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Difference between revisions of "Coexpression cluster:C4131"

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|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0001017!6.66e-24!82;UBERON:0001049!1.49e-23!57;UBERON:0005068!1.49e-23!57;UBERON:0006241!1.49e-23!57;UBERON:0007135!1.49e-23!57;UBERON:0005743!1.83e-22!86;UBERON:0000073!1.92e-21!94;UBERON:0001016!1.92e-21!94;UBERON:0001893!1.18e-20!34;UBERON:0003080!1.22e-20!42;UBERON:0002020!1.44e-20!34;UBERON:0003528!1.44e-20!34;UBERON:0002780!1.60e-20!41;UBERON:0001890!1.60e-20!41;UBERON:0006240!1.60e-20!41;UBERON:0002791!5.10e-20!33;UBERON:0000955!2.33e-19!69;UBERON:0006238!2.33e-19!69;UBERON:0001869!3.11e-19!32;UBERON:0002616!3.28e-18!59;UBERON:0007023!1.75e-17!115;UBERON:0003075!3.89e-17!86;UBERON:0007284!3.89e-17!86;UBERON:0002346!1.35e-16!90;UBERON:0000956!1.03e-14!25;UBERON:0000203!1.03e-14!25;UBERON:0003056!6.55e-14!61;UBERON:0002619!2.13e-13!22;UBERON:0000153!5.93e-13!129;UBERON:0007811!5.93e-13!129;UBERON:0004121!2.67e-12!169;UBERON:0000033!3.35e-12!123;UBERON:0000924!3.73e-12!173;UBERON:0006601!3.73e-12!173;UBERON:0001950!4.54e-12!20;UBERON:0002308!2.25e-07!9;UBERON:0000125!2.25e-07!9;UBERON:0002420!2.48e-07!9;UBERON:0007245!2.48e-07!9;UBERON:0010009!2.48e-07!9;UBERON:0010011!2.48e-07!9;UBERON:0000454!2.48e-07!9
 
