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Coexpression cluster:C1807: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.08e-34!82;UBERON:0000073!2.24e-34!94;UBERON:0001016!2.24e-34!94;UBERON:0005743!8.50e-34!86;UBERON:0001049!3.94e-32!57;UBERON:0005068!3.94e-32!57;UBERON:0006241!3.94e-32!57;UBERON:0007135!3.94e-32!57;UBERON:0002346!3.59e-30!90;UBERON:0002616!1.54e-29!59;UBERON:0000924!1.54e-28!173;UBERON:0006601!1.54e-28!173;UBERON:0003075!6.25e-28!86;UBERON:0007284!6.25e-28!86;UBERON:0000955!1.11e-26!69;UBERON:0006238!1.11e-26!69;UBERON:0004121!1.53e-26!169;UBERON:0007023!3.11e-26!115;UBERON:0003080!7.87e-25!42;UBERON:0002780!1.69e-24!41;UBERON:0001890!1.69e-24!41;UBERON:0006240!1.69e-24!41;UBERON:0000033!1.00e-22!123;UBERON:0001893!2.08e-22!34;UBERON:0002020!2.61e-22!34;UBERON:0003528!2.61e-22!34;UBERON:0000153!2.82e-22!129;UBERON:0007811!2.82e-22!129;UBERON:0002791!1.01e-21!33;UBERON:0001869!2.26e-21!32;UBERON:0003056!1.48e-19!61;UBERON:0000475!2.33e-18!365;UBERON:0000956!5.06e-17!25;UBERON:0000203!5.06e-17!25;UBERON:0002619!3.51e-15!22;UBERON:0001950!7.14e-14!20;UBERON:0000468!4.88e-11!659;UBERON:0000481!6.66e-10!347;UBERON:0000119!2.09e-08!312;UBERON:0003076!2.09e-08!15;UBERON:0003057!2.09e-08!15;UBERON:0000483!3.39e-08!309;UBERON:0000922!9.95e-08!612;UBERON:0000477!3.58e-07!286;UBERON:0004732!5.26e-07!13;UBERON:0000064!5.76e-07!219;UBERON:0002420!6.85e-07!9;UBERON:0007245!6.85e-07!9;UBERON:0010009!6.85e-07!9;UBERON:0010011!6.85e-07!9;UBERON:0000454!6.85e-07!9;UBERON:0004111!7.54e-07!241;UBERON:0004733!9.01e-07!12;UBERON:0002028!9.01e-07!12;UBERON:0007277!9.01e-07!12;UBERON:0002308!9.78e-07!9;UBERON:0000125!9.78e-07!9
|ontology_enrichment_uberon=UBERON:0001017!1.08e-34!82;UBERON:0000073!2.24e-34!94;UBERON:0001016!2.24e-34!94;UBERON:0005743!8.50e-34!86;UBERON:0001049!3.94e-32!57;UBERON:0005068!3.94e-32!57;UBERON:0006241!3.94e-32!57;UBERON:0007135!3.94e-32!57;UBERON:0002346!3.59e-30!90;UBERON:0002616!1.54e-29!59;UBERON:0000924!1.54e-28!173;UBERON:0006601!1.54e-28!173;UBERON:0003075!6.25e-28!86;UBERON:0007284!6.25e-28!86;UBERON:0000955!1.11e-26!69;UBERON:0006238!1.11e-26!69;UBERON:0004121!1.53e-26!169;UBERON:0007023!3.11e-26!115;UBERON:0003080!7.87e-25!42;UBERON:0002780!1.69e-24!41;UBERON:0001890!1.69e-24!41;UBERON:0006240!1.69e-24!41;UBERON:0000033!1.00e-22!123;UBERON:0001893!2.08e-22!34;UBERON:0002020!2.61e-22!34;UBERON:0003528!2.61e-22!34;UBERON:0000153!2.82e-22!129;UBERON:0007811!2.82e-22!129;UBERON:0002791!1.01e-21!33;UBERON:0001869!2.26e-21!32;UBERON:0003056!1.48e-19!61;UBERON:0000475!2.33e-18!365;UBERON:0000956!5.06e-17!25;UBERON:0000203!5.06e-17!25;UBERON:0002619!3.51e-15!22;UBERON:0001950!7.14e-14!20;UBERON:0000468!4.88e-11!659;UBERON:0000481!6.66e-10!347;UBERON:0000119!2.09e-08!312;UBERON:0003076!2.09e-08!15;UBERON:0003057!2.09e-08!15;UBERON:0000483!3.39e-08!309;UBERON:0000922!9.95e-08!612;UBERON:0000477!3.58e-07!286;UBERON:0004732!5.26e-07!13;UBERON:0000064!5.76e-07!219;UBERON:0002420!6.85e-07!9;UBERON:0007245!6.85e-07!9;UBERON:0010009!6.85e-07!9;UBERON:0010011!6.85e-07!9;UBERON:0000454!6.85e-07!9;UBERON:0004111!7.54e-07!241;UBERON:0004733!9.01e-07!12;UBERON:0002028!9.01e-07!12;UBERON:0007277!9.01e-07!12;UBERON:0002308!9.78e-07!9;UBERON:0000125!9.78e-07!9
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126e-06,5.37461e-06,0.218241,0.0242146,0.10708,0.327369,0.339826,0.12998,0.123097,0.254847,0.300809,0.0898207,0.126545,0.0918749,0.0686325,0.0569043,0.0639461,8.76486e-07,0.267408,0.312064,0.080156,0.274185,0.180885,0.0545112,7.06929e-08,0.00865038,0.0649137,0.0974216,0.00240882,0.195675,0.174786,0.176557,0.396547,0.0472148,7.45509e-05,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.385962,0.334921,0.296227,0.208788,0.0104864,0.36304,0.430936,0.123626,0.270619,0.132705,0.285556,6.21585e-07,0.233835,0.224471,0.262929,0.223204,0.143824,0.460679,0.431098,0.0775891,0.153079,0.257945,0.0018736,0.125701,0.175283,0.204954,0.209341,6.20756e-06,1.06019e-06,0.084895,0.160115,0.0819954,0.10091,0.122658,0.151161,0.228398,0.056055,0.