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Coexpression cluster:C4478: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
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74211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.026334,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.0355977,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.00836526,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,1.60279e-05,0.21727,0.289306,0.119215,0.192475,0.177967,0.188967,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.911304,0.936279,0.206454,0.0257531,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.0122477,0.194941,0.218271,0.000189228,0.000748789,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.0109522,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.0346616,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.00213659,0.166967,0.188651,0.0813902,0.184948,0.156261,0.0546539,0.511859,0.0590944,0.247324,0.178389,0.0257622,0.231073,0.407281,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.103051,0.36927,0.449036,0.407369,0.231447,0.18653,0.115047,0.37006,0.0189483,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.216033,0.643768,0.432035,0.0411943,0.390366,0.48809,0.153829,0.117158,0.00696618,0.616975,0.871256,0.227104,0.518585,0.250246,0.0135352,0.284625,0.504757,0.0091887,0.144318,0.28907,0.164197,0.462688,0.0461094,0.574635,0.478174,0.336276,0.132529,0.258219,0.0222932,0.243383,0.442897,0.390974,0.382874,0.029557,0.161598,0.405056,0.644754,0.496032,0.0795555,0.37357,0.200632,0.477353,0.78384,0.746954,0.771991,0.0222555,0.200493,0.00171127,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.00217346,0.0961477,0.314438,0.0720718,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.0175523,0.0442318,0.78,0.616388,0.408413,0.516511,0.322213,0.656109,0.33942,0.61031,0.387276,0.169614,0.802166,0.537348,0.222037,0.416621,0.416292,0.128937,0.734551,0.579431,0.204817,0.452428,0.138871,0.673493,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.0120568,1.17642e-06,0.408861,0.365487,0.534741,0.39088,0.363192,0.00266072,0.203486,0.273398,0.0816179,0.4466,0.351067,0.275347,0.637444,0.305885,0.241132,0.371414,0.30666,0.303709,0.0323359,0.386538,0.000833313,0.0345164,0.383276,0.125961,0.504711,0.220231,0.00608438,0.196976,0.191517,0.463751,5.00877e-05,4.10272e-05,0.459728,0.283463,0.563586,0.135386,0.399569,0.273281,0.0114705,0.275089,0.384593,0.0283414,0.0740334,0.339729,0.197805,0.0153645,0.0136044,0.0627969,0.52832,0.299887,0.0814305,0.205413,0.17639,0.0779009,0.276869,0.022685,0.0337138,0.18966,0.258854,0.188263,0.00265057,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.0358457,0.00176345,0.119514,0.179412,0.0200828,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.0186488,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.0279371,0.27872,0.0855609,0.131118,0.20837,0.0335483,0.0267847,0.0673329,0.20847,0.266544,0.0066506,0.0111711,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.0126763,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.0254879,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.0273485,0.246105,0.173026,0.0215816,0.139785,0.00149718,0.240478,0.0129343,0.13108,0.256963,0.222798,0.0157468,0.176789,0.00485777,0.202137,0.310405,0.280943,0.218161,0.0822373,0.0219487,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.00208455,0.0056723,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.0457063,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.0352561,0.177664,0.28365,0.0385243,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.0143647,0.00225856,0.0935776,0.327622,0.0276507,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.15884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}}
}}

Revision as of 15:59, 19 October 2012


Full id: C4478_hippocampus_amygdala_duodenum_temporal_occipital_parietal_cerebellum



Phase1 CAGE Peaks

Hg19::chr5:152870215..152870251,+p1@GRIA1
Hg19::chr5:152870255..152870270,+p3@GRIA1
Hg19::chr5:153175587..153175592,+p@chr5:153175587..153175592
+


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
neural tube1.53e-6756
neural rod1.53e-6756
future spinal cord1.53e-6756
neural keel1.53e-6756
central nervous system3.37e-6481
regional part of nervous system1.09e-6353
regional part of brain1.09e-6353
nervous system2.34e-5989
brain3.76e-5468
future brain3.76e-5468
regional part of forebrain3.63e-5341
forebrain3.63e-5341
anterior neural tube3.63e-5341
future forebrain3.63e-5341
telencephalon7.89e-5034
brain grey matter1.14e-4934
gray matter1.14e-4934
neural plate6.75e-4882
presumptive neural plate6.75e-4882
cerebral hemisphere1.71e-4732
regional part of telencephalon5.49e-4732
neurectoderm8.65e-4586
pre-chordal neural plate7.34e-3961
cerebral cortex5.34e-3725
pallium5.34e-3725
adult organism9.73e-35114
ecto-epithelium8.46e-34104
regional part of cerebral cortex4.52e-3322
ectoderm-derived structure3.75e-30171
ectoderm3.75e-30171
presumptive ectoderm3.75e-30171
neocortex8.52e-3020
structure with developmental contribution from neural crest2.34e-29132
organ system subdivision1.00e-25223
posterior neural tube4.93e-1515
chordal neural plate4.93e-1515
basal ganglion1.95e-149
nuclear complex of neuraxis1.95e-149
aggregate regional part of brain1.95e-149
collection of basal ganglia1.95e-149
cerebral subcortex1.95e-149
neural nucleus7.13e-149
nucleus of brain7.13e-149
tube2.60e-12192
segmental subdivision of hindbrain1.45e-1112
hindbrain1.45e-1112
presumptive hindbrain1.45e-1112
telencephalic nucleus2.58e-117
anatomical cluster4.20e-11373
organ part8.29e-11218
gyrus1.31e-106
segmental subdivision of nervous system1.78e-1013
limbic system1.51e-095
multi-tissue structure1.69e-09342
temporal lobe3.79e-096
parietal lobe4.21e-095
brainstem4.75e-096
occipital lobe7.72e-095
epithelium8.64e-09306
cell layer1.58e-08309
anatomical conduit3.77e-08240
regional part of metencephalon5.16e-089
metencephalon5.16e-089
future metencephalon5.16e-089
corpus striatum8.54e-084
striatum8.54e-084
ventral part of telencephalon8.54e-084
future corpus striatum8.54e-084
anatomical system1.96e-07624
organ2.21e-07503
anatomical group2.26e-07625
multi-cellular organism7.83e-07656


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

No analysis results for this cluster

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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