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{{Coexpression_clusters
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|full_id=C3067_medulloblastoma_lung_placenta_renal_retina_gall_rectum
|id=C3067
}}

Latest revision as of 12:18, 17 September 2013


Full id: C3067_medulloblastoma_lung_placenta_renal_retina_gall_rectum



Phase1 CAGE Peaks

Hg19::chr11:100557931..100557947,+p4@ARHGAP42
Hg19::chr11:100557958..100558008,+p2@ARHGAP42
Hg19::chr11:100558010..100558029,+p1@ARHGAP42


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
anatomical cluster2.41e-28373
organ system subdivision3.52e-27223
multi-tissue structure1.07e-26342
central nervous system8.10e-2081
nervous system1.16e-1889
adult organism1.87e-18114
brain7.61e-1768
future brain7.61e-1768
neural tube9.98e-1556
neural rod9.98e-1556
future spinal cord9.98e-1556
neural keel9.98e-1556
cell layer1.99e-14309
epithelium4.39e-14306
neural plate7.26e-1482
presumptive neural plate7.26e-1482
regional part of nervous system2.44e-1353
regional part of brain2.44e-1353
anatomical conduit3.31e-13240
tube2.15e-12192
neurectoderm5.34e-1286
structure with developmental contribution from neural crest6.32e-12132
multi-cellular organism1.12e-11656
ectoderm-derived structure1.27e-11171
ectoderm1.27e-11171
presumptive ectoderm1.27e-11171
regional part of forebrain1.44e-1141
forebrain1.44e-1141
anterior neural tube1.44e-1141
future forebrain1.44e-1141
embryo2.46e-11592
organ1.51e-10503
anatomical system2.44e-10624
ecto-epithelium3.09e-10104
pre-chordal neural plate4.12e-1061
anatomical group4.53e-10625
mesenchyme1.85e-09160
entire embryonic mesenchyme1.85e-09160
brain grey matter2.11e-0934
gray matter2.11e-0934
developing anatomical structure2.65e-09581
telencephalon2.73e-0934
digestive system4.59e-09145
digestive tract4.59e-09145
primitive gut4.59e-09145
regional part of telencephalon8.10e-0932
gastrointestinal system1.07e-0825
cerebral hemisphere1.22e-0832
subdivision of digestive tract4.36e-08118
organ part8.70e-08218
endoderm-derived structure1.50e-07160
endoderm1.50e-07160
presumptive endoderm1.50e-07160
embryonic structure3.05e-07564
cerebral cortex3.64e-0725
pallium3.64e-0725
abdomen element4.59e-0754
abdominal segment element4.59e-0754
gut epithelium5.12e-0754
intestine5.54e-0717


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.90467
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
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
MA0073.11.79391
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
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
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.12.4174
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.13.85295
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.88736
MA0065.22.13692
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.19.44515
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.70224
MA0102.21.88331
MA0258.10.519674
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
E2F1#186934.907389214879320.008460985347239390.0323541611262571
EGR1#195834.988179094810140.008056488137383440.0319030698635091
ELF1#199734.258097958807540.01295179875054610.0460030237283459
GABPB1#255337.067683836182170.002832212825417420.0153635005076492
MEF2A#4205318.74323090964410.0001518243905622470.00194748065904329
SIN3A#2594235.408884726815140.006318961977991520.027536763332198
TCF12#6938310.63446490218640.0008313523990202070.00627624788212168



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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