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{{Coexpression_clusters
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Latest revision as of 02:21, 17 September 2013


Full id: C366_heart_vagina_adipose_diaphragm_left_aorta_breast



Phase1 CAGE Peaks

Hg19::chr10:15647768..15647794,-p@chr10:15647768..15647794
-
Hg19::chr10:92678409..92678410,-p@chr10:92678409..92678410
-
Hg19::chr11:123340107..123340127,+p@chr11:123340107..123340127
+
Hg19::chr12:2386467..2386484,+p@chr12:2386467..2386484
+
Hg19::chr12:2468720..2468724,+p@chr12:2468720..2468724
+
Hg19::chr13:31729140..31729163,-p@chr13:31729140..31729163
-
Hg19::chr14:102550059..102550072,-p@chr14:102550059..102550072
-
Hg19::chr14:102551390..102551436,-p10@HSP90AA1
Hg19::chr14:102551456..102551467,-p27@HSP90AA1
Hg19::chr14:92349687..92349698,-p@chr14:92349687..92349698
-
Hg19::chr15:35082449..35082469,-p@chr15:35082449..35082469
-
Hg19::chr15:86272097..86272099,+p@chr15:86272097..86272099
+
Hg19::chr16:10783399..10783401,+p@chr16:10783399..10783401
+
Hg19::chr17:77026478..77026512,+p@chr17:77026478..77026512
+
Hg19::chr19:14628234..14628252,-p@chr19:14628234..14628252
-
Hg19::chr19:2716727..2716731,-p10@DIRAS1
Hg19::chr1:159174559..159174571,+p3@DARC
Hg19::chr22:47045714..47045722,+p@chr22:47045714..47045722
+
Hg19::chr3:46505091..46505110,-p5@LTF
Hg19::chr3:64517143..64517146,-p@chr3:64517143..64517146
-
Hg19::chr3:64673668..64673684,-p1@ADAMTS9
Hg19::chr4:95332178..95332184,+p@chr4:95332178..95332184
+
Hg19::chr5:99385820..99385831,-p@chr5:99385820..99385831
-
Hg19::chr5:99390735..99390743,-p@chr5:99390735..99390743
-
Hg19::chr6:31785440..31785544,+p@chr6:31785440..31785544
+
Hg19::chr6:31785565..31785576,+p@chr6:31785565..31785576
+
Hg19::chr6:31797870..31797898,+p6@HSPA1B
Hg19::chr7:105926145..105926185,-p7@NAMPT
Hg19::chr7:105926216..105926230,-p10@NAMPT
Hg19::chr9:124095011..124095025,+p@chr9:124095011..124095025
+


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:0042026protein refolding0.0216354645001766
GO:0030911TPR domain binding0.0260593848696238
GO:0030235nitric-oxide synthase regulator activity0.0260593848696238
GO:0009607response to biotic stimulus0.0260593848696238
GO:0045429positive regulation of nitric oxide biosynthetic process0.0346024795986266
GO:0045428regulation of nitric oxide biosynthetic process0.0360400055870461
GO:0006516glycoprotein catabolic process0.0475392087874602
GO:0006952defense response0.0475392087874602
GO:0046209nitric oxide metabolic process0.0475392087874602
GO:0006809nitric oxide biosynthetic process0.0475392087874602



