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Coexpression cluster:C618: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007100!4.60e-22!27;UBERON:0000341!5.94e-20!2;UBERON:0005090!1.06e-19!2;UBERON:0001630!1.06e-19!2;UBERON:0003103!2.08e-15!68;UBERON:0003978!5.04e-14!3;UBERON:0009751!5.04e-14!3;UBERON:0000946!5.04e-14!3;UBERON:0002523!5.04e-14!3;UBERON:0005983!5.04e-14!3;UBERON:0002165!5.04e-14!3;UBERON:0002062!5.04e-14!3;UBERON:0007280!5.04e-14!3;UBERON:0004151!6.52e-14!3;UBERON:0001723!1.70e-13!3;UBERON:0001033!1.70e-13!3;UBERON:0010056!1.70e-13!3;UBERON:0007023!4.78e-12!114;UBERON:0002146!3.08e-11!1;UBERON:0005623!3.08e-11!1;UBERON:0002079!4.15e-11!1;UBERON:0002135!4.58e-11!1;UBERON:0002084!5.05e-11!1;UBERON:0002082!5.05e-11!1;UBERON:0010226!5.05e-11!1;UBERON:0002426!6.77e-11!1;UBERON:0003831!6.77e-11!1;UBERON:0003898!6.77e-11!1;UBERON:0004830!6.77e-11!1;UBERON:0003830!6.77e-11!1;UBERON:0005175!6.77e-11!1;UBERON:0001774!6.77e-11!1;UBERON:0001103!6.77e-11!1;UBERON:0010084!6.77e-11!1;UBERON:0000989!9.97e-11!1;UBERON:0008811!9.97e-11!1;UBERON:0006258!9.97e-11!1;UBERON:0005876!9.97e-11!1;UBERON:0004874!9.97e-11!1;UBERON:0007029!1.10e-10!1;UBERON:0005418!1.46e-10!1;UBERON:0001389!1.46e-10!1;UBERON:0000026!1.46e-10!1;UBERON:0008784!1.46e-10!1;UBERON:0006058!1.46e-10!1;UBERON:0003663!1.46e-10!1;UBERON:0004256!1.46e-10!1;UBERON:0004708!1.46e-10!1;UBERON:0002101!1.46e-10!1;UBERON:0004709!1.46e-10!1;UBERON:0002529!1.46e-10!1;UBERON:0010538!1.46e-10!1;UBERON:0003661!1.46e-10!1;UBERON:0010890!1.46e-10!1;UBERON:0002471!1.46e-10!1;UBERON:0001383!1.46e-10!1;UBERON:0004357!1.46e-10!1;UBERON:0004347!1.46e-10!1;UBERON:0005420!1.46e-10!1;UBERON:0005732!1.46e-10!1;UBERON:0010758!1.46e-10!1;UBERON:0010707!1.46e-10!1;UBERON:0000978!1.46e-10!1;UBERON:0002103!1.46e-10!1;UBERON:0001665!1.46e-10!1;UBERON:0003823!1.46e-10!1;UBERON:0000154!1.46e-10!1;UBERON:0010709!1.46e-10!1;UBERON:0005733!1.46e-10!1;UBERON:0005730!1.46e-10!1;UBERON:0002372!1.77e-10!1;UBERON:0001961!1.77e-10!1;UBERON:0001744!1.77e-10!1;UBERON:0001735!1.77e-10!1;UBERON:0000948!4.48e-10!24;UBERON:0005498!4.48e-10!24;UBERON:0004140!4.48e-10!24;UBERON:0009881!4.48e-10!24;UBERON:0004141!4.48e-10!24;UBERON:0003084!4.48e-10!24;UBERON:0007005!4.48e-10!24;UBERON:0004139!4.48e-10!24;UBERON:0004291!4.48e-10!24;UBERON:0001042!5.94e-09!10;UBERON:0009145!5.94e-09!10;UBERON:0006562!3.49e-08!11
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0.0014089,0.367768,0.283437,0.0332535,0.296211,0.375214,0.342479,0.009824,0.219847,0.193816,0.000846932,8.41619e-08,0.0173116,0.391636,0.115085,0.0633558,0.0472111,0.0283153,0.0493117,0.0240205,0.0614481
|tfbs_overrepresentation_for_novel_motifs=0.18943,0.0298012,1.03473,0.297884,0.153879,1.4611,0.360887,0.569923,0.562966,0.371847,1.37072,1.81997,0.0551804,0.350994,0.152923,0.976376,0.560096,0.117033,0.220719,0.663557,1.63625,0.440546,0.290113,0.896648,0.218509,0.418678,0.173854,0.288329,0.156049,0.352289,2.01602,0.594213,0.658757,0.0562618,0.130292,0.247035,0.12818,0.29748,0.363308,0.239283,0.40562,0.676934,0.0105046,0.151865,0.0858748,0.596593,0.361827,0.727354,0.127784,0.921037,0.431291,0.372023,0.259277,0.666176,0.811691,0.353512,0.15913,0.325599,0.632877,0.324748,1.52924,0.363871,0.564331,0.534578,0.379438,0.503101,0.896916,1.25738,0.584559,1.09778,0.230809,0.987824,0.103789,0.80977,0.0530506,1.54608,0.658179,0.519091,0.581542,0.61268,0.0636623,0.533593,0.37913,0.577767,0.760489,0.00225746,0.01795,0.146775,0.454557,1.35556,0.98765,0.734737,0.609873,0.101133,0.154399,1.18021,0.218567,0.649779,0.458696,0.12702,1.7682,1.47082,0.644537,0.563483,0.492631,0.268065,0.548871,0.348037,1.16972,0.142849,0.19228,0.641937,0.179896,0.279418,0.940917,0.12714,0.0201493,0.253155,0.500972,0.336456,0.801818,0.452379,0.294241,1.00953,1.04884,0.519787,0.355419,0.614537,0.842806,0.109858,0.735394,0.256408,0.856671,1.00316,1.00021,1.32731,0.249339,0.786388,0.95886,1.80749,1.40745,0.922589,0.938959,0.646464,1.23712,0.318465,0.47912,1.64894,0.670822,0.0991414,0.437837,0.00934991,0.735758,0.0728391,0.363452,1.12781,0.440071,0.870811,0.218554,1.08507,0.921409,0.718143,0.580811,0.199028,1.26837,0.378443,0.635551,0.35974,0.0337609
}}
}}

