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Coexpression cluster:C618: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:27, 17 September 2013


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)
MA0003.10.306921
MA0004.10.757232
MA0006.10.152601
MA0007.10.260673
MA0009.10.695988
MA0014.10.045605
MA0017.10.181071
MA0019.10.403106
MA0024.10.59663
MA0025.11.92696
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.12.55883
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.267987
MA0050.10.265714
MA0051.10.359609
MA0052.10.623986
MA0055.10.0207496
MA0056.10
MA0057.10.0243088
MA0058.10.580064
MA0059.10.199079
MA0060.10.564002
MA0061.10.0626878
MA0063.10
MA0066.11.69914
MA0067.11.00375
MA0068.10.0444239
MA0069.10.681911
MA0070.15.26679
MA0071.13.30536
MA0072.10.666958
MA0073.10.777363
MA0074.10.358953
MA0076.10.212295
MA0077.10.65962
MA0078.11.13748
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.0514785
MA0089.10
MA0090.10.635809
MA0091.10.278153
MA0092.10.247341
MA0093.11.46617
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.146091
MA0105.10.0203556
MA0106.10.399649
MA0107.10.348426
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.10.339925
MA0115.10.929032
MA0116.10.354243
MA0117.10.732
MA0119.10.548507
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.789887
MA0140.10.327488
MA0141.14.06438
MA0142.10.514195
MA0143.11.06513
MA0144.10.316332
MA0145.10.0609666
MA0146.10.0782306
MA0147.10.111828
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.20.326883
MA0039.20.0118926
MA0138.20.44894
MA0002.20.531015
MA0137.20.168782
MA0104.20.265556
MA0047.21.00935
MA0112.21.47552
MA0065.20.0634018
MA0150.10.218956
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.219649
MA0155.10.744296
MA0156.10.170442
MA0157.11.22595
MA0158.10
MA0159.10.112236
MA0160.11.50795
MA0161.10
MA0162.10.03301
MA0163.10.194919
MA0164.12.85122
MA0080.20.154815
MA0018.20.400879
MA0099.20.333432
MA0079.20.000723295
MA0102.21.22472
MA0258.12.1214
MA0259.10.117259
MA0442.10



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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