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{{Coexpression_clusters
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|full_id=C1943_extraskeletal_temporal_occipital_adrenal_parietal_duodenum_bone
|id=C1943
}}

Latest revision as of 11:55, 17 September 2013


Full id: C1943_extraskeletal_temporal_occipital_adrenal_parietal_duodenum_bone



Phase1 CAGE Peaks

Hg19::chr4:66460864..66460869,-p@chr4:66460864..66460869
-
Hg19::chr4:66536057..66536071,-p5@EPHA5
Hg19::chr4:66536169..66536189,-p1@EPHA5
Hg19::chr4:66536196..66536216,-p2@EPHA5
Hg19::chr4:66536221..66536236,-p4@EPHA5


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
central nervous system1.02e-3981
nervous system5.32e-3989
neural tube2.54e-3556
neural rod2.54e-3556
future spinal cord2.54e-3556
neural keel2.54e-3556
brain3.03e-3368
future brain3.03e-3368
regional part of nervous system4.67e-3353
regional part of brain4.67e-3353
neural plate3.95e-3182
presumptive neural plate3.95e-3182
structure with developmental contribution from neural crest1.36e-30132
neurectoderm1.30e-2986
regional part of forebrain1.19e-2641
forebrain1.19e-2641
anterior neural tube1.19e-2641
future forebrain1.19e-2641
ecto-epithelium2.70e-24104
ectoderm-derived structure3.78e-24171
ectoderm3.78e-24171
presumptive ectoderm3.78e-24171
brain grey matter1.11e-2234
gray matter1.11e-2234
telencephalon2.07e-2234
pre-chordal neural plate3.25e-2261
cerebral hemisphere3.63e-2232
anatomical cluster1.61e-21373
regional part of telencephalon1.97e-2132
cerebral cortex1.79e-1825
pallium1.79e-1825
tube5.45e-18192
regional part of cerebral cortex1.15e-1722
organ system subdivision1.53e-16223
adult organism4.14e-16114
neocortex4.48e-1620
multi-tissue structure2.25e-15342
anatomical conduit6.69e-15240
epithelium7.43e-14306
cell layer2.68e-13309
embryonic structure8.43e-10564
developing anatomical structure8.84e-10581
germ layer9.59e-10560
germ layer / neural crest9.59e-10560
embryonic tissue9.59e-10560
presumptive structure9.59e-10560
germ layer / neural crest derived structure9.59e-10560
epiblast (generic)9.59e-10560
posterior neural tube1.07e-0915
chordal neural plate1.07e-0915
embryo2.02e-09592
systemic artery8.65e-0833
systemic arterial system8.65e-0833
artery1.29e-0742
arterial blood vessel1.29e-0742
arterial system1.29e-0742
segmental subdivision of hindbrain1.34e-0712
hindbrain1.34e-0712
presumptive hindbrain1.34e-0712
anatomical system1.43e-07624
anatomical group1.85e-07625
multi-cellular organism2.53e-07656
organ part7.51e-07218


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)
MA0003.10.0497246
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.369468
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.14.94778
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.11.01397
MA0056.10
MA0057.11.05691
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.12.45107
MA0073.10.0140295
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.12.13391
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.11.39943
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.16.73764
MA0062.20.284987
MA0035.20.691506
MA0039.20.311551
MA0138.20.837782
MA0002.20.30855
MA0137.22.08722
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.23503
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.03616
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
CTCF#1066444.288205098460020.005152015588243280.0239440795665957
E2F1#186943.925911371903460.007214984547106360.0298816580527121
E2F6#187644.013724585357910.006632118233933880.0283038491432584
FOS#235347.198364247115530.0006947858453382510.00559854478059421
RAD21#588548.284027116365060.0004011622639122450.00386931895832388
TRIM28#10155414.872420036214.00368496902357e-050.000734869691528739
ZNF263#1012746.577473309608540.0009875103237900160.00709462686292258



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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