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Coexpression cluster:C4474: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!7.91e-24!57;UBERON:0005068!7.91e-24!57;UBERON:0006241!7.91e-24!57;UBERON:0007135!7.91e-24!57;UBERON:0000025!1.94e-23!194;UBERON:0002780!4.69e-22!41;UBERON:0001890!4.69e-22!41;UBERON:0006240!4.69e-22!41;UBERON:0005743!2.33e-21!86;UBERON:0002616!3.32e-21!59;UBERON:0003080!4.56e-21!42;UBERON:0003075!4.84e-21!86;UBERON:0007284!4.84e-21!86;UBERON:0001869!2.51e-20!32;UBERON:0001893!2.86e-20!34;UBERON:0001017!4.39e-20!82;UBERON:0002020!5.77e-20!34;UBERON:0003528!5.77e-20!34;UBERON:0000073!8.94e-20!94;UBERON:0001016!8.94e-20!94;UBERON:0002791!1.68e-19!33;UBERON:0002346!2.37e-19!90;UBERON:0000955!4.60e-19!69;UBERON:0006238!4.60e-19!69;UBERON:0002619!1.24e-18!22;UBERON:0003056!5.42e-18!61;UBERON:0001950!3.53e-17!20;UBERON:0000483!4.04e-16!309;UBERON:0004111!5.22e-16!241;UBERON:0000956!9.47e-16!25;UBERON:0000203!9.47e-16!25;UBERON:0000119!1.95e-15!312;UBERON:0001637!2.22e-15!42;UBERON:0003509!2.22e-15!42;UBERON:0004572!2.22e-15!42;UBERON:0000477!3.26e-15!286;UBERON:0000475!1.19e-14!365;UBERON:0007023!2.60e-13!115;UBERON:0004573!6.25e-13!33;UBERON:0004571!6.25e-13!33;UBERON:0000033!4.38e-12!123;UBERON:0000153!1.09e-11!129;UBERON:0007811!1.09e-11!129;UBERON:0004872!1.81e-11!84;UBERON:0000481!2.75e-11!347;UBERON:0001981!9.35e-11!60;UBERON:0007500!9.35e-11!60;UBERON:0004537!9.35e-11!60;UBERON:0006965!9.35e-11!60;UBERON:0001134!3.27e-10!61;UBERON:0002036!3.27e-10!61;UBERON:0003082!3.27e-10!61;UBERON:0002385!9.52e-10!63;UBERON:0001015!9.52e-10!63;UBERON:0000383!9.52e-10!63;UBERON:0004121!1.36e-08!169;UBERON:0000055!4.37e-08!69;UBERON:0002049!4.49e-08!79;UBERON:0007798!4.49e-08!79;UBERON:0000924!4.88e-08!173;UBERON:0006601!4.88e-08!173;UBERON:0000468!5.52e-08!659;UBERON:0001871!3.21e-07!7;UBERON:0004290!5.99e-07!70;UBERON:0000914!6.42e-07!83;UBERON:0002329!6.42e-07!83;UBERON:0003077!6.42e-07!83;UBERON:0003059!6.42e-07!83;UBERON:0007282!6.42e-07!83;UBERON:0009618!6.42e-07!83;UBERON:0007285!6.42e-07!83;UBERON:0000064!9.06e-07!219;UBERON:0003914!9.32e-07!118;UBERON:0000947!9.56e-07!21;UBERON:0010191!9.56e-07!21
|ontology_enrichment_uberon=UBERON:0001049!7.91e-24!57;UBERON:0005068!7.91e-24!57;UBERON:0006241!7.91e-24!57;UBERON:0007135!7.91e-24!57;UBERON:0000025!1.94e-23!194;UBERON:0002780!4.69e-22!41;UBERON:0001890!4.69e-22!41;UBERON:0006240!4.69e-22!41;UBERON:0005743!2.33e-21!86;UBERON:0002616!3.32e-21!59;UBERON:0003080!4.56e-21!42;UBERON:0003075!4.84e-21!86;UBERON:0007284!4.84e-21!86;UBERON:0001869!2.51e-20!32;UBERON:0001893!2.86e-20!34;UBERON:0001017!4.39e-20!82;UBERON:0002020!5.77e-20!34;UBERON:0003528!5.77e-20!34;UBERON:0000073!8.94e-20!94;UBERON:0001016!8.94e-20!94;UBERON:0002791!1.68e-19!33;UBERON:0002346!2.37e-19!90;UBERON:0000955!4.60e-19!69;UBERON:0006238!4.60e-19!69;UBERON:0002619!1.24e-18!22;UBERON:0003056!5.42e-18!61;UBERON:0001950!3.53e-17!20;UBERON:0000483!4.04e-16!309;UBERON:0004111!5.22e-16!241;UBERON:0000956!9.47e-16!25;UBERON:0000203!9.47e-16!25;UBERON:0000119!1.95e-15!312;UBERON:0001637!2.22e-15!42;UBERON:0003509!2.22e-15!42;UBERON:0004572!2.22e-15!42;UBERON:0000477!3.26e-15!286;UBERON:0000475!1.19e-14!365;UBERON:0007023!2.60e-13!115;UBERON:0004573!6.25e-13!33;UBERON:0004571!6.25e-13!33;UBERON:0000033!4.38e-12!123;UBERON:0000153!1.09e-11!129;UBERON:0007811!1.09e-11!129;UBERON:0004872!1.81e-11!84;UBERON:0000481!2.75e-11!347;UBERON:0001981!9.35e-11!60;UBERON:0007500!9.35e-11!60;UBERON:0004537!9.35e-11!60;UBERON:0006965!9.35e-11!60;UBERON:0001134!3.27e-10!61;UBERON:0002036!3.27e-10!61;UBERON:0003082!3.27e-10!61;UBERON:0002385!9.52e-10!63;UBERON:0001015!9.52e-10!63;UBERON:0000383!9.52e-10!63;UBERON:0004121!1.36e-08!169;UBERON:0000055!4.37e-08!69;UBERON:0002049!4.49e-08!79;UBERON:0007798!4.49e-08!79;UBERON:0000924!4.88e-08!173;UBERON:0006601!4.88e-08!173;UBERON:0000468!5.52e-08!659;UBERON:0001871!3.21e-07!7;UBERON:0004290!5.99e-07!70;UBERON:0000914!6.42e-07!83;UBERON:0002329!6.42e-07!83;UBERON:0003077!6.42e-07!83;UBERON:0003059!6.42e-07!83;UBERON:0007282!6.42e-07!83;UBERON:0009618!6.42e-07!83;UBERON:0007285!6.42e-07!83;UBERON:0000064!9.06e-07!219;UBERON:0003914!9.32e-07!118;UBERON:0000947!9.56e-07!21;UBERON:0010191!9.56e-07!21
