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Coexpression cluster:C1668: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.30e-38!115;UBERON:0001049!2.31e-27!57;UBERON:0005068!2.31e-27!57;UBERON:0006241!2.31e-27!57;UBERON:0007135!2.31e-27!57;UBERON:0003075!3.04e-27!86;UBERON:0007284!3.04e-27!86;UBERON:0002346!4.64e-26!90;UBERON:0005743!2.22e-24!86;UBERON:0002616!2.10e-23!59;UBERON:0001017!6.58e-23!82;UBERON:0000073!9.42e-23!94;UBERON:0001016!9.42e-23!94;UBERON:0000955!3.28e-22!69;UBERON:0006238!3.28e-22!69;UBERON:0003080!1.85e-19!42;UBERON:0002780!2.88e-19!41;UBERON:0001890!2.88e-19!41;UBERON:0006240!2.88e-19!41;UBERON:0003056!3.29e-19!61;UBERON:0000033!5.27e-16!123;UBERON:0000153!7.94e-16!129;UBERON:0007811!7.94e-16!129;UBERON:0002020!1.78e-15!34;UBERON:0003528!1.78e-15!34;UBERON:0001893!1.83e-15!34;UBERON:0004121!2.37e-15!169;UBERON:0000924!5.21e-15!173;UBERON:0006601!5.21e-15!173;UBERON:0002791!6.81e-15!33;UBERON:0001869!3.76e-14!32;UBERON:0000475!7.51e-14!365;UBERON:0000025!8.39e-12!194;UBERON:0004111!1.01e-11!241;UBERON:0000468!1.32e-11!659;UBERON:0002619!5.45e-11!22;UBERON:0000062!7.45e-11!511;UBERON:0000956!3.77e-10!25;UBERON:0000203!3.77e-10!25;UBERON:0000483!8.00e-10!309;UBERON:0001950!8.91e-10!20;UBERON:0000480!9.05e-10!626;UBERON:0000119!1.01e-09!312;UBERON:0000481!1.07e-09!347;UBERON:0000467!2.00e-09!625;UBERON:0000477!2.08e-09!286;UBERON:0000922!2.72e-09!612;UBERON:0003076!4.34e-09!15;UBERON:0003057!4.34e-09!15;UBERON:0002050!2.97e-08!605;UBERON:0005423!2.97e-08!605;UBERON:0000923!3.99e-08!604;UBERON:0005291!3.99e-08!604;UBERON:0006598!3.99e-08!604;UBERON:0002532!3.99e-08!604;UBERON:0004732!7.09e-08!13;UBERON:0004733!2.95e-07!12;UBERON:0002028!2.95e-07!12;UBERON:0007277!2.95e-07!12;UBERON:0002308!4.14e-07!9;UBERON:0000125!4.14e-07!9;UBERON:0002420!5.09e-07!9;UBERON:0007245!5.09e-07!9;UBERON:0010009!5.09e-07!9;UBERON:0010011!5.09e-07!9;UBERON:0000454!5.09e-07!9
|ontology_enrichment_uberon=UBERON:0007023!4.16e-38!114;UBERON:0001049!3.85e-26!56;UBERON:0005068!3.85e-26!56;UBERON:0006241!3.85e-26!56;UBERON:0007135!3.85e-26!56;UBERON:0003075!1.80e-25!82;UBERON:0007284!1.80e-25!82;UBERON:0002346!2.56e-24!86;UBERON:0000073!3.18e-24!53;UBERON:0002616!3.18e-24!53;UBERON:0001017!1.40e-21!81;UBERON:0000955!1.61e-21!68;UBERON:0006238!1.61e-21!68;UBERON:0001016!3.61e-20!89;UBERON:0010314!2.05e-19!132;UBERON:0010371!7.75e-19!104;UBERON:0002780!3.08e-18!41;UBERON:0001890!3.08e-18!41;UBERON:0003080!3.08e-18!41;UBERON:0006240!3.08e-18!41;UBERON:0003056!4.07e-18!61;UBERON:0003528!2.13e-14!34;UBERON:0002020!2.13e-14!34;UBERON:0001893!2.22e-14!34;UBERON:0002791!3.39e-13!32;UBERON:0001869!4.35e-13!32;UBERON:0004121!4.80e-13!171;UBERON:0000924!4.80e-13!171;UBERON:0006601!4.80e-13!171;UBERON:0000062!9.21e-12!503;UBERON:0000025!5.82e-11!192;UBERON:0002619!3.83e-10!22;UBERON:0000468!4.38e-10!656;UBERON:0004111