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{{Coexpression_clusters
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guanyl-nucleotide exchange factor activity!0.0332038149063935!23263$GO:0035023!regulation of Rho protein signal transduction!0.0332038149063935!23263$GO:0005088!Ras guanyl-nucleotide exchange factor activity!0.0332038149063935!23263$GO:0007266!Rho protein signal transduction!0.0332038149063935!23263$GO:0005085!guanyl-nucleotide exchange factor activity!0.0372071117390792!23263$GO:0046578!regulation of Ras protein signal transduction!0.0372071117390792!23263$GO:0007265!Ras protein signal transduction!0.0372071117390792!23263$GO:0005083!small GTPase regulator activity!0.0372071117390792!23263$GO:0051056!regulation of small GTPase mediated signal transduction!0.0372071117390792!23263$GO:0030695!GTPase regulator 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|full_id=C3355_cerebellum_Neural_occipital_small_parietal_Neurons_neuroblastoma
|gostat_on_coexpression_clusters=GO:0005089!Rho guanyl-nucleotide exchange factor activity!0.0332038149063935!23263$GO:0035023!regulation of Rho protein signal transduction!0.0332038149063935!23263$GO:0005088!Ras guanyl-nucleotide exchange factor activity!0.0332038149063935!23263$GO:0007266!Rho protein signal transduction!0.0332038149063935!23263$GO:0005085!guanyl-nucleotide exchange factor activity!0.0372071117390792!23263$GO:0046578!regulation of Ras protein signal transduction!0.0372071117390792!23263$GO:0007265!Ras protein signal transduction!0.0372071117390792!23263$GO:0005083!small GTPase regulator activity!0.0372071117390792!23263$GO:0051056!regulation of small GTPase mediated signal transduction!0.0372071117390792!23263$GO:0030695!GTPase regulator activity!0.049452490286118!23263
|id=C3355
|ontology_enrichment_celltype=CL:0002319!1.82e-07!25
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!3.90e-58!82;UBERON:0001049!2.81e-57!57;UBERON:0005068!2.81e-57!57;UBERON:0006241!2.81e-57!57;UBERON:0007135!2.81e-57!57;UBERON:0000073!5.95e-57!94;UBERON:0001016!5.95e-57!94;UBERON:0005743!4.82e-56!86;UBERON:0002616!1.74e-49!59;UBERON:0000955!2.37e-49!69;UBERON:0006238!2.37e-49!69;UBERON:0003075!6.93e-46!86;UBERON:0007284!6.93e-46!86;UBERON:0002346!2.19e-45!90;UBERON:0007023!3.49e-45!115;UBERON:0002780!9.52e-45!41;UBERON:0001890!9.52e-45!41;UBERON:0006240!9.52e-45!41;UBERON:0003080!2.79e-43!42;UBERON:0001893!5.63e-37!34;UBERON:0002020!5.96e-37!34;UBERON:0003528!5.96e-37!34;UBERON:0002791!6.56e-36!33;UBERON:0001869!3.79e-35!32;UBERON:0000924!7.01e-35!173;UBERON:0006601!7.01e-35!173;UBERON:0003056!1.07e-34!61;UBERON:0004121!1.23e-34!169;UBERON:0000153!2.27e-31!129;UBERON:0007811!2.27e-31!129;UBERON:0000033!2.70e-30!123;UBERON:0000956!9.63e-28!25;UBERON:0000203!9.63e-28!25;UBERON:0002619!1.42e-25!22;UBERON:0001950!1.62e-23!20;UBERON:0000025!2.22e-15!194;UBERON:0000064!2.30e-15!219;UBERON:0003076!1.40e-14!15;UBERON:0003057!1.40e-14!15;UBERON:0000483!4.90e-13!309;UBERON:0000481!6.27e-13!347;UBERON:0004111!6.38e-13!241;UBERON:0000475!7.80e-13!365;UBERON:0000119!1.28e-12!312;UBERON:0004732!1.41e-12!13;UBERON:0000477!4.57e-12!286;UBERON:0004733!7.48e-12!12;UBERON:0002028!7.48e-12!12;UBERON:0007277!7.48e-12!12;UBERON:0002420!1.39e-10!9;UBERON:0007245!1.39e-10!9;UBERON:0010009!1.39e-10!9;UBERON:0010011!1.39e-10!9;UBERON:0000454!1.39e-10!9;UBERON:0000922!1.39e-10!612;UBERON:0002308!1.52e-10!9;UBERON:0000125!1.52e-10!9;UBERON:0001871!1.31e-09!7;UBERON:0000062!3.70e-09!511;UBERON:0002680!4.46e-09!9;UBERON:0001895!4.46e-09!9;UBERON:0010092!4.46e-09!9;UBERON:0001894!4.79e-09!7;UBERON:0006222!4.79e-09!7;UBERON:0009663!1.21e-08!7;UBERON:0000923!1.67e-08!604;UBERON:0005291!1.67e-08!604;UBERON:0006598!1.67e-08!604;UBERON:0002532!1.67e-08!604;UBERON:0000468!1.74e-08!659;UBERON:0002050!2.04e-08!605;UBERON:0005423!2.04e-08!605;UBERON:0000200!5.07e-08!6;UBERON:0000467!1.41e-07!625;UBERON:0000480!1.70e-07!626;UBERON:0001872!5.60e-07!5;UBERON:0002298!6.40e-07!8;UBERON:0002021!7.25e-07!5
}}