120552,0.41771,3.14148e-10,0.529713,0.335207,0.020181,0.190688,0.299739,0.278645,0.000447255,0.0940982,0.0780533,1.54794e-09,0.0993772,0.274769,2.32542e-07,0.11602,0.344528,0.436413,0.0585992,0.20045,0.000341918,2.31456e-19,3.18745e-15,0.319826,0.336512,0.173868,0.109708,0.174594,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.114361,0.000989686,0.242462,0.0620267,0.211111,0.0738743,0.0882327,0.183058,0.150073,0.270522,0.16872,0.341388,0.0934526,0.359135,0.123404,0.430769,0.240825,0.3033,0.336623,0.163542,0.483244,0.27134,0.500871,0.239667,0.10226,0.049649,0.235147,3.15253e-18,0.245965,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.244789,0.267391,0.301441,0.21807,0.350528,0.382904,0.432408,0.190404,0.135865,0.488841,0.18137,0.180609,0.291283,0.273972,0.153023,0.400137,0.37958,0.22307,0.160699,0.0891264,0.166736,0.181253,0.0422294,0.00381527,0.146486,0.769574,0.000281014,0.00544137,0.131936,0.288826,0.246621,0.00383169,2.69881e-13,0.0965376,0.0124605,8.62288e-14,0.336564,0.0720023,0.00204488,6.98061e-18,0.0594155,0.587524,0.208795,0.0713793,0.212621,0.228454,0.1798,0.629713,0.581874,0.355154,0.730614,0.619037,0.537088,0.603804,0.629445,0.306963,0.569605,0.526495,0.580285,0.550495,0.0592373,0.00041888,0.610475,0.00638184,0.561689,0.102829,0.00125038,0.623136,0.708698,2.27584e-18,1.24735e-17,0.349068,0.124522,0.0238618,0.557035,0.427789,0.000217126,0.0119463,0.0238314,0.433702,0.258394,0.644878,0.432123,2.61912e-06,0.661773,0.494975,0.651196,0.392155,0.626931,0.371758,4.78786e-14,0.562417,2.08199e-05,0.00360419,0.254547,3.78834e-09,5.86589e-12,0.680843,2.25109e-15,0.541378,8.37308e-15,8.99467e-13,8.20264e-16,7.36108e-13,3.49965e-14,0.315485,0.0544455,0.318577,0.4488,0.389888,0.603509,0.511254,0.553178,0.246387,0.224252,0.587237,0.155054,0.466978,0.518234,0.257848,0.353942,0.192234,0.427276,0.0133812,0.000488347,0.283682,0.424668,3.2757e-11,0.00132111,0.583101,0.00804138,0.477016,0.263776,0.498956,3.94273e-05,0.55798,0.708394,4.79393e-09,0.367723,0.34194,0.592696,0.592314,0.0212338,1.9559e-09,2.06495e-05,0.317485,0.265627,0.220564,4.36248e-06,0.262394,0.307462,0.135076,0.469588,0.0979706,0.274593,0.490712,0.541363,0.709432,0.00208999,1.38414e-06,0.720644,0.00162326,0.00736363,0.361524,0.31558,0.412744,0.54408,0.259136,0.513592,0.415367,0.00182035,0.45585,0.36864,0.538745,0.456862,0.453004,0.680686,0.557093,0.693441,0.382214,0.00929457,0.639572,0.11429,0.339393,0.117434,0.306231,0.298354,0.646049,0.199987,0.457741,0.0851712,0.426239,0.0135524,0.656093,0.572661,0.412586,0.534679,0.0172799,0.55475,0.66153,0.523749,0.499347,0.307426,0.0216268,0.557732,0.490527,6.81431e-06,0.44799,0.813041,0.318338,0.276338,0.126433,0.417412,0.318174,0.0555558,0.048795,0.393022,0.293641,0.116969,0.401231,0.255983,0.297663,0.256708,0.338258,0.322052,0.145568,0.153833,0.0375572,0.38389,0.54721,0.388459,0.321362,0.627637,0.280757,0.301366,0.340343,0.343265,0.501812,0.462092,0.336254,0.308589,0.291523,0.19697,0.309816,0.0537285,0.15063,0.198077,0.281455,0.348739,0.419895,0.138495,0.208834,0.32256,0.377566,0.0667472,0.109684,0.322704,0.403482,0.181288,0.230841,0.352328,0.255358,0.0707105,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.0968383,0.312881,0.512825,0.244656,0.192188,0.158985,0.174153,0.0972854,0.333309,0.249919,0.339517,0.303699,0.0211134,0.394084,0.458518,0.282501,0.252005,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.117618,0.392533,0.396962,0.316002,0.330317,0.321404,0.0274786,0.300542,0.379651,0.185715,0.345505,0.375521,0.271405,0.311201,0.221943,0.00622106,0.367733,0.246925,0.208775,0.390438,0.343014,0.00411518,0.276922,0.156279,0.313647,0.461742,0.10563,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.0148259,0.060398,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.116796,0.430541,0.508546,0.224871,0.398887,0.389061,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.297596,0.42392,0.425912,0.380826,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,0.13907,0.470121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}}
}}

