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Difference between revisions of "Coexpression cluster:C467"

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|gostat_on_coexpression_clusters=GO:0008043!ferritin complex!0.0242541980461979!2512$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.0470088123859172!9391;8804
 
|gostat_on_coexpression_clusters=GO:0008043!ferritin complex!0.0242541980461979!2512$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.0470088123859172!9391;8804
 
|id=C467
 
|id=C467
|ontology_enrichment_celltype=CL:0002194!3.30e-26!63;CL:0000576!3.30e-26!63;CL:0000040!3.30e-26!63;CL:0000559!3.30e-26!63;CL:0002009!2.94e-25!65;CL:0000839!1.25e-24!70;CL:0000766!3.55e-23!76;CL:0000557!1.03e-22!71;CL:0002057!3.42e-22!42;CL:0000860!1.72e-20!45;CL:0000048!6.32e-20!430;CL:0000723!1.36e-18!436;CL:0000763!8.06e-18!112;CL:0000049!8.06e-18!112;CL:0000034!8.39e-18!444;CL:0002371!2.32e-16!591;CL:0002320!5.11e-15!365;CL:0000144!1.95e-14!625;CL:0000134!2.95e-13!358;CL:0000548!3.31e-13!679;CL:0000004!3.31e-13!679;CL:0000255!3.31e-13!679;CL:0000012!9.02e-13!682;CL:0000063!2.48e-09!578;CL:0000219!3.80e-09!390;CL:0000003!3.40e-08!722
+
|ontology_enrichment_celltype=CL:0002194!1.00e-27!59;CL:0000576!1.00e-27!59;CL:0000040!1.00e-27!59;CL:0000559!1.00e-27!59;CL:0002009!9.28e-27!61;CL:0000473!1.12e-25!48;CL:0000234!1.12e-25!48;CL:0000839!1.98e-25!66;CL:0000557!1.22e-23!67;CL:0000766!6.75e-23!72;CL:0000860!1.44e-21!42;CL:0002057!1.44e-21!42;CL:0000325!3.71e-21!87;CL:0000048!3.91e-19!427;CL:0000723!4.29e-18!433;CL:0002371!7.54e-18!588;CL:0000034!1.45e-17!441;CL:0000763!3.60e-16!108;CL:0000049!3.60e-16!108;CL:0000548!1.92e-15!679;CL:0000255!1.92e-15!679;CL:0002320!3.76e-14!361;CL:0000134!2.58e-12!354;CL:0000003!2.74e-11!722;CL:0000219!3.97e-09!386
 
|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002405!1.73e-25!115;UBERON:0002204!9.04e-23!167;UBERON:0002371!1.41e-22!80;UBERON:0000926!2.20e-22!448;UBERON:0004120!2.20e-22!448;UBERON:0006603!2.20e-22!448;UBERON:0002193!1.45e-21!112;UBERON:0002390!1.14e-20!102;UBERON:0003061!1.14e-20!102;UBERON:0001474!1.22e-19!86;UBERON:0003081!1.02e-18!216;UBERON:0004765!1.87e-18!101;UBERON:0001434!1.87e-18!101;UBERON:0002384!1.46e-14!375;UBERON:0000468!6.98e-07!659
+
|ontology_enrichment_uberon=UBERON:0002204!2.10e-24!167;UBERON:0002371!5.92e-23!76;UBERON:0000926!1.44e-21!315;UBERON:0004120!1.44e-21!315;UBERON:0006603!1.44e-21!315;UBERON:0002405!4.77e-21!93;UBERON:0002193!5.43e-21!108;UBERON:0004765!9.77e-21!90;UBERON:0002390!2.34e-20!98;UBERON:0003061!2.34e-20!98;UBERON:0001434!3.17e-20!100;UBERON:0001474!5.95e-20!82;UBERON:0003081!1.98e-17!203;UBERON:0002384!3.21e-13!371
 
|tf_chipseq_enrich=CHD2#1106;9:4.43315264319294:7.30842829241517e-05:0.00114745180762409!CTCF#10664;12:3.06300364175716:9.61865604962896e-05:0.0013695471290623!EP300#2033;9:2.90311788266709:0.00179788483493483:0.0110270903380173!HEY1#23462;13:2.50102112192258:0.000333939791046434:0.00339991595214452!RDBP#7936;3:21.9483434271464:0.000335136345525603:0.00341143321543357!SP1#6667;9:2.44216344777467:0.00604709026326707:0.02709361046784
 
|tf_chipseq_enrich=CHD2#1106;9:4.43315264319294:7.30842829241517e-05:0.00114745180762409!CTCF#10664;12:3.06300364175716:9.61865604962896e-05:0.0013695471290623!EP300#2033;9:2.90311788266709:0.00179788483493483:0.0110270903380173!HEY1#23462;13:2.50102112192258:0.000333939791046434:0.00339991595214452!RDBP#7936;3:21.9483434271464:0.000335136345525603:0.00341143321543357!SP1#6667;9:2.44216344777467:0.00604709026326707:0.02709361046784
 
