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Coexpression cluster:C2266: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.01e-59!115;UBERON:0001049!2.06e-28!57;UBERON:0005068!2.06e-28!57;UBERON:0006241!2.06e-28!57;UBERON:0007135!2.06e-28!57;UBERON:0002616!4.03e-24!59;UBERON:0003080!3.92e-23!42;UBERON:0002780!1.23e-22!41;UBERON:0001890!1.23e-22!41;UBERON:0006240!1.23e-22!41;UBERON:0000955!2.93e-20!69;UBERON:0006238!2.93e-20!69;UBERON:0001017!1.08e-19!82;UBERON:0005743!2.38e-19!86;UBERON:0001893!1.84e-18!34;UBERON:0003075!2.70e-18!86;UBERON:0007284!2.70e-18!86;UBERON:0002020!2.92e-18!34;UBERON:0003528!2.92e-18!34;UBERON:0002791!1.04e-17!33;UBERON:0000073!1.45e-17!94;UBERON:0001016!1.45e-17!94;UBERON:0001869!5.21e-17!32;UBERON:0002346!1.89e-16!90;UBERON:0002619!4.68e-15!22;UBERON:0000153!3.26e-14!129;UBERON:0007811!3.26e-14!129;UBERON:0000033!1.77e-13!123;UBERON:0001950!2.08e-13!20;UBERON:0003056!6.06e-13!61;UBERON:0000956!3.52e-12!25;UBERON:0000203!3.52e-12!25;UBERON:0004121!6.21e-11!169;UBERON:0000924!4.43e-10!173;UBERON:0006601!4.43e-10!173;UBERON:0002420!4.69e-08!9;UBERON:0007245!4.69e-08!9;UBERON:0010009!4.69e-08!9;UBERON:0010011!4.69e-08!9;UBERON:0000454!4.69e-08!9;UBERON:0000062!4.93e-08!511;UBERON:0002308!8.27e-08!9;UBERON:0000125!8.27e-08!9;UBERON:0002298!4.19e-07!8;UBERON:0004111!9.33e-07!241;UBERON:0000064!9.43e-07!219
|ontology_enrichment_uberon=UBERON:0007023!2.94e-74!114;UBERON:0001049!1.74e-35!56;UBERON:0005068!1.74e-35!56;UBERON:0006241!1.74e-35!56;UBERON:0007135!1.74e-35!56;UBERON:0000073!8.99e-33!53;UBERON:0002616!8.99e-33!53;UBERON:0002780!2.22e-29!41;UBERON:0001890!2.22e-29!41;UBERON:0003080!2.22e-29!41;UBERON:0006240!2.22e-29!41;UBERON:0000955!4.79e-25!68;UBERON:0006238!4.79e-25!68;UBERON:0001017!1.71e-24!81;UBERON:0001893!5.59e-24!34;UBERON:0003528!1.01e-23!34;UBERON:0002020!1.01e-23!34;UBERON:0003075!2.90e-22!82;UBERON:0007284!2.90e-22!82;UBERON:0001869!3.60e-22!32;UBERON:0002791!4.16e-22!32;UBERON:0001016!5.01e-22!89;UBERON:0002346!2.14e-20!86;UBERON:0002619!8.03e-19!22;UBERON:0011216!5.86e-18!223;UBERON:0001950!1.15e-16!20;UBERON:0003056!1.60e-16!61;UBERON:0000956!1.00e-15!25;UBERON:0000203!1.00e-15!25;UBERON:0010371!1.05e-15!104;UBERON:0010314!3.31e-14!132;UBERON:0004121!3.84e-12!171;UBERON:0000924!3.84e-12!171;UBERON:0006601!3.84e-12!171;UBERON:0000064!1.55e-10!218;UBERON:0000477!2.22e-10!373;UBERON:0002420!5.61e-10!9;UBERON:0007245!5.61e-10!9;UBERON:0010009!5.61e-10!9;UBERON:0010011!5.61e-10!9;UBERON:0000454!5.61e-10!9;UBERON:0000125!9.52e-10!9;UBERON:0002308!9.52e-10!9;UBERON:0004111!1.68e-09!240;UBERON:0000025!7.01e-09!192;UBERON:0000481!2.11e-08!342;UBERON:0009663!3.61e-08!7;UBERON:0000200!8.48e-08!6;UBERON:0003076!1.67e-07!15;UBERON:0003057!1.67e-07!15;UBERON:0000062!2.07e-07!503;UBERON:0002298!3.09e-07!6;UBERON:0001894!8.11e-07!7;UBERON:0006222!8.11e-07!7
|tf_chipseq_enrich=FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.0010692990143322!GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.7576989869892e-05!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249277514817408
|tf_chipseq_enrich=FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.0010692990143322!GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.7576989869892e-05!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249277514817408
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48988,0.00641248,0.224626,0.183585,0.0407862,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.357807,0.621787,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.000178798,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.0367692,0.064656,0.226143,0.12751,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,2.14704e-05,0.332403,0.0379537,0.6545,0.187953,0.051459,0.000276381,0.0726892,0.18732,0.00740893,2.35047e-05,0.003001,1.64608e-06,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.00265514,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.0757944,6.89614e-07,0.124464,0.186295,0.0159364,0.101893,0.142875,0.167635,0.0155918,0.787798,0.189107,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.00979133,0.535567,4.15088e-10,0.278645,0.365775,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.00233636,0.379174,0.0939463,0.0457255,0.0779623,0.0471607,0.163865,0.226359,0.960445,0.974549,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.0385301,0.0994829,0.0604041,0.144185,0.0925862,0.00516485,0.199201,0.049937,0.172796,0.0595495,6.36345e-05,0.149346,0.121978,0.22302,0.000482136,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.0988568,0.0271325,0.426452,0.196838,0.0826805,0.246601,0.0199582,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.00159724,0.220353,0.00318161,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.0114255,0.0316373,0.00231398,0.124417,0.0639386,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.00204396,0.119015,4.08996e-06,0.21618,0.243266,0.107021,0.238657,0.0016367,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.0487563,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.459091,0.0466753,0.0338476,0.296013,0.000760863,0.181196,3.91181e-06,0.523209,0.189126,0.25423,0.490559,0.45013,0.500698,0.472542,0.685908,0.399934,0.000134583,0.818701,0.029441,0.590496,0.603763,0.541914,0.259354,0.938109,0.934991,0.00523185,0.254935,0.722684,0.139104,0.00116273,0.608176,0.657141,0.824761,0.365494,0.00190736,0.56318,0.364079,0.680099,0.579886,0.421038,0.569409,0.328518,0.545608,0.0065017,0.324103,0.483764,0.829658,0.0698158,0.209437,0.55323,0.401218,0.598945,0.361291,0.464001,0.336867,0.579004,0.334776,0.113944,0.860705,0.261575,0.00026034,0.264245,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,8.35813e-07,0.126097,0.3955,0.442469,0.000111592,0.294954,0.0130252,0.00115593,0.667777,0.39549,0.0298727,0.357409,0.146291,0.721266,0.00575146,0.0171443,0.404625,0.172147,0.424691,0.132999,0.479581,0.62689,0.884725,0.274432,0.284496,0.512545,0.162017,0.563206,0.260945,0.0299859,0.263302,0.192292,0.0174164,0.775168,0.216102,0.254659,0.109605,1.53532e-05,0.0121932,7.52123e-06,0.417131,0.463987,0.260097,0.00578014,0.454761,0.639483,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.741477,0.385425,0.307816,0.461541,0.386339,0.0849889,0.598787,0.478745,5.90805e-05,0.000676019,0.00431644,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.00168296,0.000156291,0.559969,0.0105234,0.668972,0.574252,0.493455,0.0685505,0.125876,0.348802,6.22125e-12,0.579645,3.06683e-06,0.42505,0.254628,0.713293,0.139532,0.416962,0.632833,0.0828233,0.738545,0.0384092,0.22798,0.102495,0.350933,0.263896,0.0446972,1.14442e-05,4.00904e-06,0.242783,0.0947248,2.56773e-11,0.210656,0.000212417,0.02408,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.187728,0.231754,0.00317894,0.283107,0.000408231,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.00657048,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.000605968,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.0442657,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.0205476,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.000420752,0.000621734,0.223773,0.25788,0.181895,0.000242325,0.30702,9.21284e-05,0.170837,0.327002,0.28543,0.222656,0.00239762,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.0371525,0.139723,0.0708274,0.0710478,0.0206568,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.00297709,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.00173808,0.088258,0.117657,0.0486914,0.00104239,0.262778,0.000126367,0.0755696,0.0201006,0.00121144,0.00831677,0.325785,0.00352332,0.291176,0.376537,3.49391e-06,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.0109327,0.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}}
}}