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043,0.0043762,0.00481323,0.0160457,0.141119,2.04645e-07,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.000777797,0.123526,0.0906475,0.0558058,2.5572e-05,0.000112257,0.000481141,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,1.72988e-06,0.122476,0.108872,0.000241884,0.000276129,0.0286025,0.0470027,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.0353101,0.217069,0.190048,0.131088,0.00176415,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.00502301,0.0473033,0.094881,0.445524,1.53696e-05,0.0774373,0.109194,0.128564,0.131452,0.687347,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.0232393,0.21727,0.289306,0.119215,0.192475,0.0168693,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.00525614,0.0355833,0.00824114,0.175094,0.43617,0.00739585,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,4.46154e-06,0.0755808,0.045654,0.110216,0.070276,0.00232088,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.00771936,0.000990951,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.000166026,0.15503,0.170295,0.00141547,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.0622625,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.000516956,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.000874248,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.252227,0.0360851,0.0168763,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.544776,0.115047,0.00131691,0.42622,0.022688,0.197484,0.0148336,0.36145,0.406019,0.381071,0.00201312,0.643768,0.11074,0.138468,0.0140037,0.48809,0.0334527,0.0217093,0.00696618,0.158867,0.151996,0.227104,0.518585,0.617852,0.38649,0.00488219,0.504757,0.55194,0.144318,0.28907,0.164197,0.00379441,0.287881,0.0113427,6.0419e-05,0.336276,0.468444,0.258219,0.446557,0.243383,0.191695,0.390974,0.382874,0.683217,0.161598,0.405056,0.644754,8.02175e-05,0.21803,0.37357,0.0203982,0.477353,0.069689,0.746954,0.43491,0.20342,0.200493,9.7305e-05,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.0168417,0.0961477,0.314438,0.0101316,0.163828,0.230581,0.120226,0.00486063,0.0513026,0.314429,0.00115141,0.00475227,0.0674279,0.00047615,0.408413,0.000110203,5.37085e-05,0.28903,0.00873429,0.000436901,0.0871388,0.522605,0.221908,1.56204e-06,0.222037,0.00229284,0.0174635,0.000461257,0.0457685,0.057399,0.204817,0.0233392,0.138871,0.308032,0.000885521,0.19783,0.0833851,0.056391,0.00457272,0.175199,0.332919,0.373557,0.170369,0.408861,0.365487,0.534741,0.0889149,0.363192,0.236011,0.203486,0.000336234,0.375787,0.4466,0.351067,0.275347,0.019895,0.305885,1.0599e-05,0.0118241,0.30666,0.303709,0.15059,0.0867777,0.035296,0.250964,2.57023e-09,0.457886,0.0344603,0.0262575,0.509064,0.196976,3.2343e-09,0.463751,0.601877,0.000565784,0.459728,0.283463,0.0102434,0.472935,0.0932845,0.273281,0.368095,0.275089,0.384593,0.138622,0.0740334,0.339729,0.00151397,0.0153645,0.387069,0.000809836,0.173874,0.299887,0.266492,0.205413,0.0165618,8.36739e-05,0.00446098,0.022685,0.0337138,0.18966,0.258854,0.00129444,0.0719199,1.78112e-05,0.00081525,0.19104,0.163057,0.00210664,4.73583e-06,0.0900729,0.0953646,0.000872573,0.00329437,0.378361,0.255516,0.20753,0.0224033,0.0171537,0.193601,0.0264253,0.0269454,0.000913176,0.00651011,0.0257082,0.0015337,0.186804,0.000344402,0.00155473,0.0325925,0.00449563,0.00803363,0.179889,0.226869,0.00455899,0.0855609,0.131118,0.20837,1.22576e-05,0.0267847,0.0673329,0.20847,0.00394192,0.113092,0.145701,0.00242972,0.162145,0.00241368,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.00160819,0.350452,0.154941,0.120196,0.000172898,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.0370716,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,8.36878e-07,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.00149718,0.240478,0.156465,0.00899301,0.256963,0.222798,0.0157468,0.0166394,0.0969345,0.202137,0.00649151,0.280943,0.00206803,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.0577193,0.0377035,0.00186843,0.187731,0.0297055,0.0192232,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.0488311,0.286691,0.347036,0.141729,0.0037817,0.255956,0.200105,0.0280973,0.0497481,0.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}}
}}