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5956,0.739703,0.628162,0.209764,0.577281,0.517622,0.245643,0.349815,0.527376,0.599307,0.553749,0.557758,0.356136,0.183833,0.112513,0.298419,0.242217,0.473023,0.327127,0.663428,0.336403,0.819671,0.771327,0.626036,0.864842,0.294769,0.421857,0.425492,0.734289,0.450078,0.756406,0.942524,0.673297,0.656195,0.722323,0.653831,0.479088,0.731312,0.906425,0.287668,0.502332,0.235201,0.631419,0.431185,0.194591,0.618365,0.627132,0.908034,0.785669,0.311066,0.519466,0.30185,0.360303,0.422823,0.497581,0.663448,0.215169,0.41698,0.396338,0.345044,0.864653,0.511329,0.219313,0.0609922,0.190268,0.746356,0.322836,0.339701,0.289172,0.678096,0.355712,0.740581,0.918136,0.404258,0.830361,0.0969277,0.224015,0.609203,0.740084,0.71578,0.119242,0.801846,0.821475,0.551659,0.386187,0.0482739,0.298603,0.506047,0.80058,0.423124,0.278991,0.558436,0.399548,0.535624,0.325146,0.235812,0.630625,0.275541,0.321558,0.208986,0.494871,0.734142,0.539808,0.523339,0.337722,0.5573,0.424881,0.421533,0.685633,0.448141,0.249054,0.527648,0.764245,0.73539,0.17124,0.683615,0.364328,0.773858,0.310443,0.723073,0.694477,0.406809,0.490748,0.0711456,0.664079,0.681083,0.0362667,0.329836,0.729315,0.778358,0.64412,0.836788,0.601378,0.686889,0.58816,0.458446,0.772055,0.20584,0.204426,0.764502,0.739382,0.502194,0.883099,0.595321,0.653578,0.520868,0.875699,0.535179,0.568253,0.165746,0.72382,0.485857,0.984939,0.721621,0.768552,0.120014,0.761055,0.695591,0.485632,0.56302,0.347137,0.863146,0.747266,0.821534,0.548758,0.880204,0.669143,0.226837,0.172696,0.62605,0.267308,0.265709,0.524621,0.832178,0.404844,0.708129,0.549754,0.912164,0.982634,0.960636,0.979525,0.598937,0.785624,0.282283,0.820794,0.494594,0.965207,0.0895314,0.727126,0.755958,0.539719,0.968704,0.846414,0.714792,0.775999,0.759371,0.104051,0.466553,0.835241,0.40459,0.903248,0.967285,0.904118,0.36982,0.491495,0.69263,0.688995,0.132773,0.15001,0.424159,0.71275,0.175793,0.780449,0.159292,0.876425,0.918234,0.858051,0.95006,0.0630948,0.709199,0.903014,0.708817,0.98748,0.586065,0.857147,0.967473,0.413917,0.956805,0.989347,0.193657,0.986365,0.584857,0.472478,0.791188,0.800313,0.918059,0.874478,0.899658,0.0338542,0.252757,0.333061,0.655787,0.172276,0.507187,0.928825,0.591706,0.714194,0.547448,0.592058,0.088601,0.0699326,0.74072,0.408599,0.901902,0.980244,0.505764,0.710248,0.0350975,0.934287,0.00994798,0.945112,0.131079,0.967577,0.994349,0.695455,0.625962,0.82753,0.977004,0.976913,0.00523005,0.32821,0.264743,0.798965,0.791846,0.648862,0.793189,0.721476,0.786271,0.456364,0.0538225,0.180156,0.740317,0.941218,0.962141,0.266222,0.711154,0.616807,0.446275,0.860926,0.611476,0.561806,0.0777931,0.654033,0.841261,0.398826,0.804845,0.658504,0.416487,0.922372,0.575134,0.961225,0.922976,0.464857,0.704955,0.0237932,0.23284,0.867712,0.127361,0.620314,0.545054,0.519472,0.873661,0.200139,0.774214,0.810307,0.465108,0.726857,0.624601,0.412766,0.830446,0.65483,0.69204,0.653763,0.959769,0.657914,0.659933,0.831962,0.602204,0.945291,0.786224,0.782828,0.665349,0.941128,0.161921,0.711797,0.10159,0.478142,0.393725,0.11139,0.395765,0.477816,0.213424,0.770559,0.160772,0.428718,0.0970903,0.634099,0.711167,0.773279,0.712346,0.82344,0.804555,0.483529,0.50419,0.363117,0.869213,0.42579,0.611419,0.803718,0.126783,0.74946,0.778257,0.825765,0.828983,0.789596,0.926044,0.821183,0.787728,0.764838,0.23533,0.789306,0.207013,0.00071683,0.604308,0.750479,0.834891,0.666158,0.465333,0.258296,0.4865,0.863481,0.525232,0.386116,0.226119,0.885812,0.205688,0.30182,0.838679,0.710145,0.837984,0.725761,0.240267,0.38041,0.312897,0.27845,0.37485,0.210468,0.803871,0.692242,0.591961,0.165318,0.192521,0.349403,0.507623,0.701148,0.519713,0.196263,0.237934,0.621479,0.258889,0.752002,0.704624,0.345556,0.316926,0.246307,0.60389,0.759758,0.761849,0.408769,0.876747,0.880478,0.797125,0.814368,0.803769,0.29033,0.777157,0.324782,0.0568831,0.531289,0.587875,0.383724,0.207838,0.284102,0.784927,0.573443,0.696107,0.62601,0.344713,0.828709,0.733486,0.39491,0.510182,0.468821,0.925842,0.202425,0.821425,0.451581,0.0760947,0.546215,0.320004,0.320851,0.682393,0.433678,0.252507,0.320659,0.932716,0.165929,0.810215,0.42716,0.844731,0.183969,0.4476,0.514645,0.371276,0.597501,0.369981,0.538566,0.381461,0.42605,0.251247,0.554795,0.270785,0.384359,0.481683,0.230538,0.637576,0.798214,0.102832,0.213971,0.798393,0.656939,0.62998,0.873762,0.790478,0.271194,0.916294,0.151382,0.7457,0.903199,0.88347,0.628059,0.706525,0.0811475,0.788886,0.906223,0.848712,0.297589,0.57753,0.248535,0.262347,0.211967,0.448259,0.187057,0.901365,0.676205,0.326937,0.716128,0.830946,0.497294,0.937871,0.833214,0.224556,0.506147,0.466831,0.745372,0.732468,0.341299,0.649123,0.095206,0.890164,0.52549,0.828321,0.392372,0.69814,0.81746,0.869961,0.80097,0.956705
 
