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Coexpression cluster:C3463: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324444429681427
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324444429681427
|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.0190579,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.0250931,0.209392,0.0907212,0.143747,0.0933697,0.0226057,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.000210711,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.0180778,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.0279481,0.000916199,0.114846,0.291327,0.0347684,0.064341,0.209032,0.0028047,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0594776,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.0259741,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.0177901,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.001669,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.0283286,0.0516985,0.0337251,0.227719,0.0952829,0.00708381,0.147788,0.273479,0.114283,0.0008122,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.0284396,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.0859236,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.00596775,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.0223286,0.0865903,0.0380459,0.130174,0.584917,0.131316,0.198118,0.268011,0.563047,0.517782,0.0263372,0.335423,0.629514,0.0376513,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.615744,0.271958,0.292154,0.405773,0.39729,0.581713,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.0620388,0.218329,0.107929,0.376924,0.129235,0.00436109,0.528324,0.168255,0.370782,0.0173702,0.484505,0.253571,0.0424424,0.301787,0.481778,0.316882,0.223503,0.503224,0.0669244,0.283727,0.314747,0.21363,0.291709,0.448095,0.212757,0.416816,0.292835,0.476744,0.115044,0.373868,0.57762,0.241757,0.18237,0.126021,0.0310069,0.0133926,0.0419647,0.236471,0.0184133,0.0684159,0.179399,0.270984,0.0179843,0.503058,0.163222,0.0389686,0.248634,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.176034,0.581837,0.412837,0.305671,0.546839,0.551561,0.0225539,0.0258593,0.0550136,0.032738,0.0451077,0.0747529,0.229003,0.000764752,0.0129683,0.0338328,0.294698,0.34331,0.138202,0.289204,0.327108,0.683186,0.278044,0.085507,0.428671,0.228096,0.336314,0.19763,0.15631,0.0106166,0.421464,0.48267,0.420626,0.0374607,0.000203002,0.0637439,0.144809,0.145539,0.385517,0.376191,0.119597,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.18767,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.522888,0.284629,0.0379506,0.359455,0.226257,0.0965765,0.41707,0.0110128,0.464871,0.0142811,0.206222,0.171685,0.0905337,0.437176,0.269226,0.339277,0.192529,0.281425,0.141758,0.455379,0.168058,0.159617,0.238587,0.0799758,0.232251,0.189515,0.0891382,0.0595618,0.0397695,0.625309,0.347298,0.539392,0.34988,0.475069,0.0958562,0.6408,0.0186811,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.11631,0.191777,0.111931,0.28934,0.0435386,0.0515253,0.126478,0.134852,0.10689,0.000335843,0.0627924,0.0129363,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.0135136,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.000107423,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.0190418,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.000155001,0.0112557,0.222432,0.107043,0.0419304,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.0235128,0.153187,0.0797897,0.0974211,0.1601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}}
}}

Revision as of 16:09, 26 November 2012


Full id: C3463_pineal_optic_colon_spinal_substantia_globus_locus



Phase1 CAGE Peaks

Hg19::chr14:94254821..94254836,-p2@PRIMA1
Hg19::chr14:94255332..94255348,-p@chr14:94255332..94255348
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Hg19::chr14:94255350..94255382,-p@chr14:94255350..94255382
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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 organism1.51e-92114
neural tube4.16e-4756
neural rod4.16e-4756
future spinal cord4.16e-4756
neural keel4.16e-4756
regional part of nervous system1.14e-4253
regional part of brain1.14e-4253
nervous system1.93e-3789
central nervous system1.68e-3681
neural plate5.61e-3682
presumptive neural plate5.61e-3682
neurectoderm5.69e-3586
brain9.60e-3568
future brain9.60e-3568
regional part of forebrain2.39e-3341
forebrain2.39e-3341
anterior neural tube2.39e-3341
future forebrain2.39e-3341
brain grey matter1.08e-2834
gray matter1.08e-2834
ecto-epithelium1.20e-28104
telencephalon2.18e-2834
organ system subdivision2.74e-26223
regional part of telencephalon1.05e-2532
cerebral hemisphere2.09e-2532
structure with developmental contribution from neural crest2.30e-25132
pre-chordal neural plate8.11e-2461
ectoderm-derived structure1.35e-21171
ectoderm1.35e-21171
presumptive ectoderm1.35e-21171
regional part of cerebral cortex1.81e-1922
neocortex4.76e-1720
cerebral cortex1.51e-1625
pallium1.51e-1625
anatomical cluster1.82e-16373
neural nucleus6.19e-159
nucleus of brain6.19e-159
posterior neural tube1.50e-1415
chordal neural plate1.50e-1415
tube8.76e-14192
anatomical conduit1.04e-13240
multi-tissue structure3.01e-13342
segmental subdivision of nervous system8.18e-1213
telencephalic nucleus1.05e-117
brainstem4.39e-116
basal ganglion4.98e-119
nuclear complex of neuraxis4.98e-119
aggregate regional part of brain4.98e-119
collection of basal ganglia4.98e-119
cerebral subcortex4.98e-119
organ1.30e-10503
segmental subdivision of hindbrain2.52e-1012
hindbrain2.52e-1012
presumptive hindbrain2.52e-1012
embryo4.49e-10592
multi-cellular organism2.14e-09656
developing anatomical structure2.34e-09581
embryonic structure3.30e-09564
germ layer5.95e-09560
germ layer / neural crest5.95e-09560
embryonic tissue5.95e-09560
presumptive structure5.95e-09560
germ layer / neural crest derived structure5.95e-09560
epiblast (generic)5.95e-09560
gyrus7.09e-096
organ part1.57e-08218
epithelium5.35e-08306
regional part of diencephalon8.00e-084
cell layer9.39e-08309
anatomical system4.56e-07624
corpus striatum4.65e-074
striatum4.65e-074
ventral part of telencephalon4.65e-074
future corpus striatum4.65e-074
anatomical group5.22e-07625


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#186934.907389214879320.008460985347239390.0324444429681427



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.