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Coexpression cluster:C4508: Difference between revisions

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|full_id=C4508_cervical_acute_gastric_medial_gall_bile_large
|full_id=C4508_cervical_acute_gastric_medial_gall_bile_large
|id=C4508
|id=C4508
|ontology_enrichment_celltype=CL:0002139!2.83e-09!24;CL:0000115!4.20e-08!35
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.73e-35!115;UBERON:0001049!7.27e-18!57;UBERON:0005068!7.27e-18!57;UBERON:0006241!7.27e-18!57;UBERON:0007135!7.27e-18!57;UBERON:0002780!1.49e-17!41;UBERON:0001890!1.49e-17!41;UBERON:0006240!1.49e-17!41;UBERON:0003080!7.52e-17!42;UBERON:0001950!4.34e-16!20;UBERON:0002616!8.42e-16!59;UBERON:0002619!1.38e-15!22;UBERON:0001893!1.63e-15!34;UBERON:0000477!1.83e-15!286;UBERON:0002020!3.56e-15!34;UBERON:0003528!3.56e-15!34;UBERON:0003075!3.63e-15!86;UBERON:0007284!3.63e-15!86;UBERON:0001869!4.90e-15!32;UBERON:0002791!1.11e-14!33;UBERON:0002346!9.80e-14!90;UBERON:0000955!1.10e-13!69;UBERON:0006238!1.10e-13!69;UBERON:0001017!7.06e-13!82;UBERON:0000956!7.51e-13!25;UBERON:0000203!7.51e-13!25;UBERON:0005743!2.10e-12!86;UBERON:0000064!5.62e-12!219;UBERON:0003056!2.03e-11!61;UBERON:0004111!2.57e-11!241;UBERON:0001737!1.82e-10!9;UBERON:0000073!7.82e-10!94;UBERON:0001016!7.82e-10!94;UBERON:0000025!3.94e-09!194;UBERON:0000481!2.05e-08!347;UBERON:0000062!3.37e-08!511;UBERON:0000059!8.43e-08!11;UBERON:0000467!5.36e-07!625;UBERON:0000480!6.57e-07!626;UBERON:0000200!7.64e-07!6;UBERON:0000153!9.03e-07!129;UBERON:0007811!9.03e-07!129
|ontology_enrichment_uberon=UBERON:0007023!7.63e-34!114;UBERON:0001737!1.28e-13!9;UBERON:0011216!3.79e-13!223;UBERON:0000477!4.80e-13!373;UBERON:0001950!4.86e-13!20;UBERON:0002619!5.39e-13!22;UBERON:0000073!1.74e-11!53;UBERON:0002616!1.74e-11!53;UBERON:0001049!2.52e-11!56;UBERON:0005068!2.52e-11!56;UBERON:0006241!2.52e-11!56;UBERON:0007135!2.52e-11!56;UBERON:0000956!6.66e-11!25;UBERON:0000203!6.66e-11!25;UBERON:0002780!1.80e-10!41;UBERON:0001890!1.80e-10!41;UBERON:0003080!1.80e-10!41;UBERON:0006240!1.80e-10!41;UBERON:0001893!4.50e-10!34;UBERON:0001869!5.15e-10!32;UBERON:0000064!8.86e-10!218;UBERON:0003528!5.92e-09!34;UBERON:0002020!5.92e-09!34;UBERON:0002791!9.46e-09!32;UBERON:0000955!1.01e-08!68;UBERON:0006238!1.01e-08!68;UBERON:0004921!1.50e-08!118;UBERON:0000481!2.65e-08!342;UBERON:0001017!5.23e-08!81;UBERON:0008947!6.57e-08!38;UBERON:0003258!6.57e-08!38;UBERON:0003075!1.12e-07!82;UBERON:0007284!1.12e-07!82;UBERON:0004111!2.39e-07!240;UBERON:0001557!3.24e-07!19;UBERON:0001007!5.75e-07!145;UBERON:0001555!5.75e-07!145;UBERON:0007026!5.75e-07!145;UBERON:0002346!6.04e-07!86
|tf_chipseq_enrich=NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460724558377492
|tf_chipseq_enrich=NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460724558377492
|tfbs_overrepresentation=0.147255,0.0586687,0.35968,0.0477154,0.0214323,0.287811,0.0430074,0.101122,0.03272,0.0257057,0.139423,0.0275521,0.00130551,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.000431173,0.081977,0.0948982,0.0415721,0.0250931,0.00181435,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,1.03704e-05,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.0125303,0.0541794,0.0701653,0.00446469,0.198787,0.0384161,0.000224888,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.00481292,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.00180443,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.00087036,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.005305,0.0337525,0.0203386,3.16521e-05,0.139021,0.0838393,0.16671,0.214708,0.000512275,0.0857827,0.000193634,0.0166632,0.0906875,0.0147934,0.0843604,0.000455452,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.0085119,0.0223702,0.000716344,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.0076135,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.00708381,0.147788,0.273479,0.114283,0.0400322,0.00847953,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.000758098,0.00033709,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.00127354,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.00411171,0.060398,0.0308319,0.0606036,0.136451,0.00360981,0.27358,0.0121616,0.00173038,0.178359,0.0458667,0.104357,0.121154,0.1129,0.00664287,0.169057,0.164202,0.100942,0.062995,0.00549554,0.0105855,0.00135672,0.15606,0.161026,7.1088e-05,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,1.82002e-05,0.0381183,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0802194,0.117027,0.159052,0.0183114,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.0356268,0.446759,0.0865903,0.0380459,0.130174,3.7536e-05,0.713218,0.782949,1.10207e-05,0.20128,0.823736,0.807281,0.335423,0.629514,1.66024e-05,0.446302,0.373681,0.309233,0.49143,0.0619618,0.0914012,0.329568,0.53472,0.615744,0.271958,0.292154,0.00202409,0.000182319,0.0582602,0.597171,0.187251,0.362792,0.00115743,0.10624,0.109988,0.330894,0.218329,0.427027,0.0821552,0.463191,0.0883629,0.528324,0.520763,0.370782,0.101703,0.484505,0.253571,0.276829,0.301787,0.481778,4.88271e-05,0.223503,0.155672,0.603208,0.0447111,0.314747,0.577664,0.291709,0.448095,0.212757,0.416816,0.292835,0.0280875,0.439556,0.0807167,0.57762,5.64141e-05,0.00117064,0.706298,0.821217,0.747852,0.0419647,0.236471,0.185661,0.346319,0.00117453,0.00415948,0.625945,0.503058,0.163222,0.522083,0.248634,2.50472e-05,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.00243366,0.176034,0.581837,0.412837,0.671377,0.546839,0.00142658,0.448039,0.218623,0.312808,0.00142673,0.0451077,0.0747529,0.229003,0.650179,0.589326,0.50215,0.294698,0.34331,0.477304,0.0465597,0.327108,0.109738,0.278044,0.807485,0.108847,0.228096,0.336314,0.0209597,0.15631,0.0530502,0.421464,0.48267,0.420626,0.516462,0.858756,0.335105,0.144809,0.0111455,0.385517,0.376191,0.447325,0.00044427,0.252232,0.152681,0.0465712,0.137098,0.259235,0.000453938,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.00202838,0.41707,0.363685,0.130283,0.166672,0.206222,0.525396,0.00455998,0.437176,0.269226,0.339277,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.0192138,0.0891382,0.0595618,1.31517e-05,0.257493,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.630264,0.000642687,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.00223077,0.203656,0.0216577,0.441735,0.191777,0.111931,0.28934,0.0435386,3.80918e-05,0.126478,0.134852,0.000221257,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.00016427,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.000397518,0.210369,0.193675,0.0684384,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.0190418,0.0481795,0.199971,0.0966069,0.127758,0.00104242,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.21159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}}
}}