Revision as of 11:31, 5 September 2012


Full id: C1807_Chondrocyte_brain_Neural_basal_Astrocyte_mature_Neurons



Phase1 CAGE Peaks

Hg19::chr19:10047047..10047080,-p5@OLFM2
Hg19::chr19:10047087..10047098,-p7@OLFM2
Hg19::chr19:10047099..10047125,-p3@OLFM2
Hg19::chr19:10047135..10047164,-p2@OLFM2
Hg19::chr19:10047177..10047201,-p1@OLFM2


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>

Cell Type
Ontology termp-valuen
fat cell1.73e-0715
neuronal stem cell8.88e-078
Uber Anatomy
Ontology termp-valuen
central nervous system1.08e-3482
regional part of nervous system2.24e-3494
nervous system2.24e-3494
neural tube3.94e-3257
neural rod3.94e-3257
future spinal cord3.94e-3257
neural keel3.94e-3257
neurectoderm3.59e-3090
regional part of brain1.54e-2959
ectoderm1.54e-28173
presumptive ectoderm1.54e-28173
neural plate6.25e-2886
presumptive neural plate6.25e-2886
brain1.11e-2669
future brain1.11e-2669
ectoderm-derived structure1.53e-26169
adult organism3.11e-26115
anterior neural tube7.87e-2542
regional part of forebrain1.69e-2441
forebrain1.69e-2441
future forebrain1.69e-2441
head1.00e-22123
telencephalon2.08e-2234
gray matter2.61e-2234
brain grey matter2.61e-2234
anterior region of body2.82e-22129
craniocervical region2.82e-22129
regional part of telencephalon1.01e-2133
cerebral hemisphere2.26e-2132
pre-chordal neural plate1.48e-1961
organism subdivision2.33e-18365
cerebral cortex5.06e-1725
pallium5.06e-1725
regional part of cerebral cortex3.51e-1522
neocortex7.14e-1420
multi-cellular organism4.88e-11659
multi-tissue structure6.66e-10347
cell layer2.09e-08312
posterior neural tube2.09e-0815
chordal neural plate2.09e-0815
epithelium3.39e-08309
embryo9.95e-08612
anatomical cluster3.58e-07286
segmental subdivision of nervous system5.26e-0713
organ part5.76e-07219
basal ganglion6.85e-079
nuclear complex of neuraxis6.85e-079
aggregate regional part of brain6.85e-079
collection of basal ganglia6.85e-079
cerebral subcortex6.85e-079
anatomical conduit7.54e-07241
segmental subdivision of hindbrain9.01e-0712
hindbrain9.01e-0712
presumptive hindbrain9.01e-0712
nucleus of brain9.78e-079
neural nucleus9.78e-079


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
USF1#739156.361499277207969.59569864925045e-050.00136851723505267
USF2#7392512.99219738506962.69963551658264e-069.4233701108414e-05
ZBTB7A#5134157.35190930787594.65425347594289e-050.000815853606535749



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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