|ontology_enrichment_uberon=UBERON:0001017!6.66e-24!82;UBERON:0001049!1.49e-23!57;UBERON:0005068!1.49e-23!57;UBERON:0006241!1.49e-23!57;UBERON:0007135!1.49e-23!57;UBERON:0005743!1.83e-22!86;UBERON:0000073!1.92e-21!94;UBERON:0001016!1.92e-21!94;UBERON:0001893!1.18e-20!34;UBERON:0003080!1.22e-20!42;UBERON:0002020!1.44e-20!34;UBERON:0003528!1.44e-20!34;UBERON:0002780!1.60e-20!41;UBERON:0001890!1.60e-20!41;UBERON:0006240!1.60e-20!41;UBERON:0002791!5.10e-20!33;UBERON:0000955!2.33e-19!69;UBERON:0006238!2.33e-19!69;UBERON:0001869!3.11e-19!32;UBERON:0002616!3.28e-18!59;UBERON:0007023!1.75e-17!115;UBERON:0003075!3.89e-17!86;UBERON:0007284!3.89e-17!86;UBERON:0002346!1.35e-16!90;UBERON:0000956!1.03e-14!25;UBERON:0000203!1.03e-14!25;UBERON:0003056!6.55e-14!61;UBERON:0002619!2.13e-13!22;UBERON:0000153!5.93e-13!129;UBERON:0007811!5.93e-13!129;UBERON:0004121!2.67e-12!169;UBERON:0000033!3.35e-12!123;UBERON:0000924!3.73e-12!173;UBERON:0006601!3.73e-12!173;UBERON:0001950!4.54e-12!20;UBERON:0002308!2.25e-07!9;UBERON:0000125!2.25e-07!9;UBERON:0002420!2.48e-07!9;UBERON:0007245!2.48e-07!9;UBERON:0010009!2.48e-07!9;UBERON:0010011!2.48e-07!9;UBERON:0000454!2.48e-07!9
 +
|tfbs_overrepresentation=0.0114172,0.00175569,0.039404,0.0477154,0.199763,0.287811,0.0430074,0.0172144,0.03272,2.8866e-06,0.0102054,0.225367,2.89859e-09,0.125978,2.46009e-05,0.0619003,0.000522123,0.0982016,0.00142191,0.00606063,0.00130254,0.132577,0.081977,0.00465244,0.0415721,0.0250931,0.00181435,0.00424558,0.0108656,0.000145865,9.60364e-05,8.1328e-06,0.0180314,0.208242,0.00226357,2.3557e-06,0.0308399,0.0429682,0.00755159,0.00227592,8.23283e-08,0.0246116,0.0102981,0.00120442,0.000323983,0.0362416,0.0380166,0.00115331,0.111283,2.69421e-07,0.154071,0.0541794,0.00252127,0.000144073,0.0212153,9.72924e-06,0.000224888,0.0244227,0.0783235,5.90617e-06,4.34423e-06,0.0117644,0.00612307,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.000113601,4.0202e-05,0.00146949,0.00234364,0.000126043,9.83413e-06,0.00747605,0.0171177,0.0964936,0.000968819,0.0372495,0.00725252,0.00472557,0.0279481,0.000916199,0.000276216,0.000445554,0.00327964,0.00211576,0.0235519,0.0028047,0.062747,0.0857568,0.0495878,7.75986e-08,0.00114029,2.4625e-06,0.00688504,0.000303831,0.000682869,0.0927458,5.19747e-08,0.0574857,0.0422457,1.10356e-13,0.0370665,2.57091e-07,0.0409286,0.00229559,0.0649715,0.144217,0.000314695,7.85272e-08,6.72027e-06,0.149552,0.0176855,0.101221,0.000576135,0.0203386,0.0566549,0.000499822,2.28403e-06,0.00088228,2.33085e-10,0.000512275,0.0857827,0.00542817,0.0166632,0.00424238,2.03148e-09,4.11752e-08,0.134932,0.00181106,0.0748346,0.001669,0.0227861,0.0082662,1.4847e-07,0.00215071,2.9462e-05,0.0330399,0.00395526,0.022776,0.0085119,0.0223702,0.000716344,0.0641358,5.85505e-05,0.00505227,4.08421e-08,0.0389418,0.120833,0.200647,0.000553889,0.0174119,0.0265818,0.0427088,0.000296839,0.0747594,0.00239446,0.0516985,0.0337251,0.227719,0.00469088,8.92948e-06,2.39879e-05,1.12411e-06,0.114283,0.0400322,7.90463e-09,1.12941e-05,2.82586e-10,0.0172085,1.78489e-05,0.12972,0.0014925,0.0799324,0.000130634,0.00051468,0.181817,5.31756e-05,0.0356339,3.2496e-05,0.122474,0.000379027,0.115574,7.06907e-05,0.118847,0.00118409,1.11433e-05,0.0828697,0.00100145,0.107145,0.187297,2.90176e-07,0.000154392,0.000260351,1.80204e-05,1.72108e-06,0.0602859,0.00234165,0.000239533,0.0893019,0.060398,0.000480264,3.88622e-05,5.0123e-07,0.00360981,0.0413967,0.0121616,9.87732e-05,0.0169462,0.0458667,0.104357,0.0076549,0.1129,0.0549274,0.000921916,0.0142864,0.00527533,0.062995,0.10299,0.14193,6.30027e-07,0.000717242,0.161026,2.07919e-08,0.00837667,0.138852,0.000113199,0.060453,3.74959e-05,0.206862,0.00157828,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.00377835,0.000830039,0.0249262,0.182472,0.0695582,0.00500828,0.000101961,8.81579e-06,0.00982118,0.0815104,0.111647,0.372804,0.000292777,3.23556e-08,0.0183114,0.00124042,0.000169443,4.35895e-06,3.3218e-05,0.107242,0.201859,0.0024791,3.22083e-08,0.0619218,0.0163125,0.000828043,8.19345e-09,0.0345133,1.9896e-06,0.0033867,0.0920653,0.118078,0.0755168,5.86736e-08,0.063292,0.000246553,0.119261,0.000115712,0.000733101,0.130174,0.00212189,0.355018,0.782949,0.0821962,0.051522,0.0986134,0.00156905,0.00083951,0.0185583,0.0376513,0.446302,0.0120704,4.24877e-05,4.43809e-08,0.000787222,0.395854,0.000775053,0.0078057,0.000471837,2.06255e-05,1.75933e-06,0.000206884,3.82487e-09,0.000290219,0.0643874,0.187251,0.000106625,0.00115743,0.10624,6.99818e-06,0.330894,6.15811e-06,1.40118e-07,0.000133444,0.000464237,0.647576,0.0407001,0.00682286,0.000121147,2.11212e-05,0.0297533,0.00335333,0.000355279,0.301787,0.141124,1.66079e-07,0.00223433,0.00078363,0.000394966,1.44183e-06,4.69813e-05,0.0116619,0.0474194,0.000378092,0.576651,0.416816,0.000455917,0.476744,0.0210941,0.0120909,3.33907e-07,0.0694028,0.00117064,0.126021,0.248484,0.0133926,0.000346968,0.00267743,0.0012387,0.00934251,1.50687e-06,1.05674e-06,0.258117,0.0340542,0.0367769,0.000119998,0.00314692,1.36933e-06,0.0271848,0.163244,5.28973e-05,0.0027389,2.46678e-09,0.0641718,0.176034,0.217247,0.0021959,0.305671,0.188159,0.00142658,0.0225539,6.20339e-06,0.00665903,0.032738,1.5832e-05,1.42689e-06,0.000154952,0.650179,0.061213,0.154921,0.000468976,0.000933193,0.00441816,0.289204,0.000749204,0.109738,8.5025e-11,0.00692297,0.108847,0.000152311,4.6451e-06,4.10714e-09,0.15631,0.0106166,0.421464,0.48267,0.00239933,0.00654277,0.582303,0.00836919,0.144809,0.145539,0.0134194,0.000131921,0.0032214,0.00368553,6.53253e-07,0.0122989,0.00110167,0.137098,0.000266053,0.134788,0.0985856,0.00133722,0.048108,0.00488039,0.00911104,0.00055939,0.000553055,0.2348,0.00573447,0.169823,2.66079e-05,0.000281257,0.00115172,0.226257,0.0965765,0.102469,0.00121543,0.00388249,0.0538047,0.0228979,1.22049e-06,0.000779217,0.020698,0.269226,0.00872205,0.0479524,0.0439467,0.0105593,0.455379,0.00680512,3.30973e-08,0.00275523,0.00135387,0.0293409,9.98681e-08,0.00409641,7.06687e-11,0.0397695,0.000539973,8.26983e-05,0.0081614,6.12973e-06,2.96498e-08,1.73352e-05,0.00403911,0.0186811,0.316179,0.0697683,4.28879e-07,0.00138994,3.7158e-10,0.0575676,0.010955,0.0270501,9.34563e-05,0.00307017,0.441735,3.26786e-09,0.111931,0.046606,0.0435386,0.051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}}
 