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
adult organism2.14e-54114
neural tube4.06e-1856
neural rod4.06e-1856
future spinal cord4.06e-1856
neural keel4.06e-1856
neurectoderm6.81e-1886
neural plate2.23e-1782
presumptive neural plate2.23e-1782
brainstem3.39e-156
regional part of nervous system3.48e-1553
regional part of brain3.48e-1553
structure with developmental contribution from neural crest4.10e-13132
valve9.86e-133
cardiac mesenchyme9.86e-133
cardial valve9.86e-133
tunica intima9.86e-133
heart layer9.86e-133
endocardium9.86e-133
endocardial cushion9.86e-133
presumptive endocardium9.86e-133
ecto-epithelium1.53e-12104
male genital duct4.59e-123
internal male genitalia4.59e-123
medulla oblongata2.35e-113
myelencephalon2.35e-113
future myelencephalon2.35e-113
posterior neural tube5.33e-1115
chordal neural plate5.33e-1115
central nervous system5.39e-1181
brain8.65e-1168
future brain8.65e-1168
brain grey matter2.50e-1034
gray matter2.50e-1034
anatomical cluster6.79e-10373
regional part of forebrain9.48e-1041
forebrain9.48e-1041
anterior neural tube9.48e-1041
future forebrain9.48e-1041
neural nucleus9.87e-109
nucleus of brain9.87e-109
nervous system1.74e-0989
anatomical conduit3.33e-09240
duct of male reproductive system3.79e-094
atrioventricular valve4.31e-092
organ system subdivision4.63e-09223
open tracheal system trachea8.23e-092
compound organ8.50e-0968
tube1.05e-08192
locus ceruleus1.15e-082
brainstem nucleus1.15e-082
hindbrain nucleus1.15e-082
telencephalon2.69e-0834
multi-tissue structure4.94e-08342
segmental subdivision of hindbrain1.99e-0712
hindbrain1.99e-0712
presumptive hindbrain1.99e-0712
regional part of telencephalon2.92e-0732
pre-chordal neural plate6.84e-0761
segmental subdivision of nervous system7.89e-0713
ectoderm-derived structure7.93e-07171
ectoderm7.93e-07171
presumptive ectoderm7.93e-07171


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)
MA0003.11.47648e-05
MA0004.10.31844
MA0006.10.134363
MA0007.10.0871398
MA0009.10.417521
MA0014.10.0116099
MA0017.10.694981
MA0019.11.02157
MA0024.10.332558
MA0025.10.531977
MA0027.11.95983
MA0028.10.0380705
MA0029.10.347825
MA0030.10.898657
MA0031.10.786656
MA0038.10.464214
MA0040.10.352485
MA0041.11.15504
MA0042.10.300789
MA0043.10.417784
MA0046.10.408463
MA0048.10.0261535
MA0050.10.626734
MA0051.10.457885
MA0052.10.355576
MA0055.10.0919169
MA0056.10
MA0057.10.227938
MA0058.10.443744
MA0059.10.199599
MA0060.10.0459286
MA0061.10.579374
MA0063.10
MA0066.10.907141
MA0067.10.697961
MA0068.10.416765
MA0069.10.405267
MA0070.11.02498
MA0071.10.407159
MA0072.10.392323
MA0073.10.191062
MA0074.10.89351
MA0076.10.060743
MA0077.11.00303
MA0078.10.612611
MA0081.10.19978
MA0083.11.08548
MA0084.10.873335
MA0087.10.390315
MA0088.10.00585586
MA0089.10
MA0090.10.236197
MA0091.10.321927
MA0092.10.9717
MA0093.10.585007
MA0095.10
MA0098.10
MA0100.10.161006
MA0101.10.594807
MA0103.10.125753
MA0105.10.189462
MA0106.10.527317
MA0107.10.640153
MA0108.20.781414
MA0109.10
MA0111.10.0723215
MA0113.11.05411
MA0114.10.191937
MA0115.10.62811
MA0116.10.0177927
MA0117.10.449155
MA0119.11.10716
MA0122.10.471243
MA0124.10.590699
MA0125.10.516292
MA0130.10
MA0131.10.226279
MA0132.10
MA0133.10
MA0135.10.443024
MA0136.10.474844
MA0139.10.0271546
MA0140.10.403323
MA0141.10.197657
MA0142.10.732627
MA0143.10.553308
MA0144.11.19581
MA0145.10.0579147
MA0146.10.00106014
MA0147.10.0831159
MA0148.11.17714
MA0149.13.20749
MA0062.20.00542453
MA0035.20.801096
MA0039.20.000106231
MA0138.20.214585
MA0002.20.238419
MA0137.21.42719
MA0104.20.0455118
MA0047.20.980224
MA0112.20.27967
MA0065.20.206209
MA0150.10.229194
MA0151.10
MA0152.10.412817
MA0153.10.501603
MA0154.10.450486
MA0155.10.0882858
MA0156.10.15867
MA0157.10.686763
MA0158.10
MA0159.10.0835942
MA0160.10.373329
MA0161.10
MA0162.10.000754431
MA0163.10.190215
MA0164.10.196993
MA0080.20.0341882
MA0018.20.179075
MA0099.20.132386
MA0079.22.1449e-07
MA0102.22.09985
MA0258.10.532714
MA0259.10.0895432
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.