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Coexpression cluster:C2746: Difference between revisions

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|full_id=C2746_mature_breast_colon_uterus_vagina_hippocampus_smooth
|full_id=C2746_mature_breast_colon_uterus_vagina_hippocampus_smooth
|id=C2746
|id=C2746
|ontology_enrichment_celltype=CL:0000055!2.84e-15!180;CL:0000680!3.68e-08!57;CL:0000056!3.68e-08!57;CL:0000355!3.68e-08!57;CL:0000136!3.87e-08!15;CL:0000187!6.06e-08!54;CL:0000183!9.54e-08!59;CL:0000057!2.17e-07!75;CL:0000393!8.16e-07!60;CL:0000211!8.16e-07!60
|ontology_enrichment_celltype=CL:0000183!6.87e-08!59;CL:0000187!1.12e-07!55;CL:0000055!1.19e-07!106;CL:0000680!1.20e-07!58;CL:0000056!1.20e-07!58;CL:0000355!1.20e-07!58;CL:0000136!2.75e-07!15;CL:0000057!4.08e-07!76
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!9.84e-33!365;UBERON:0000119!6.04e-26!312;UBERON:0007023!7.84e-26!115;UBERON:0000033!8.01e-26!123;UBERON:0000955!1.14e-25!69;UBERON:0006238!1.14e-25!69;UBERON:0000483!1.43e-25!309;UBERON:0003075!5.24e-25!86;UBERON:0007284!5.24e-25!86;UBERON:0001017!5.93e-25!82;UBERON:0000153!7.55e-25!129;UBERON:0007811!7.55e-25!129;UBERON:0004121!8.24e-25!169;UBERON:0000481!1.00e-24!347;UBERON:0005743!1.02e-24!86;UBERON:0002616!8.63e-24!59;UBERON:0001049!3.22e-23!57;UBERON:0005068!3.22e-23!57;UBERON:0006241!3.22e-23!57;UBERON:0007135!3.22e-23!57;UBERON:0000924!5.31e-23!173;UBERON:0006601!5.31e-23!173;UBERON:0002346!2.89e-22!90;UBERON:0000073!4.63e-21!94;UBERON:0001016!4.63e-21!94;UBERON:0003056!3.74e-20!61;UBERON:0003080!3.83e-20!42;UBERON:0000468!1.24e-19!659;UBERON:0002780!1.87e-19!41;UBERON:0001890!1.87e-19!41;UBERON:0006240!1.87e-19!41;UBERON:0000477!3.07e-19!286;UBERON:0004111!3.95e-19!241;UBERON:0000025!2.77e-17!194;UBERON:0002020!3.82e-17!34;UBERON:0003528!3.82e-17!34;UBERON:0001893!8.60e-17!34;UBERON:0001869!1.00e-16!32;UBERON:0002791!3.18e-16!33;UBERON:0000467!8.14e-16!625;UBERON:0000480!1.53e-15!626;UBERON:0000922!3.90e-14!612;UBERON:0002050!1.01e-13!605;UBERON:0005423!1.01e-13!605;UBERON:0000956!1.88e-13!25;UBERON:0000203!1.88e-13!25;UBERON:0000923!2.45e-13!604;UBERON:0005291!2.45e-13!604;UBERON:0006598!2.45e-13!604;UBERON:0002532!2.45e-13!604;UBERON:0002619!1.27e-12!22;UBERON:0000914!8.37e-12!83;UBERON:0002329!8.37e-12!83;UBERON:0003077!8.37e-12!83;UBERON:0003059!8.37e-12!83;UBERON:0007282!8.37e-12!83;UBERON:0009618!8.37e-12!83;UBERON:0007285!8.37e-12!83;UBERON:0000062!1.83e-11!511;UBERON:0001950!2.48e-11!20;UBERON:0000064!1.35e-10!219;UBERON:0005256!1.80e-10!143;UBERON:0004290!2.41e-10!70;UBERON:0002385!1.69e-09!63;UBERON:0001015!1.69e-09!63;UBERON:0000383!1.69e-09!63;UBERON:0000486!1.70e-09!82;UBERON:0000479!3.78e-09!787;UBERON:0001134!6.24e-09!61;UBERON:0002036!6.24e-09!61;UBERON:0003082!6.24e-09!61;UBERON:0002100!1.22e-07!216
|ontology_enrichment_uberon=UBERON:0010314!3.03e-30!132;UBERON:0000481!8.68e-30!342;UBERON:0007023!1.80e-26!114;UBERON:0000955!6.89e-26!68;UBERON:0006238!6.89e-26!68;UBERON:0000119!1.21e-25!309;UBERON:0000483!3.69e-25!306;UBERON:0010371!3.98e-25!104;UBERON:0003075!5.98e-25!82;UBERON:0007284!5.98e-25!82;UBERON:0001017!6.18e-25!81;UBERON:0004121!7.04e-25!171;UBERON:0000924!7.04e-25!171;UBERON:0006601!7.04e-25!171;UBERON:0000477!7.05e-25!373;UBERON:0001049!2.54e-23!56;UBERON:0005068!2.54e-23!56;UBERON:0006241!2.54e-23!56;UBERON:0007135!2.54e-23!56;UBERON:0000073!2.02e-22!53;UBERON:0002616!2.02e-22!53;UBERON:0002346!3.73e-22!86;UBERON:0001016!4.97e-21!89;UBERON:0002780!1.46e-20!41;UBERON:0001890!1.46e-20!41;UBERON:0003080!1.46e-20!41;UBERON:0006240!1.46e-20!41;UBERON:0000468!2.42e-20!656;UBERON:0003056!3.73e-20!61;UBERON:0004111!1.07e-18!240;UBERON:0003528!9.94e-18!34;UBERON:0002020!9.94e-18!34;UBERON:0001893!1.88e-17!34;UBERON:0001869!2.34e-17!32;UBERON:0002050!4.04e-17!564;UBERON:0002791!6.80e-17!32;UBERON:0005423!8.07e-17!581;UBERON:0000025!9.01e-17!192;UBERON:0000467!2.67e-16!624;UBERON:0000922!3.03e-16!592;UBERON:0000480!4.96e-16!625;UBERON:0000923!6.81e-16!560;UBERON:0010316!6.81e-16!560;UBERON:0005291!6.81e-16!560;UBERON:0006598!6.81e-16!560;UBERON:0010317!6.81e-16!560;UBERON:0002532!6.81e-16!560;UBERON:0011216!4.29e-15!223;UBERON:0000956!3.92e-14!25;UBERON:0000203!3.92e-14!25;UBERON:0002619!2.51e-13!22;UBERON:0001950!4.59e-12!20;UBERON:0000479!1.68e-11!773;UBERON:0000062!3.02e-11!503;UBERON:0000064!8.89e-11!218;UBERON:0003077!2.15e-10!72;UBERON:0007285!2.15e-10!72;UBERON:0007524!2.44e-10!73;UBERON:0002329!6.17e-10!71;UBERON:0003059!6.17e-10!71;UBERON:0007282!6.17e-10!71;UBERON:0004290!6.17e-10!71;UBERON:0009618!6.17e-10!71;UBERON:0003104!7.71e-10!160;UBERON:0009142!7.71e-10!160;UBERON:0000475!1.38e-09!264;UBERON:0000486!2.55e-09!83;UBERON:0007503!4.19e-09!78;UBERON:0002385!5.51e-09!64;UBERON:0001015!5.51e-09!64;UBERON:0000383!5.51e-09!64;UBERON:0005256!1.37e-08!122;UBERON:0001134!1.72e-08!62;UBERON:0002036!1.72e-08!62;UBERON:0003082!1.72e-08!62