Revision as of 16:00, 19 October 2012


Full id: C4508_cervical_acute_gastric_medial_gall_bile_large



Phase1 CAGE Peaks

Hg19::chr5:58571396..58571416,-p2@uc003jsd.1
Hg19::chr5:58571425..58571440,-p3@uc003jsd.1
Hg19::chr5:58571461..58571474,-p4@uc003jsd.1


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 organism7.63e-34114
larynx1.28e-139
organ system subdivision3.79e-13223
anatomical cluster4.80e-13373
neocortex4.86e-1320
regional part of cerebral cortex5.39e-1322
regional part of nervous system1.74e-1153
regional part of brain1.74e-1153
neural tube2.52e-1156
neural rod2.52e-1156
future spinal cord2.52e-1156
neural keel2.52e-1156
cerebral cortex6.66e-1125
pallium6.66e-1125
regional part of forebrain1.80e-1041
forebrain1.80e-1041
anterior neural tube1.80e-1041
future forebrain1.80e-1041
telencephalon4.50e-1034
cerebral hemisphere5.15e-1032
organ part8.86e-10218
brain grey matter5.92e-0934
gray matter5.92e-0934
regional part of telencephalon9.46e-0932
brain1.01e-0868
future brain1.01e-0868
subdivision of digestive tract1.50e-08118
multi-tissue structure2.65e-08342
central nervous system5.23e-0881
respiratory primordium6.57e-0838
endoderm of foregut6.57e-0838
neural plate1.12e-0782
presumptive neural plate1.12e-0782
anatomical conduit2.39e-07240
upper respiratory tract3.24e-0719
digestive system5.75e-07145
digestive tract5.75e-07145
primitive gut5.75e-07145
neurectoderm6.04e-0786


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
NR3C1#290829.982015554115360.01278474365547170.0460724558377492



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.