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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0724992894770213

Latest revision as of 14:21, 17 September 2013


Full id: C4871_Mesenchymal_astrocytoma_tubular_melanoma_Prostate_MCF7_mesenchymal



Phase1 CAGE Peaks

Hg19::chrX:37765302..37765334,+p1@ENST00000449263
Hg19::chrX:37765335..37765354,+p5@ENST00000449263
Hg19::chrX:37765364..37765390,+p3@ENST00000449263


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>

Cell Type
Ontology termp-valuen
neural cell3.69e-0925
oligodendrocyte3.09e-087
macroglial cell3.09e-087
astrocyte3.09e-087
oligodendrocyte precursor cell3.09e-087
neurectodermal cell5.48e-0859
Uber Anatomy
Ontology termp-valuen
central nervous system2.19e-2481
nervous system6.83e-2289
neurectoderm6.89e-2186
neural plate3.59e-2082
presumptive neural plate3.59e-2082
ectoderm-derived structure6.13e-19171
ectoderm6.13e-19171
presumptive ectoderm6.13e-19171
brain2.58e-1868
future brain2.58e-1868
pre-chordal neural plate9.37e-1861
ecto-epithelium3.90e-17104
neural tube4.37e-1656
neural rod4.37e-1656
future spinal cord4.37e-1656
neural keel4.37e-1656
cerebral hemisphere8.89e-1532
brain grey matter7.57e-1434
gray matter7.57e-1434
pigment epithelium of eye7.89e-1411
regional part of nervous system1.26e-1353
regional part of brain1.26e-1353
telencephalon1.45e-1334
regional part of telencephalon2.13e-1332
cerebral cortex2.08e-1125
pallium2.08e-1125
structure with developmental contribution from neural crest2.36e-11132
regional part of forebrain2.72e-1141
forebrain2.72e-1141
anterior neural tube2.72e-1141
future forebrain2.72e-1141
regional part of cerebral cortex1.66e-0822
vasculature of organ6.77e-0811
limbic system9.01e-085
camera-type eye9.04e-0820
simple eye9.04e-0820
immature eye9.04e-0820
ocular region9.04e-0820
eyeball of camera-type eye9.04e-0820
optic cup9.04e-0820
optic vesicle9.04e-0820
eye primordium9.04e-0820
organ system subdivision1.15e-07223
eye2.91e-0721
visual system2.91e-0721
atypical epithelium4.90e-074
face8.38e-0722


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)
MA0003.10.708947
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.990225
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.11.93651
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.13.4624
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.13.97071
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.15.65642
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.23.44359
MA0079.22.28794
MA0102.21.88331
MA0258.11.29138
MA0259.10.575594
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#1066435.360256373075030.0064925092527670.0281848521842935
E2F1#186934.907389214879320.008460985347239390.0328350493712966
FOSL2#2355316.93020060456170.0002060162053171620.00244251634318527
JUN#3725312.51282919233630.0005103313992726250.00446722831352223
JUND#372736.994663941871030.002921845042734990.0157849459144527
RAD21#5885310.35503389545630.0009004912073565420.00669846162429557
ZNF263#1012738.221841637010680.001799043925565870.0110322558007266



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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