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{{Coexpression_clusters
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wall catabolic process!0.0150194937569828!55074$GO:0010382!cell wall metabolic process!0.0150194937569828!55074$GO:0007047!cell wall organization and biogenesis!0.0150194937569828!55074$GO:0007215!glutamate signaling pathway!0.0150194937569828!2893$GO:0045229!external encapsulating structure organization and biogenesis!0.0150194937569828!55074$GO:0004970!ionotropic glutamate receptor activity!0.019013430069202!2893$GO:0005234!extracellular-glutamate-gated ion channel activity!0.019013430069202!2893$GO:0005231!excitatory extracellular ligand-gated ion channel activity!0.0306990760222157!2893$GO:0008066!glutamate receptor activity!0.0356145402287207!2893$GO:0006979!response to oxidative stress!0.0372431402806523!55074$GO:0005230!extracellular ligand-gated ion channel activity!0.0372431402806523!2893$GO:0045211!postsynaptic membrane!0.0372431402806523!2893$GO:0044456!synapse part!0.0372431402806523!2893$GO:0015276!ligand-gated ion channel 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317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;1.38935,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.8915,MA0163.1;1.84145,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;1.22771,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3078_pineal_extraskeletal_occipital_medial_cerebellum_amygdala_parietal
|gostat_on_coexpression_clusters=GO:0016998!cell wall catabolic process!0.0150194937569828!55074$GO:0010382!cell wall metabolic process!0.0150194937569828!55074$GO:0007047!cell wall organization and biogenesis!0.0150194937569828!55074$GO:0007215!glutamate signaling pathway!0.0150194937569828!2893$GO:0045229!external encapsulating structure organization and biogenesis!0.0150194937569828!55074$GO:0004970!ionotropic glutamate receptor activity!0.019013430069202!2893$GO:0005234!extracellular-glutamate-gated ion channel activity!0.019013430069202!2893$GO:0005231!excitatory extracellular ligand-gated ion channel activity!0.0306990760222157!2893$GO:0008066!glutamate receptor activity!0.0356145402287207!2893$GO:0006979!response to oxidative stress!0.0372431402806523!55074$GO:0005230!extracellular ligand-gated ion channel activity!0.0372431402806523!2893$GO:0045211!postsynaptic membrane!0.0372431402806523!2893$GO:0044456!synapse part!0.0372431402806523!2893$GO:0015276!ligand-gated ion channel activity!0.0372431402806523!2893$GO:0022834!ligand-gated channel activity!0.0372431402806523!2893
|id=C3078
}}

Latest revision as of 12:18, 17 September 2013


Full id: C3078_pineal_extraskeletal_occipital_medial_cerebellum_amygdala_parietal



Phase1 CAGE Peaks

Hg19::chr11:105480996..105481007,+p13@GRIA4
Hg19::chr8:107282368..107282379,+p5@OXR1
Hg19::chr8:107282389..107282493,+p1@OXR1


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:0016998cell wall catabolic process0.0150194937569828
GO:0010382cell wall metabolic process0.0150194937569828
GO:0007047cell wall organization and biogenesis0.0150194937569828
GO:0007215glutamate signaling pathway0.0150194937569828
GO:0045229external encapsulating structure organization and biogenesis0.0150194937569828
GO:0004970ionotropic glutamate receptor activity0.019013430069202
GO:0005234extracellular-glutamate-gated ion channel activity0.019013430069202
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0306990760222157
GO:0008066glutamate receptor activity0.0356145402287207
GO:0006979response to oxidative stress0.0372431402806523
GO:0005230extracellular ligand-gated ion channel activity0.0372431402806523
GO:0045211postsynaptic membrane0.0372431402806523
GO:0044456synapse part0.0372431402806523
GO:0015276ligand-gated ion channel activity0.0372431402806523
GO:0022834ligand-gated channel activity0.0372431402806523



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
fibroblast3.87e-1176
skin fibroblast2.14e-0723
Uber Anatomy
Ontology termp-valuen
central nervous system2.10e-3381
nervous system6.22e-3189
brain3.84e-3068
future brain3.84e-3068
neural tube2.36e-2956
neural rod2.36e-2956
future spinal cord2.36e-2956
neural keel2.36e-2956
regional part of nervous system1.17e-2753
regional part of brain1.17e-2753
regional part of forebrain1.41e-2541
forebrain1.41e-2541
anterior neural tube1.41e-2541
future forebrain1.41e-2541
neurectoderm1.82e-2186
telencephalon3.28e-2134
neural plate7.41e-2182
presumptive neural plate7.41e-2182
ectoderm-derived structure9.43e-21171
ectoderm9.43e-21171
presumptive ectoderm9.43e-21171
brain grey matter9.86e-2134
gray matter9.86e-2134
cerebral hemisphere1.37e-2032
regional part of telencephalon5.99e-2032
regional part of cerebral cortex5.65e-1922
adult organism2.23e-18114
cerebral cortex5.88e-1825
pallium5.88e-1825
structure with developmental contribution from neural crest8.15e-18132
neocortex2.55e-1720
pre-chordal neural plate8.41e-1761
ecto-epithelium1.22e-16104
organ system subdivision5.18e-16223
multi-cellular organism5.50e-09656
multi-tissue structure1.04e-08342
cell layer5.04e-08309
anatomical cluster5.41e-08373
epithelium7.60e-08306
gyrus5.58e-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)
MA0003.15.30359
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
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
MA0052.12.78861
MA0055.11.67416
MA0056.10
MA0057.11.59304
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
MA0073.10.0185922
MA0074.12.15449
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
MA0103.10.628063
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
MA0116.10.560723
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
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
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
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.22771
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
CTCF#1066435.360256373075030.0064925092527670.027822870372563
CTCFL#140690213.16431623931620.007433367036996010.0306669334377573
MEF2A#4205212.4954872730960.008235029478029740.0324721831781299
MEF2C#4208227.54090299508270.001729119938369690.010645968121405
SMC3#9126210.02995522995520.0126656379767470.0457094773369322
TFAP2A#7020211.01242291536330.01054990655215560.0389928757617788



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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