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{{Coexpression_clusters
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|full_id=C3408_cerebellum_pineal_rhabdomyosarcoma_neuroectodermal_brain_Pericytes_iPS
|id=C3408
|ontology_enrichment_celltype=CL:0000133!4.31e-07!59
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.39e-41!94;UBERON:0001016!1.39e-41!94;UBERON:0005743!2.09e-41!86;UBERON:0001017!8.87e-40!82;UBERON:0002346!1.38e-37!90;UBERON:0003075!1.58e-35!86;UBERON:0007284!1.58e-35!86;UBERON:0001049!3.30e-33!57;UBERON:0005068!3.30e-33!57;UBERON:0006241!3.30e-33!57;UBERON:0007135!3.30e-33!57;UBERON:0000955!4.41e-33!69;UBERON:0006238!4.41e-33!69;UBERON:0000924!6.64e-32!173;UBERON:0006601!6.64e-32!173;UBERON:0002616!9.73e-32!59;UBERON:0004121!5.01e-30!169;UBERON:0007023!5.89e-29!115;UBERON:0000033!8.06e-27!123;UBERON:0003056!1.09e-26!61;UBERON:0000153!1.10e-26!129;UBERON:0007811!1.10e-26!129;UBERON:0003080!2.32e-24!42;UBERON:0002780!3.94e-24!41;UBERON:0001890!3.94e-24!41;UBERON:0006240!3.94e-24!41;UBERON:0000481!1.18e-23!347;UBERON:0002020!4.12e-20!34;UBERON:0003528!4.12e-20!34;UBERON:0001893!8.02e-20!34;UBERON:0000119!8.24e-20!312;UBERON:0000475!1.08e-19!365;UBERON:0002791!2.45e-19!33;UBERON:0000483!4.10e-19!309;UBERON:0001869!9.20e-19!32;UBERON:0000025!2.38e-15!194;UBERON:0000477!4.10e-15!286;UBERON:0004111!8.67e-15!241;UBERON:0000956!1.13e-14!25;UBERON:0000203!1.13e-14!25;UBERON:0002619!5.03e-14!22;UBERON:0001950!6.85e-13!20;UBERON:0000064!8.53e-11!219;UBERON:0000922!2.23e-10!612;UBERON:0003076!6.93e-10!15;UBERON:0003057!6.93e-10!15;UBERON:0004732!1.54e-08!13;UBERON:0002050!2.55e-08!605;UBERON:0005423!2.55e-08!605;UBERON:0004733!4.00e-08!12;UBERON:0002028!4.00e-08!12;UBERON:0007277!4.00e-08!12;UBERON:0000923!4.60e-08!604;UBERON:0005291!4.60e-08!604;UBERON:0006598!4.60e-08!604;UBERON:0002532!4.60e-08!604;UBERON:0000468!8.65e-08!659;UBERON:0003103!3.79e-07!69;UBERON:0002308!6.30e-07!9;UBERON:0000125!6.30e-07!9
}}

Latest revision as of 12:25, 17 September 2013


Full id: C3408_cerebellum_pineal_rhabdomyosarcoma_neuroectodermal_brain_Pericytes_iPS



Phase1 CAGE Peaks

Hg19::chr14:21994337..21994442,-p1@SALL2
Hg19::chr14:21994449..21994524,-p2@SALL2
Hg19::chr19:49149553..49149602,-p4@CA11


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
neurectodermal cell1.53e-0759
neural cell7.25e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system1.60e-3981
nervous system1.83e-3989
neurectoderm5.83e-3786
neural plate7.65e-3582
presumptive neural plate7.65e-3582
brain1.08e-3268
future brain1.08e-3268
neural tube1.18e-3256
neural rod1.18e-3256
future spinal cord1.18e-3256
neural keel1.18e-3256
regional part of nervous system7.96e-3153
regional part of brain7.96e-3153
ectoderm-derived structure9.82e-31171
ectoderm9.82e-31171
presumptive ectoderm9.82e-31171
anatomical cluster2.71e-29373
adult organism2.84e-28114
structure with developmental contribution from neural crest2.23e-27132
pre-chordal neural plate1.31e-2661
ecto-epithelium1.40e-25104
organ system subdivision1.47e-25223
multi-tissue structure1.26e-24342
regional part of forebrain1.19e-2341
forebrain1.19e-2341
anterior neural tube1.19e-2341
future forebrain1.19e-2341
cell layer5.56e-20309
brain grey matter1.18e-1934
gray matter1.18e-1934
telencephalon2.52e-1934
epithelium3.83e-19306
regional part of telencephalon2.20e-1832
cerebral hemisphere2.61e-1832
tube1.52e-15192
anatomical conduit7.62e-15240
cerebral cortex2.61e-1425
pallium2.61e-1425
regional part of cerebral cortex1.37e-1322
neocortex1.54e-1220
posterior neural tube4.58e-1015
chordal neural plate4.58e-1015
embryo7.19e-10592
organ part1.72e-09218
segmental subdivision of nervous system9.20e-0913
multi-cellular organism1.02e-08656
segmental subdivision of hindbrain2.31e-0812
hindbrain2.31e-0812
presumptive hindbrain2.31e-0812
developing anatomical structure1.38e-07581
compound organ7.23e-0768
neural nucleus7.74e-079
nucleus of brain7.74e-079
regional part of metencephalon7.89e-079
metencephalon7.89e-079
future metencephalon7.89e-079


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
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.14.3182
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
MA0073.10.668628
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
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
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
MA0116.10.560723
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.22.38017
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.214.6003
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
BCL3#602223.03140186915890.002464674760842910.0138495731920624
CTBP2#1488241.81133355955210.0007543408259914850.00593376527270654
E2F6#187635.017155731697390.00791769806886330.0321207453625705
EGR1#195834.988179094810140.008056488137383440.0319685244901288
GATA3#2625218.15767757147070.003944546819279620.0189426395649597
JUND#372736.994663941871030.002921845042734990.0156401298968889
SP1#666735.69838137814090.005403962701712170.0245887012854144
TCF12#6938310.63446490218640.0008313523990202070.00628487971055167
YY1#752834.911170749853860.008441455341808260.0328544814207018
ZBTB7A#5134137.35190930787590.002516255860282270.0139829331590944
ZNF263#1012738.221841637010680.001799043925565870.0109118037366963



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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