Revision as of 14:21, 26 November 2012


Full id: C618_skeletal_heart_left_diaphragm_throat_skin_maxillary



Phase1 CAGE Peaks

Hg19::chr10:919094..919101,-p@chr10:919094..919101
-
Hg19::chr10:919161..919172,-p@chr10:919161..919172
-
Hg19::chr18:3219935..3219940,-p5@MYOM1
Hg19::chr19:3950387..3950398,+p@chr19:3950387..3950398
+
Hg19::chr20:33565724..33565728,+p3@MYH7B
Hg19::chr2:179494327..179494343,-p@chr2:179494327..179494343
-
Hg19::chr2:179494358..179494367,-p@chr2:179494358..179494367
-
Hg19::chr2:179494375..179494392,-p@chr2:179494375..179494392
-
Hg19::chr2:179494404..179494433,-p@chr2:179494404..179494433
-
Hg19::chr2:179665435..179665442,-p@chr2:179665435..179665442
-
Hg19::chr5:191638..191646,+p9@LRRC14B
Hg19::chr6:73471730..73471745,+p@chr6:73471730..73471745
+
Hg19::chr7:123241658..123241669,-p@chr7:123241658..123241669
-
Hg19::chr8:124665994..124666002,-p@chr8:124665994..124666002
-