}}
 
}}

Revision as of 07:08, 19 October 2012


Full id: C467_CD14_Monocytederived_Mesenchymal_Macrophage_Dendritic_mucinous_liver



Phase1 CAGE Peaks

  Short description
Hg19::chr11:64570565..64570568,+ p@chr11:64570565..64570568
+
Hg19::chr15:82336075..82336082,- p2@MEX3B
Hg19::chr16:86227253..86227256,- p@chr16:86227253..86227256
-
Hg19::chr18:43418864..43418874,- p@chr18:43418864..43418874
-
Hg19::chr19:3870787..3870791,+ p@chr19:3870787..3870791
+
Hg19::chr19:49468563..49468567,+ p1@FTL
Hg19::chr19:49468653..49468695,- p@chr19:49468653..49468695
-
Hg19::chr19:49469582..49469598,- p@chr19:49469582..49469598
-
Hg19::chr19:49469909..49469927,- p3@BC007552
Hg19::chr19:49469928..49469955,- p1@BC007552
Hg19::chr19:49470000..49470017,- p4@BC007552
Hg19::chr19:49470100..49470134,- p2@BC007552
Hg19::chr1:167522982..167523017,- p1@CREG1
Hg19::chr1:229478625..229478628,+ p@chr1:229478625..229478628
+
Hg19::chr20:4004363..4004364,+ p1@FTLP3
Hg19::chr20:4004638..4004661,+ p3@FTLP3
Hg19::chr22:21058481..21058484,+ +
p@chr22:21058481..21058484
Hg19::chr2:96931834..96931847,+ p3@CIAO1
Hg19::chr5:139555310..139555313,+ p@chr5:139555310..139555313
+
Hg19::chr9:108505287..108505289,+ +
p@chr9:108505287..108505289
Hg19::chrX:30648208..30648217,+ p1@FTLP2


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:0008043ferritin complex0.0242541980461979
GO:0006357regulation of transcription from RNA polymerase II promoter0.0470088123859172



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


Uber Anatomy
Ontology termp-valuen
musculoskeletal system2.10e-24167
bone marrow5.92e-2376
mesoderm1.44e-21315
mesoderm-derived structure1.44e-21315
presumptive mesoderm1.44e-21315
immune system4.77e-2193
hemolymphoid system5.43e-21108
skeletal element9.77e-2190
hematopoietic system2.34e-2098
blood island2.34e-2098
skeletal system3.17e-20100
bone element5.95e-2082
lateral plate mesoderm1.98e-17203
connective tissue3.21e-13371


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CHD2#110694.433152643192947.30842829241517e-050.00114745180762409
CTCF#10664123.063003641757169.61865604962896e-050.0013695471290623
EP300#203392.903117882667090.001797884834934830.0110270903380173
HEY1#23462132.501021121922580.0003339397910464340.00339991595214452
RDBP#7936321.94834342714640.0003351363455256030.00341143321543357
SP1#666792.442163447774670.006047090263267070.02709361046784



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.