!5.57e-10!240;UBERON:0000477!9.05e-10!373;UBERON:0000481!1.02e-09!342;UBERON:0000956!2.59e-09!25;UBERON:0000203!2.59e-09!25;UBERON:0003076!3.84e-09!15;UBERON:0003057!3.84e-09!15;UBERON:0001950!5.64e-09!20;UBERON:0000480!1.39e-08!625;UBERON:0000483!1.56e-08!306;UBERON:0000119!1.67e-08!309;UBERON:0000467!2.98e-08!624;UBERON:0004732!5.65e-08!13;UBERON:0011216!6.22e-08!223;UBERON:0000922!9.65e-08!592;UBERON:0004733!2.71e-07!12;UBERON:0002028!2.71e-07!12;UBERON:0007277!2.71e-07!12;UBERON:0000125!6.49e-07!9;UBERON:0002308!6.49e-07!9;UBERON:0002420!9.28e-07!9;UBERON:0007245!9.28e-07!9;UBERON:0010009!9.28e-07!9;UBERON:0010011!9.28e-07!9;UBERON:0000454!9.28e-07!9
|tf_chipseq_enrich=JUND#3727;4:5.59573115349682:0.00184959330175546:0.0109308326642168!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130602667652118!SUZ12#23512;5:50.1157809110629:3.15480790456198e-09:2.61288646109872e-07!TRIM28#10155;4:14.87242003621:4.00368496902357e-05:0.000734482442437822!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.0013675834760222
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17,0.272406,0.223952,0.00772611,0.0496113,0.20949,0.0730994,0.0857377,0.0590174,0.24204,0.129414,0.157037,0.252398,0.197279,0.146467,0.0912686,0.425114,0.000270913,0.218241,0.0242146,0.10708,0.000751917,0.000890811,0.12998,0.123097,0.254847,0.300809,0.0898207,0.126545,0.0918749,0.0686325,0.0569043,0.0639461,0.387306,0.267408,0.312064,0.080156,0.274185,0.53753,0.0545112,0.510703,0.33844,0.0649137,0.0974216,0.0137454,0.195675,0.174786,0.176557,0.00181673,0.0472148,1.69502e-07,0.229138,0.0639045,0.00052768,0.0900204,0.228387,0.000153505,0.0636691,0.296227,0.208788,0.0525834,0.36304,0.430936,0.123626,0.270619,0.132705,0.285556,0.000691181,0.233835,0.224471,0.262929,0.223204,0.143824,4.54693e-05,0.11021,0.0775891,0.153079,0.0771804,0.211515,0.125701,0.0163476,0.204954,0.209341,0.00018873,1.06019e-06,0.084895,0.160115,0.0819954,0.10091,0.122658,0.151161,0.228398,0.056055,0.120552,0.102815,0.00824561,0.00974414,0.335207,2.90692e-05,0.00134794,0.299739,0.278645,0.733648,0.0940982,0.0780533,0.00167259,0.0993772,0.0417776,0.448923,0.11602,7.89507e-05,0.0205723,0.0585992,0.20045,0.274438,0.000298744,4.06619e-09,0.319826,0.336512,0.173868,0.109708,0.174594,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.114361,0.347759,0.242462,0.0620267,0.00186222,0.0738743,0.0882327,0.183058,0.150073,0.270522,0.16872,0.341388,0.0934526,0.359135,0.123404,2.18978e-06,0.240825,0.3033,0.0643653,0.163542,0.142089,0.27134,0.500871,0.239667,0.10226,0.29809,0.235147,0.000216511,0.0330886,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.244789,0.0394446,0.301441,0.000125416,0.350528,0.382904,0.000303886,0.190404,0.135865,0.488841,0.18137,0.180609,0.291283,0.273972,0.153023,0.400137,0.0834173,0.22307,0.160699,0.391307,0.166736,0.181253,0.0422294,0.263877,0.146486,0