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Revision as of 10:45, 8 August 2012


Full id: C4131_Mast_corpus_optic_thalamus_substantia_spinal_globus



Phase1 CAGE Peaks

  Short description
Hg19::chr2:145188503..145188517,- p40@ZEB2
Hg19::chr2:145188568..145188590,- p27@ZEB2
Hg19::chr4:48782217..48782228,- p2@FRYL


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0046332SMAD binding0.0480289559837234



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
CD14-positive, CD16-negative classical monocyte1.02e-0742
classical monocyte1.45e-0745
Uber Anatomy
Ontology termp-valuen
central nervous system6.66e-2482
neural tube1.49e-2357
neural rod1.49e-2357
future spinal cord1.49e-2357
neural keel1.49e-2357
regional part of nervous system1.92e-2194
nervous system1.92e-2194
telencephalon1.18e-2034
anterior neural tube1.22e-2042
gray matter1.44e-2034
brain grey matter1.44e-2034
regional part of forebrain1.60e-2041
forebrain1.60e-2041
future forebrain1.60e-2041
regional part of telencephalon5.10e-2033
brain2.33e-1969
future brain2.33e-1969
cerebral hemisphere3.11e-1932
regional part of brain3.28e-1859
adult organism1.75e-17115
neural plate3.89e-1786
presumptive neural plate3.89e-1786
neurectoderm1.35e-1690
cerebral cortex1.03e-1425
pallium1.03e-1425
pre-chordal neural plate6.55e-1461
regional part of cerebral cortex2.13e-1322
anterior region of body5.93e-13129
craniocervical region5.93e-13129
ectoderm-derived structure2.67e-12169
head3.35e-12123
ectoderm3.73e-12173
presumptive ectoderm3.73e-12173
neocortex4.54e-1220
nucleus of brain2.25e-079
neural nucleus2.25e-079
basal ganglion2.48e-079
nuclear complex of neuraxis2.48e-079
aggregate regional part of brain2.48e-079
collection of basal ganglia2.48e-079
cerebral subcortex2.48e-079


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.