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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:27, 17 September 2013


Full id: C626_penis_skeletal_tongue_diaphragm_salivary_throat_Adipocyte



Phase1 CAGE Peaks

Hg19::chr12:53068552..53068579,-p@chr12:53068552..53068579
-
Hg19::chr12:53068835..53068874,-p@chr12:53068835..53068874
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Hg19::chr12:53068889..53068898,-p@chr12:53068889..53068898
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Hg19::chr12:53068923..53068932,-p@chr12:53068923..53068932
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Hg19::chr17:10401094..10401106,-p@chr17:10401094..10401106
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Hg19::chr17:38974394..38974440,-p@chr17:38974394..38974440
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Hg19::chr17:4448859..4448864,-p@chr17:4448859..4448864
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Hg19::chr20:33451391..33451397,-p6@GGT7
Hg19::chr2:178753478..178753487,-p10@PDE11A
Hg19::chr2:179433518..179433530,-p@chr2:179433518..179433530
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Hg19::chr2:179595422..179595432,-p@chr2:179595422..179595432
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Hg19::chr2:179640441..179640449,-p107@TTN
Hg19::chr3:155838361..155838382,+p10@KCNAB1
Hg19::chrX:135292261..135292285,+p@chrX:135292261..135292285
+


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:0051393alpha-actinin binding0.0168507433336938
GO:0042805actinin binding0.0168507433336938
GO:00475553',5'-cyclic-GMP phosphodiesterase activity0.0168507433336938
GO:0030239myofibril assembly0.0168507433336938
GO:0055001muscle cell development0.0168507433336938
GO:0055002striated muscle cell development0.0168507433336938
GO:0017022myosin binding0.0168507433336938
GO:0048628myoblast maturation0.0180193423251079
GO:0048627myoblast development0.0180193423251079
GO:0030018Z disc0.0204093141395362
GO:0051146striated muscle cell differentiation0.0204093141395362
GO:0031674I band0.0204093141395362
GO:0015459potassium channel regulator activity0.0204093141395362
GO:0031032actomyosin structure organization and biogenesis0.0221081374747377
GO:0045445myoblast differentiation0.025174788347535
GO:0000794condensed nuclear chromosome0.025174788347535
GO:0016247channel regulator activity0.025174788347535
GO:0006941striated muscle contraction0.025174788347535
GO:0048741skeletal muscle fiber development0.025174788347535
GO:0008307structural constituent of muscle0.025174788347535
GO:0048747muscle fiber development0.025174788347535
GO:0046777protein amino acid autophosphorylation0.025174788347535
GO:0048469cell maturation0.025174788347535
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.025174788347535
GO:0042692muscle cell differentiation0.025174788347535
GO:0016540protein autoprocessing0.025174788347535
GO:0004112cyclic-nucleotide phosphodiesterase activity0.025174788347535
GO:0030017sarcomere0.025174788347535
GO:0000793condensed chromosome0.025174788347535
GO:0030016myofibril0.025174788347535
GO:0021700developmental maturation0.025174788347535
GO:0044449contractile fiber part0.0276034512261386
GO:0043292contractile fiber0.0285480848324906
GO:0007519skeletal muscle development0.0290047049993703
GO:0014706striated muscle development0.036984395187087
GO:0016485protein processing0.0393456394331647
GO:0000228nuclear chromosome0.0393456394331647
GO:0005737cytoplasm0.0469339209353349



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
muscle structure2.97e-312
muscle organ2.97e-312
tongue1.76e-213
gustatory system1.76e-213
future tongue1.76e-213
penis4.72e-171
intromittent organ4.72e-171
lateral plate mesenchyme4.72e-171
undifferentiated genital tubercle4.72e-171
somatopleure4.72e-171
surface6.47e-171
chest muscle1.41e-161
respiratory system muscle1.41e-161
skeletal muscle of trunk1.41e-161
respiratory system skeletal muscle1.41e-161
thoracic segment muscle1.41e-161
chest organ1.41e-161
muscle of trunk1.41e-161
diaphragm1.41e-161
future diaphragm1.41e-161
hindlimb bud1.65e-161
soleus muscle1.65e-161
appendage1.65e-161
lower limb segment1.65e-161
multi-limb segment region1.65e-161
hindlimb muscle1.65e-161
hindlimb zeugopod muscle1.65e-161
paired limb/fin1.65e-161
limb1.65e-161
pelvic appendage1.65e-161
limb segment1.65e-161
paired limb/fin segment1.65e-161
limb muscle1.65e-161
pelvic complex muscle1.65e-161
zeugopod1.65e-161
muscle of leg1.65e-161
paired limb/fin bud1.65e-161
limb bud1.65e-161
pelvic appendage bud1.65e-161
limb/fin field1.65e-161
subdivision of organism along appendicular axis1.65e-161
appendage girdle complex1.65e-161
leg1.65e-161
hindlimb1.65e-161
triceps surae1.65e-161
hindlimb zeugopod1.65e-161
posterior region of body1.65e-161
pelvic complex1.65e-161
limb field1.65e-161
hindlimb/pelvic fin field1.65e-161
epididymis2.25e-161
pharyngeal arch system7.19e-1418
thyroid gland4.66e-135
pharyngeal pouch4.66e-135
thyroid diverticulum4.66e-135
pharyngeal pouch 24.66e-135
thyroid primordium4.66e-135
throat4.34e-092
open tracheal system trachea8.09e-092
adult organism6.12e-08114
chordate pharynx4.26e-0710
pharyngeal region of foregut4.26e-0710


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)
MA0003.10.000725818
MA0004.10.275994
MA0006.10.152601
MA0007.10.260673
MA0009.10.695988
MA0014.10.000542531
MA0017.10.181071
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.492785
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.110534
MA0050.10.265714
MA0051.10.359609
MA0052.10.623986
MA0055.10.0654733
MA0056.10
MA0057.10.0243088
MA0058.10.200063
MA0059.10.199079
MA0060.10.0773489
MA0061.10.224865
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.169955
MA0069.12.75043
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.10.00376762
MA0074.10.358953
MA0076.10.609177
MA0077.10.65962
MA0078.10.447828
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.0514785
MA0089.10
MA0090.10.223576
MA0091.10.278153
MA0092.10.247341
MA0093.10.154754
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.448026
MA0105.10.0899037
MA0106.10.399649
MA0107.10.107387
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.10.104181
MA0115.10.929032
MA0116.10.354243
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.0564547
MA0140.11.572
MA0141.10.197753
MA0142.10.514195
MA0143.11.06513
MA0144.10.316332
MA0145.10.0609666
MA0146.10.248894
MA0147.10.111828
MA0148.10.804328
MA0149.10.319221
MA0062.20.216892
MA0035.20.872194
MA0039.20.0567934
MA0138.20.44894
MA0002.20.248488
MA0137.20.504333
MA0104.20.0769208
MA0047.20.388882
MA0112.20.0554275
MA0065.20.0133095
MA0150.10.218956
MA0151.10
MA0152.10.886132
MA0153.10.790794
MA0154.10.0872435
MA0155.10.0101184
MA0156.10.508404
MA0157.10.489002
MA0158.10
MA0159.10.730396
MA0160.10.30953
MA0161.10
MA0162.10.03301
MA0163.10.0183776
MA0164.11.08899
MA0080.20.154815
MA0018.20.400879
MA0099.20.333432
MA0079.20.027534
MA0102.21.22472
MA0258.10.300766
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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