Latest revision as of 12:24, 17 September 2013


Full id: C3355_cerebellum_Neural_occipital_small_parietal_Neurons_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr13:113656022..113656041,+p9@MCF2L
Hg19::chr13:113656047..113656064,+p13@MCF2L
Hg19::chr8:62200509..62200590,+p1@CLVS1


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


GO IDGO nameFDR corrected p-value
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0332038149063935
GO:0035023regulation of Rho protein signal transduction0.0332038149063935
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0332038149063935
GO:0007266Rho protein signal transduction0.0332038149063935
GO:0005085guanyl-nucleotide exchange factor activity0.0372071117390792
GO:0046578regulation of Ras protein signal transduction0.0372071117390792
GO:0007265Ras protein signal transduction0.0372071117390792
GO:0005083small GTPase regulator activity0.0372071117390792
GO:0051056regulation of small GTPase mediated signal transduction0.0372071117390792
GO:0030695GTPase regulator activity0.049452490286118



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>disease_data<br>


Cell Type
Ontology termp-valuen
neural cell5.15e-0725
Uber Anatomy
Ontology termp-valuen
neural tube7.46e-7056
neural rod7.46e-7056
future spinal cord7.46e-7056
neural keel7.46e-7056
nervous system1.35e-6989
central nervous system2.07e-6881
regional part of nervous system7.29e-6553
regional part of brain7.29e-6553
brain1.09e-5568
future brain1.09e-5568
regional part of forebrain3.48e-5541
forebrain3.48e-5541
anterior neural tube3.48e-5541
future forebrain3.48e-5541
neural plate2.00e-5482
presumptive neural plate2.00e-5482
neurectoderm4.54e-5386
telencephalon4.88e-4634
brain grey matter7.63e-4634
gray matter7.63e-4634
pre-chordal neural plate3.81e-4561
ecto-epithelium9.36e-45104
cerebral hemisphere6.62e-4332
regional part of telencephalon7.17e-4332
ectoderm-derived structure4.75e-42171
ectoderm4.75e-42171
presumptive ectoderm4.75e-42171
adult organism2.86e-38114
organ system subdivision1.11e-35223
cerebral cortex5.11e-3525
pallium5.11e-3525
regional part of cerebral cortex2.30e-3122
structure with developmental contribution from neural crest9.38e-30132
neocortex2.34e-2820
anatomical cluster2.63e-19373
posterior neural tube2.53e-1515
chordal neural plate2.53e-1515
tube9.79e-15192
anatomical conduit3.34e-12240
neural nucleus4.29e-129
nucleus of brain4.29e-129
organ part5.90e-12218
multi-tissue structure2.54e-11342
epithelium4.47e-11306
gyrus4.76e-116
segmental subdivision of hindbrain6.34e-1112
hindbrain6.34e-1112
presumptive hindbrain6.34e-1112
cell layer8.55e-11309
brainstem1.53e-106
diencephalon2.53e-107
future diencephalon2.53e-107
segmental subdivision of nervous system6.34e-1013
parietal lobe1.09e-095
occipital lobe1.64e-095
basal ganglion1.97e-099
nuclear complex of neuraxis1.97e-099
aggregate regional part of brain1.97e-099
collection of basal ganglia1.97e-099
cerebral subcortex1.97e-099
telencephalic nucleus2.95e-097
gland of diencephalon6.16e-094
neuroendocrine gland6.16e-094
embryo1.84e-08592
corpus striatum4.83e-084
striatum4.83e-084
ventral part of telencephalon4.83e-084
future corpus striatum4.83e-084
germ layer5.51e-08560
germ layer / neural crest5.51e-08560
embryonic tissue5.51e-08560
presumptive structure5.51e-08560
germ layer / neural crest derived structure5.51e-08560
epiblast (generic)5.51e-08560
embryonic structure9.32e-08564
developing anatomical structure1.14e-07581
multi-cellular organism2.77e-07656
regional part of metencephalon6.52e-079
metencephalon6.52e-079
future metencephalon6.52e-079
organ6.55e-07503
anatomical system9.85e-07624
Disease
Ontology termp-valuen
neuroendocrine tumor2.00e-076


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
MA0014.10.377374
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
MA0055.10.190716
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
MA0073.10.0834661
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
MA0090.11.77664
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
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
MA0145.11.37817
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
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
MA0154.10.312019
MA0155.10.711948
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
MA0099.20.902716
MA0079.20.00160703
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
GATA3#2625218.15767757147070.003944546819279620.0189417685989583
NR3C1#290829.982015554115360.01278474365547170.0460248127480545
ZNF263#1012738.221841637010680.001799043925565870.0109092694967296



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.