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{{Coexpression_clusters
{
|full_id=C749_Wilms_rhabdomyosarcoma_medulloblastoma_fibrous_retinoblastoma_endometrial_schwannoma

Latest revision as of 11:30, 17 September 2013


Full id: C749_Wilms_rhabdomyosarcoma_medulloblastoma_fibrous_retinoblastoma_endometrial_schwannoma



Phase1 CAGE Peaks

Hg19::chr12:66218152..66218174,+p10@HMGA2
Hg19::chr12:66218183..66218209,+p4@HMGA2
Hg19::chr12:66218212..66218244,+p5@HMGA2
Hg19::chr12:66218255..66218304,+p3@HMGA2
Hg19::chr12:66218378..66218401,+p6@HMGA2
Hg19::chr12:66218413..66218418,+p17@HMGA2
Hg19::chr12:66218420..66218439,+p12@HMGA2
Hg19::chr12:66218443..66218461,+p8@HMGA2
Hg19::chr12:66218469..66218477,+p16@HMGA2
Hg19::chr12:66218573..66218596,+p7@HMGA2
Hg19::chr12:66218598..66218645,+p2@HMGA2


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

No GOStat results

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>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
organism subdivision2.76e-20264
unilaminar epithelium7.18e-18148
mesenchyme1.42e-16160
entire embryonic mesenchyme1.42e-16160
multilaminar epithelium2.06e-1683
epithelial vesicle4.00e-1578
cell layer9.56e-15309
epithelium7.58e-14306
epithelial tube1.16e-13117
trunk mesenchyme2.29e-13122
somite3.98e-1371
presomitic mesoderm3.98e-1371
presumptive segmental plate3.98e-1371
dermomyotome3.98e-1371
trunk paraxial mesoderm3.98e-1371
dense mesenchyme tissue5.97e-1373
trunk7.07e-13199
paraxial mesoderm7.99e-1372
presumptive paraxial mesoderm7.99e-1372
vasculature3.74e-1278
vascular system3.74e-1278
skeletal muscle tissue1.08e-1062
striated muscle tissue1.08e-1062
myotome1.08e-1062
surface structure5.05e-1099
muscle tissue6.61e-1064
musculature6.61e-1064
musculature of body6.61e-1064
multi-tissue structure7.81e-10342
multi-cellular organism8.43e-10656
head2.78e-0956
epithelial tube open at both ends8.01e-0959
blood vessel8.01e-0959
blood vasculature8.01e-0959
vascular cord8.01e-0959
subdivision of head1.05e-0849
artery1.59e-0842
arterial blood vessel1.59e-0842
arterial system1.59e-0842
vessel1.67e-0868
anatomical system3.50e-08624
anatomical cluster4.38e-08373
anatomical group5.42e-08625
splanchnic layer of lateral plate mesoderm6.20e-0883
anterior region of body1.38e-0762
craniocervical region1.38e-0762
embryo2.22e-07592
ectodermal placode2.27e-0731
camera-type eye3.98e-0720
simple eye3.98e-0720
immature eye3.98e-0720
ocular region3.98e-0720
eyeball of camera-type eye3.98e-0720
optic cup3.98e-0720
optic vesicle3.98e-0720
eye primordium3.98e-0720
eye9.00e-0721
visual system9.00e-0721


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)
MA0003.10.65925
MA0004.11.64978
MA0006.13.32778
MA0007.10.885261
MA0009.10.79061
MA0014.11.72362
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.0494179
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.00989454
MA0056.10
MA0057.16.83288
MA0058.12.07342
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.13.90436
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.147.2561
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.11.51073
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.11.15029
MA0095.10
MA0098.10
MA0100.12.01706
MA0101.10.216017
MA0103.10.203171
MA0105.11.91523
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.13.64606
MA0117.10.827487
MA0119.16.6312
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.637178
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.02761
MA0146.10.700193
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.166893
MA0138.20.534556
MA0002.20.111226
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.20.784016
MA0065.20.0286783
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.0391503
MA0155.10.0230394
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.761942
MA0163.10.0158063
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.210.9787
MA0102.21.32663
MA0258.10.135061
MA0259.15.51383
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

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

TF#promotersEnrichmentp-valueq-value
BHLHE40#8553416.31702310799187.16950673576926e-050.0011276748704473
CTCF#10664104.872960339159114.65999095504339e-072.20418838475442e-05
E2F1#1869114.907389214879322.51269297258347e-081.75416538344683e-06
HEY1#23462114.040111043105712.1344242734918e-071.13733233009801e-05
HNF4G#3174410.4557900096170.0003962302175651170.00387434581895733
JUND#372774.451149781190650.0002363774257855520.00257532046438736
NR3C1#29081114.9730233311731.17432722508375e-131.82780269836844e-11
POLR2A#5430112.147453176558070.0002231983422387430.00248487492432279
TAF1#6872113.343046285745291.71447392661505e-066.47821788790697e-05
TCF7L2#693465.874641761711280.0001957148425876120.00235432647373964
TFAP2C#7022109.82657146350934.61610782404372e-104.48884250498419e-08
ZNF263#10127118.221841637010688.59817612641675e-119.4128397952499e-09
ZZZ3#260097152.3538624587857.02064328878409e-151.22408842143126e-12



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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