.769574,8.52916e-07,0.294204,0.131936,0.288826,0.246621,0.463617,4.70839e-06,0.0965376,0.0124605,0.0432352,0.336564,0.35463,3.55683e-05,4.80709e-05,0.0594155,0.587524,0.208795,0.0713793,0.212621,0.228454,0.53612,0.261842,0.0121192,0.355154,0.145569,0.619037,0.537088,0.236988,0.629445,0.306963,0.206759,0.526495,0.0119447,0.00906483,0.0162156,0.820986,0.610475,7.90608e-05,0.200159,0.00576733,0.685628,0.623136,0.708698,1.71009e-07,0.000842093,0.349068,0.70429,0.0238618,0.557035,0.427789,0.0313227,0.0469865,9.2707e-05,0.433702,0.258394,0.0212289,0.432123,0.0565478,0.0051179,0.494975,0.28382,0.392155,0.259088,0.371758,6.24073e-05,0.20076,1.44444e-08,0.00017372,0.254547,0.000678098,0.0969507,0.0011703,2.426e-05,0.183869,1.6012e-05,0.660884,2.11647e-09,2.83956e-05,8.76506e-09,0.315485,0.311289,0.318577,0.120474,0.389888,0.0670531,0.511254,0.553178,0.246387,0.224252,0.0603905,0.155054,0.466978,0.000947122,0.257848,0.353942,0.192234,0.427276,1.77565e-13,0.466967,0.283682,0.424668,0.111989,0.474058,0.218352,0.0015715,0.477016,0.0098429,0.498956,0.792095,0.55798,0.127604,0.0567757,0.139363,0.34194,0.592696,0.0133236,0.644904,2.06614e-05,0.0160438,0.00699419,0.0809958,0.220564,9.49168e-08,0.262394,0.307462,0.135076,0.133253,0.0251525,0.274593,0.490712,0.183857,0.0369687,0.583627,0.531474,0.0406675,0.562305,1.30554e-06,0.361524,0.31558,0.412744,0.54408,0.62698,0.163034,0.415367,0.240393,0.0035295,0.36864,0.181824,0.456862,0.453004,0.00116776,0.0495146,0.116707,0.0130321,0.553161,0.00398326,0.11429,0.000885649,0.00141312,0.306231,0.000495492,0.0214465,3.30908e-05,0.125872,0.273855,0.0189513,0.748909,0.656093,0.572661,0.412586,0.00780261,0.41502,0.00148253,0.00510396,0.523749,0.499347,0.307426,0.0736126,0.196912,0.490527,0.714189,0.44799,0.028167,0.318338,0.276338,0.126433,0.417412,0.318174,0.0555558,0.295666,0.393022,0.00540731,0.116969,0.401231,0.255983,0.297663,0.256708,0.0086349,0.322052,0.145568,0.153833,0.261242,0.38389,0.188453,0.00164979,3.38549e-06,0.00347751,0.280757,0.00588893,0.340343,7.72901e-05,0.154685,0.128553,0.0642137,0.308589,0.0473553,0.19697,0.309816,0.0537285,0.15063,0.198077,0.281455,8.47082e-05,0.419895,0.0100666,0.208834,0.32256,0.00144526,0.342366,0.109684,0.322704,0.00197084,0.181288,0.230841,0.352328,0.255358,0.351665,0.00387354,0.0633313,0.10772,0.0854747,0.0747609,0.0160823,0.312881,0.0365105,0.244656,0.192188,0.158985,0.174153,0.0972854,0.0630133,0.000226651,0.339517,0.303699,0.0211134,0.394084,0.458518,0.282501,0.252005,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.117618,0.014271,3.78987e-09,0.316002,0.330317,0.000691958,0.225079,0.300542,0.379651,0.185715,0.345505,0.00140931,0.271405,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.343014,0.270094,0.276922,0.156279,0.313647,0.461742,0.422872,0.336468,0.13327,0.000618953,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.00045615,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.109896,0.000838419,0.224871,0.398887,0.389061,0.310732,0.00964357,0.445995,0.385709,0.278202,0.0189898,0.400591,0.209809,0.253154,0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}}