|tf_chipseq_enrich=NANOG#79923;4:29.2447784810127:1.36586687657858e-06:5.34669305558436e-05!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322894738686762
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38,0.207615,0.161213,0.118999,0.0737069,0.357807,0.621787,0.178782,0.019419,0.0866228,0.0408454,0.00477271,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.0248217,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.00648069,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.00740893,0.278397,0.245002,0.170848,0.144756,0.302909,2.84648e-08,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.000544303,0.167635,0.0155918,0.0721023,0.189107,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.833813,0.415079,0.278645,0.0769795,0.155708,0.248017,0.22995,0.00463504,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.404165,0.499775,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.00384141,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.0988568,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.0219712,0.0946865,0.00758581,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.000681832,0.00122546,0.0127656,0.110256,0.415419,0.14794,2.36613e-05,0.240761,0.225961,0.124417,0.0639386,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.000185372,0.20272,0.392453,0.61565,0.00312482,0.315336,0.230477,0.279823,0.295555,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.459091,0.000178027,8.68892e-06,0.296013,0.282366,0.181196,0.127256,0.523209,0.548059,0.25423,0.146971,0.45013,0.153911,0.472542,0.0302459,0.0133357,0.174869,0.818701,0.483077,0.00226518,0.603763,0.541914,0.0181844,0.304145,0.934991,0.290703,0.622694,0.366999,0.0284983,0.360199,0.241059,0.657141,0.253797,0.365494,0.0244211,0.0515679,0.364079,0.0287777,0.579886,0.421038,2.87521e-05,0.000763941,0.545608,0.310552,0.594773,0.00472069,0.528161,0.453065,0.209437,0.843495,0.0514874,0.598945,0.882403,0.464001,0.871271,0.0118057,0.605327,0.839946,0.860705,1.66105e-05,0.257956,0.264245,0.0126705,0.326516,0.522925,0.113006,0.0277366,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,3.09341e-05,0.35974,0.0999766,0.39549,0.234254,0.357409,0.00116299,0.0408829,0.000785185,0.000504793,0.404625,0.0034658,0.00251166,0.132999,0.0286876,0.62689,0.884725,0.274432,0.284496,0.512545,0.512178,2.58222e-05,0.260945,0.321001,0.263302,0.00919591,0.180735,0.0646927,0.216102,0.254659,0.109605,0.0924199,0.217863,0.226491,0.102502,0.463987,0.627953,0.000790209,0.454761,0.0840572,0.0295677,0.0232851,0.301581,0.261657,0.346776,0.00395053,1.89949e-05,0.438176,0.00959742,0.0124698,0.385425,0.307816,0.00374881,0.386339,0.382854,0.598787,0.478745,0.0158475,0.319747,0.475047,0.00972177,0.608127,0.282281,7.02953e-06,0.2536,0.246827,0.564333,0.70712,0.387134,0.559969,0.358813,0.000153433,0.00187124,0.148933,0.346636,0.00360135,0.0694762,0.476541,0.0574793,0.447581,0.106831,0.254628,4.88736e-05,0.139532,0.416962,0.0806585,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.0613938,0.242783,0.0947248,0.336551,0.210656,0.00304995,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.187728,0.231754,0.249415,0.283107,0.00493982,0.427316,0.391071,0.279553,0.25563,0.240967,0.000790138,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.0191872,0.293546,0.210125,0.00536668,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.0662546,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.0617695,0.387837,0.233244,0.207281,0.0606443,0.195748,0.00454462,0.161712,0.00272873,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,2.41686e-08,0.31749,0.15156,0.287598,0.313858,0.223773,0.036547,0.181895,0.253768,0.30702,0.00164332,0.170837,0.00771419,0.28543,0.00220735,0.228479,0.127111,0.000269465,0.390754,0.355805,0.279739,0.00606762,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.0107262,0.0583767,0.088258,0.000297685,0.0486914,0.175784,0.262778,0.373453,0.0755696,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.00304766,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.28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}}
}}