Revision as of 13:24, 5 September 2012


Full id: C4474_occipital_medial_Smooth_insula_Mesenchymal_hippocampus_parietal



Phase1 CAGE Peaks

Hg19::chr5:143584901..143584987,+p1@KCTD16
Hg19::chr5:143584993..143585004,+p4@KCTD16
Hg19::chr5:143585025..143585036,+p6@KCTD16


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>

Uber Anatomy
Ontology termp-valuen
neural tube7.91e-2457
neural rod7.91e-2457
future spinal cord7.91e-2457
neural keel7.91e-2457
tube1.94e-23194
regional part of forebrain4.69e-2241
forebrain4.69e-2241
future forebrain4.69e-2241
regional part of brain3.32e-2159
anterior neural tube4.56e-2142
neural plate4.84e-2186
presumptive neural plate4.84e-2186
cerebral hemisphere2.51e-2032
telencephalon2.86e-2034
central nervous system4.39e-2082
gray matter5.77e-2034
brain grey matter5.77e-2034
regional part of nervous system8.94e-2094
nervous system8.94e-2094
regional part of telencephalon1.68e-1933
neurectoderm2.37e-1990
brain4.60e-1969
future brain4.60e-1969
regional part of cerebral cortex1.24e-1822
pre-chordal neural plate5.42e-1861
neocortex3.53e-1720
epithelium4.04e-16309
anatomical conduit5.22e-16241
cerebral cortex9.47e-1625
pallium9.47e-1625
cell layer1.95e-15312
artery2.22e-1542
arterial blood vessel2.22e-1542
arterial system2.22e-1542
anatomical cluster3.26e-15286
organism subdivision1.19e-14365
adult organism2.60e-13115
systemic artery6.25e-1333
systemic arterial system6.25e-1333
head4.38e-12123
anterior region of body1.09e-11129
craniocervical region1.09e-11129
splanchnic layer of lateral plate mesoderm1.81e-1184
multi-tissue structure2.75e-11347
blood vessel9.35e-1160
epithelial tube open at both ends9.35e-1160
blood vasculature9.35e-1160
vascular cord9.35e-1160
skeletal muscle tissue3.27e-1061
striated muscle tissue3.27e-1061
myotome3.27e-1061
muscle tissue9.52e-1063
musculature9.52e-1063
musculature of body9.52e-1063
ectoderm-derived structure1.36e-08169
vessel4.37e-0869
vasculature4.49e-0879
vascular system4.49e-0879
ectoderm4.88e-08173
presumptive ectoderm4.88e-08173
multi-cellular organism5.52e-08659
temporal lobe3.21e-077
dermomyotome5.99e-0770
somite6.42e-0783
paraxial mesoderm6.42e-0783
presomitic mesoderm6.42e-0783
presumptive segmental plate6.42e-0783
trunk paraxial mesoderm6.42e-0783
presumptive paraxial mesoderm6.42e-0783
organ part9.06e-07219
epithelial tube9.32e-07118
aorta9.56e-0721
aortic system9.56e-0721


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)

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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
CEBPB#105137.971147625824820.001974187055288560.0115624787947107



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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