Revision as of 13:48, 19 October 2012


Full id: C2266_rectal_extraskeletal_basal_heart_medulla_adipose_ductus



Phase1 CAGE Peaks

Hg19::chr13:49975564..49975588,-p7@CAB39L
Hg19::chr13:49975590..49975605,-p8@CAB39L
Hg19::chr13:49975606..49975627,-p5@CAB39L
Hg19::chr13:49975632..49975694,-p2@CAB39L


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 organism2.94e-74114
neural tube1.74e-3556
neural rod1.74e-3556
future spinal cord1.74e-3556
neural keel1.74e-3556
regional part of nervous system8.99e-3353
regional part of brain8.99e-3353
regional part of forebrain2.22e-2941
forebrain2.22e-2941
anterior neural tube2.22e-2941
future forebrain2.22e-2941
brain4.79e-2568
future brain4.79e-2568
central nervous system1.71e-2481
telencephalon5.59e-2434
brain grey matter1.01e-2334
gray matter1.01e-2334
neural plate2.90e-2282
presumptive neural plate2.90e-2282
cerebral hemisphere3.60e-2232
regional part of telencephalon4.16e-2232
nervous system5.01e-2289
neurectoderm2.14e-2086
regional part of cerebral cortex8.03e-1922
organ system subdivision5.86e-18223
neocortex1.15e-1620
pre-chordal neural plate1.60e-1661
cerebral cortex1.00e-1525
pallium1.00e-1525
ecto-epithelium1.05e-15104
structure with developmental contribution from neural crest3.31e-14132
ectoderm-derived structure3.84e-12171
ectoderm3.84e-12171
presumptive ectoderm3.84e-12171
organ part1.55e-10218
anatomical cluster2.22e-10373
basal ganglion5.61e-109
nuclear complex of neuraxis5.61e-109
aggregate regional part of brain5.61e-109
collection of basal ganglia5.61e-109
cerebral subcortex5.61e-109
neural nucleus9.52e-109
nucleus of brain9.52e-109
anatomical conduit1.68e-09240
tube7.01e-09192
multi-tissue structure2.11e-08342
telencephalic nucleus3.61e-087
gyrus8.48e-086
posterior neural tube1.67e-0715
chordal neural plate1.67e-0715
organ2.07e-07503
brainstem3.09e-076
diencephalon8.11e-077
future diencephalon8.11e-077


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
FOXA1#3169411.08141974938556.62943068949433e-050.0010692990143322
GATA3#2625427.2365163572061.81561517799785e-066.7576989869892e-05
SPI1#668848.204323508522730.000220661881527680.00249277514817408



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.