Revision as of 14:22, 19 October 2012


Full id: C2746_mature_breast_colon_uterus_vagina_hippocampus_smooth



Phase1 CAGE Peaks

Hg19::chr3:64253787..64253799,-p5@PRICKLE2
Hg19::chr3:64253805..64253834,-p2@PRICKLE2
Hg19::chr3:64253837..64253863,-p1@PRICKLE2
Hg19::chr3:64253867..64253883,-p3@PRICKLE2


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
contractile cell6.87e-0859
muscle cell1.12e-0755
non-terminally differentiated cell1.19e-07106
muscle precursor cell1.20e-0758
myoblast1.20e-0758
multi-potent skeletal muscle stem cell1.20e-0758
fat cell2.75e-0715
fibroblast4.08e-0776
Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest3.03e-30132
multi-tissue structure8.68e-30342
adult organism1.80e-26114
brain6.89e-2668
future brain6.89e-2668
cell layer1.21e-25309
epithelium3.69e-25306
ecto-epithelium3.98e-25104
neural plate5.98e-2582
presumptive neural plate5.98e-2582
central nervous system6.18e-2581
ectoderm-derived structure7.04e-25171
ectoderm7.04e-25171
presumptive ectoderm7.04e-25171
anatomical cluster7.05e-25373
neural tube2.54e-2356
neural rod2.54e-2356
future spinal cord2.54e-2356
neural keel2.54e-2356
regional part of nervous system2.02e-2253
regional part of brain2.02e-2253
neurectoderm3.73e-2286
nervous system4.97e-2189
regional part of forebrain1.46e-2041
forebrain1.46e-2041
anterior neural tube1.46e-2041
future forebrain1.46e-2041
multi-cellular organism2.42e-20656
pre-chordal neural plate3.73e-2061
anatomical conduit1.07e-18240
brain grey matter9.94e-1834
gray matter9.94e-1834
telencephalon1.88e-1734
cerebral hemisphere2.34e-1732
embryonic structure4.04e-17564
regional part of telencephalon6.80e-1732
developing anatomical structure8.07e-17581
tube9.01e-17192
anatomical system2.67e-16624
embryo3.03e-16592
anatomical group4.96e-16625
germ layer6.81e-16560
germ layer / neural crest6.81e-16560
embryonic tissue6.81e-16560
presumptive structure6.81e-16560
germ layer / neural crest derived structure6.81e-16560
epiblast (generic)6.81e-16560
organ system subdivision4.29e-15223
cerebral cortex3.92e-1425
pallium3.92e-1425
regional part of cerebral cortex2.51e-1322
neocortex4.59e-1220
tissue1.68e-11773
organ3.02e-11503
organ part8.89e-11218
paraxial mesoderm2.15e-1072
presumptive paraxial mesoderm2.15e-1072
dense mesenchyme tissue2.44e-1073
somite6.17e-1071
presomitic mesoderm6.17e-1071
presumptive segmental plate6.17e-1071
dermomyotome6.17e-1071
trunk paraxial mesoderm6.17e-1071
mesenchyme7.71e-10160
entire embryonic mesenchyme7.71e-10160
organism subdivision1.38e-09264
multilaminar epithelium2.55e-0983
epithelial vesicle4.19e-0978
muscle tissue5.51e-0964
musculature5.51e-0964
musculature of body5.51e-0964
trunk mesenchyme1.37e-08122
skeletal muscle tissue1.72e-0862
striated muscle tissue1.72e-0862
myotome1.72e-0862


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
NANOG#79923429.24477848101271.36586687657858e-065.34669305558436e-05
TAF1#687243.343046285745290.008005664898701650.0322894738686762



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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