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

GO IDGO nameFDR corrected p-value
GO:0016459myosin complex0.000402943405822179
GO:0015629actin cytoskeleton0.00155109408377679
GO:0044430cytoskeletal part0.00772230272679474
GO:0032982myosin filament0.00772230272679474
GO:0005863striated muscle thick filament0.00772230272679474
GO:0005859muscle myosin complex0.00891040668937179
GO:0016460myosin II complex0.00891040668937179
GO:0005856cytoskeleton0.00891040668937179
GO:0006941striated muscle contraction0.00991794678464657
GO:0008307structural constituent of muscle0.0101316428173755
GO:0030017sarcomere0.010525451995305
GO:0030016myofibril0.0106525809272849
GO:0044449contractile fiber part0.0110240654734831
GO:0043292contractile fiber0.0110240654734831
GO:0043234protein complex0.0178123998291474
GO:0043232intracellular non-membrane-bound organelle0.0178123998291474
GO:0043228non-membrane-bound organelle0.0178123998291474
GO:0003012muscle system process0.0209109374396495
GO:0006936muscle contraction0.0209109374396495
GO:0032991macromolecular complex0.0267761009008234
GO:0044446intracellular organelle part0.0275376365500003
GO:0044422organelle part0.0275376365500003
GO:0003779actin binding0.0456705904149696



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
primary circulatory organ4.60e-2227
throat5.94e-202
muscle structure1.06e-192
muscle organ1.06e-192
compound organ2.08e-1568
valve5.04e-143
cardiac mesenchyme5.04e-143
cardial valve5.04e-143
tunica intima5.04e-143
heart layer5.04e-143
endocardium5.04e-143
endocardial cushion5.04e-143
presumptive endocardium5.04e-143
cardiac chamber6.52e-143
tongue1.70e-133
gustatory system1.70e-133
future tongue1.70e-133
adult organism4.78e-12114
pulmonary valve3.08e-111
semi-lunar valve3.08e-111
left cardiac atrium4.15e-111
mitral valve4.58e-111
heart left ventricle5.05e-111
cardiac ventricle5.05e-111
future cardiac ventricle5.05e-111
chest muscle6.77e-111
respiratory system muscle6.77e-111
skeletal muscle of trunk6.77e-111
respiratory system skeletal muscle6.77e-111
thoracic segment muscle6.77e-111
chest organ6.77e-111
muscle of trunk6.77e-111
diaphragm6.77e-111
future diaphragm6.77e-111
penis9.97e-111
intromittent organ9.97e-111
lateral plate mesenchyme9.97e-111
undifferentiated genital tubercle9.97e-111
somatopleure9.97e-111
surface1.10e-101
hindlimb bud1.46e-101
soleus muscle1.46e-101
appendage1.46e-101
lower limb segment1.46e-101
multi-limb segment region1.46e-101
hindlimb muscle1.46e-101
hindlimb zeugopod muscle1.46e-101
paired limb/fin1.46e-101
limb1.46e-101
pelvic appendage1.46e-101
limb segment1.46e-101
paired limb/fin segment1.46e-101
limb muscle1.46e-101
pelvic complex muscle1.46e-101
zeugopod1.46e-101
muscle of leg1.46e-101
paired limb/fin bud1.46e-101
limb bud1.46e-101
pelvic appendage bud1.46e-101
limb/fin field1.46e-101
subdivision of organism along appendicular axis1.46e-101
appendage girdle complex1.46e-101
leg1.46e-101
hindlimb1.46e-101
triceps surae1.46e-101
hindlimb zeugopod1.46e-101
posterior region of body1.46e-101
pelvic complex1.46e-101
limb field1.46e-101
hindlimb/pelvic fin field1.46e-101
tonsil1.77e-101
mucosa-associated lymphoid tissue1.77e-101
lymphoid tissue1.77e-101
tonsillar ring1.77e-101
heart4.48e-1024
primitive heart tube4.48e-1024
primary heart field4.48e-1024
anterior lateral plate mesoderm4.48e-1024
heart tube4.48e-1024
heart primordium4.48e-1024
cardiac mesoderm4.48e-1024
cardiogenic plate4.48e-1024
heart rudiment4.48e-1024
chordate pharynx5.94e-0910
pharyngeal region of foregut5.94e-0910
pharynx3.49e-0811
Disease
Ontology termp-valuen
heart disease3.33e-202
vascular disease8.22e-111
ischemia8.22e-111
extrinsic cardiomyopathy8.22e-111
myocardial ischemia8.22e-111
myocardial infarction8.22e-111
cardiovascular system disease1.40e-104


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

No analysis results for this cluster

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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