006238!2.95e-16!68;UBERON:0003075!4.53e-16!82;UBERON:0007284!4.53e-16!82;UBERON:0002780!1.69e-15!41;UBERON:0001890!1.69e-15!41;UBERON:0003080!1.69e-15!41;UBERON:0006240!1.69e-15!41;UBERON:0002346!3.00e-14!86;UBERON:0001016!6.99e-14!89;UBERON:0004121!9.56e-13!171;UBERON:0000924!9.56e-13!171;UBERON:0006601!9.56e-13!171;UBERON:0003528!5.02e-12!34;UBERON:0002020!5.02e-12!34;UBERON:0001893!8.84e-12!34;UBERON:0003056!1.37e-11!61;UBERON:0001869!2.28e-11!32;UBERON:0010314!3.08e-11!132;UBERON:0002791!4.86e-11!32;UBERON:0007023!1.14e-10!114;UBERON:0011216!5.56e-10!223;UBERON:0002619!8.07e-10!22;UBERON:0000062!1.05e-09!503;UBERON:0001950!1.24e-08!20;UBERON:0000956!4.87e-08!25;UBERON:0000203!4.87e-08!25
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324456342456521!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321332271941406!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319818907818689!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470277111904673!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109149731928764
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324456342456521!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321332271941406!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319818907818689!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470277111904673!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109149731928764
|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.0226057,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.113083,0.0429682,0.120351,0.00227592,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.00686288,0.291327,0.251834,0.064341,0.209032,0.0154619,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0124566,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.00056041,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,4.57719e-05,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.12972,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.119261,0.0865903,0.0380459,0.130174,0.584917,0.713218,0.782949,0.635872,0.563047,0.517782,1.3468e-06,0.335423,0.629514,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.0724671,0.271958,0.292154,0.0964816,0.39729,0.0582602,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.0883629,0.528324,0.03861,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.0669244,0.283727,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.292835,0.476744,0.439556,0.373868,0.213592,0.608919,0.18237,0.706298,2.05465e-06,0.161148,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.513852,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.581837,0.412837,0.305671,0.546839,0.551561,0.448039,0.218623,0.0550136,0.695172,0.0451077,0.0747529,0.229003,0.0897888,0.223844,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,2.73928e-05,0.278044,0.490301,0.428671,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.48267,0.420626,0.516462,3.5356e-10,0.335105,0.144809,0.145539,0.385517,0.376191,0.119597,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.464871,0.40841,0.206222,0.525396,0.651524,0.437176,0.269226,0.339277,0.552319,0.281425,0.141758,0.455379,0.0385377,0.159617,0.238587,0.0799758,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.136757,0.404569,0.273024,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.0214618,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.0129363,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.0190418,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,4.63571e-06,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,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}}
}}

Revision as of 15:07, 19 October 2012


Full id: C3464_Small_granulosa_Fibroblast_squamous_amygdala_thalamus_epidermoid



Phase1 CAGE Peaks

Hg19::chr14:94640633..94640667,+p1@PPP4R4
Hg19::chr14:94640671..94640694,+p2@PPP4R4
Hg19::chr14:94640699..94640709,+p3@PPP4R4


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
endo-epithelial cell1.08e-0742
Uber Anatomy
Ontology termp-valuen
neural tube1.72e-2056
neural rod1.72e-2056
future spinal cord1.72e-2056
neural keel1.72e-2056
regional part of nervous system3.33e-1953
regional part of brain3.33e-1953
ecto-epithelium3.54e-17104
central nervous system5.74e-1781
brain2.95e-1668
future brain2.95e-1668
neural plate4.53e-1682
presumptive neural plate4.53e-1682
regional part of forebrain1.69e-1541
forebrain1.69e-1541
anterior neural tube1.69e-1541
future forebrain1.69e-1541
neurectoderm3.00e-1486
nervous system6.99e-1489
ectoderm-derived structure9.56e-13171
ectoderm9.56e-13171
presumptive ectoderm9.56e-13171
brain grey matter5.02e-1234
gray matter5.02e-1234
telencephalon8.84e-1234
pre-chordal neural plate1.37e-1161
cerebral hemisphere2.28e-1132
structure with developmental contribution from neural crest3.08e-11132
regional part of telencephalon4.86e-1132
adult organism1.14e-10114
organ system subdivision5.56e-10223
regional part of cerebral cortex8.07e-1022
organ1.05e-09503
neocortex1.24e-0820
cerebral cortex4.87e-0825
pallium4.87e-0825


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#186934.907389214879320.008460985347239390.0324456342456521
E2F6#187635.017155731697390.00791769806886330.0321332271941406
EGR1#195834.988179094810140.008056488137383440.0319818907818689
NRF1#4899312.21027944771090.0005492172401020010.00470277111904673
ZNF263#1012738.221841637010680.001799043925565870.0109149731928764



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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