}}

Revision as of 11:33, 19 October 2012


Full id: C1668_spinal_thalamus_substantia_pineal_lymphangiectasia_globus_renal



Phase1 CAGE Peaks

Hg19::chr12:26276068..26276086,-p1@AK311258
Hg19::chr12:26277798..26277809,-p5@BHLHE41
Hg19::chr12:26277817..26277863,-p2@BHLHE41
Hg19::chr12:26277929..26277955,-p3@BHLHE41
Hg19::chr12:26277956..26277980,-p1@BHLHE41


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 organism4.16e-38114
neural tube3.85e-2656
neural rod3.85e-2656
future spinal cord3.85e-2656
neural keel3.85e-2656
neural plate1.80e-2582
presumptive neural plate1.80e-2582
neurectoderm2.56e-2486
regional part of nervous system3.18e-2453
regional part of brain3.18e-2453
central nervous system1.40e-2181
brain1.61e-2168
future brain1.61e-2168
nervous system3.61e-2089
structure with developmental contribution from neural crest2.05e-19132
ecto-epithelium7.75e-19104
regional part of forebrain3.08e-1841
forebrain3.08e-1841
anterior neural tube3.08e-1841
future forebrain3.08e-1841
pre-chordal neural plate4.07e-1861
brain grey matter2.13e-1434
gray matter2.13e-1434
telencephalon2.22e-1434
regional part of telencephalon3.39e-1332
cerebral hemisphere4.35e-1332
ectoderm-derived structure4.80e-13171
ectoderm4.80e-13171
presumptive ectoderm4.80e-13171
organ9.21e-12503
tube5.82e-11192
regional part of cerebral cortex3.83e-1022
multi-cellular organism4.38e-10656
anatomical conduit5.57e-10240
anatomical cluster9.05e-10373
multi-tissue structure1.02e-09342
cerebral cortex2.59e-0925
pallium2.59e-0925
posterior neural tube3.84e-0915
chordal neural plate3.84e-0915
neocortex5.64e-0920
anatomical group1.39e-08625
epithelium1.56e-08306
cell layer1.67e-08309
anatomical system2.98e-08624
segmental subdivision of nervous system5.65e-0813
organ system subdivision6.22e-08223
embryo9.65e-08592
segmental subdivision of hindbrain2.71e-0712
hindbrain2.71e-0712
presumptive hindbrain2.71e-0712
neural nucleus6.49e-079
nucleus of brain6.49e-079
basal ganglion9.28e-079
nuclear complex of neuraxis9.28e-079
aggregate regional part of brain9.28e-079
collection of basal ganglia9.28e-079
cerebral subcortex9.28e-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
JUND#372745.595731153496820.001849593301755460.0109308326642168
MAX#414956.452555509007128.93743970843928e-050.00130602667652118
SUZ12#23512550.11578091106293.15480790456198e-092.61288646109872e-07
TRIM28#10155414.872420036214.00368496902357e-050.000734482442437822
USF1#739156.361499277207969.59569864925045e-050.0013675834760222



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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