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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:43, 17 September 2013


Full id: C1367_optic_extraskeletal_brain_rhabdomyosarcoma_substantia_corpus_thalamus



Phase1 CAGE Peaks

Hg19::chr12:70760058..70760085,+p1@KCNMB4
Hg19::chr12:70760380..70760395,+p6@KCNMB4
Hg19::chr12:70760508..70760600,+p4@KCNMB4
Hg19::chr17:36759531..36759542,+p@chr17:36759531..36759542
+
Hg19::chr19:1450095..1450102,+p4@APC2
Hg19::chr19:36370460..36370479,+p@chr19:36370460..36370479
+


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:0016342catenin complex0.00600494524902861
GO:0019228generation of action potential0.0108076287272309
GO:0005513detection of calcium ion0.0108076287272309
GO:0019229regulation of vasoconstriction0.0108076287272309
GO:0008013beta-catenin binding0.0108076287272309
GO:0046928regulation of neurotransmitter secretion0.0120079460631646
GO:0042310vasoconstriction0.0135077461451033
GO:0009593detection of chemical stimulus0.0135077461451033
GO:0042391regulation of membrane potential0.015179589722366
GO:0015269calcium-activated potassium channel activity0.015179589722366
GO:0022839ion gated channel activity0.015179589722366
GO:0005227calcium activated cation channel activity0.015179589722366
GO:0001508regulation of action potential0.015179589722366
GO:0007269neurotransmitter secretion0.015179589722366
GO:0035150regulation of tube size0.015179589722366
GO:0050880regulation of blood vessel size0.015179589722366
GO:0003018vascular process in circulatory system0.015179589722366
GO:0008017microtubule binding0.0157910906900584
GO:0019897extrinsic to plasma membrane0.0157910906900584
GO:0045055regulated secretory pathway0.0159009256768253
GO:0051046regulation of secretion0.0168566343658797
GO:0015631tubulin binding0.0182573598082459
GO:0003001generation of a signal involved in cell-cell signaling0.0182573598082459
GO:0044459plasma membrane part0.0184552706464487
GO:0001505regulation of neurotransmitter levels0.0184552706464487
GO:0051606detection of stimulus0.0184552706464487
GO:0035239tube morphogenesis0.0186592293268234
GO:0019898extrinsic to membrane0.0229116677526957
GO:0035295tube development0.0237832898150614
GO:0043234protein complex0.0237832898150614
GO:0008076voltage-gated potassium channel complex0.0237832898150614
GO:0016055Wnt receptor signaling pathway0.027152237988412
GO:0016043cellular component organization and biogenesis0.0273869361726116
GO:0008015blood circulation0.0273869361726116
GO:0003013circulatory system process0.0273869361726116
GO:0005267potassium channel activity0.0347753819963962
GO:0005886plasma membrane0.0347753819963962
GO:0032991macromolecular complex0.0350272484805176
GO:0055082cellular chemical homeostasis0.0350272484805176
GO:0006873cellular ion homeostasis0.0350272484805176
GO:0045045secretory pathway0.0350272484805176
GO:0006813potassium ion transport0.0364641979791503
GO:0050801ion homeostasis0.0371405398920149
GO:0051239regulation of multicellular organismal process0.0376502896809556
GO:0007268synaptic transmission0.0384140263190828
GO:0032940secretion by cell0.0384140263190828
GO:0048878chemical homeostasis0.0384140263190828
GO:0019226transmission of nerve impulse0.0410840863746678
GO:0006461protein complex assembly0.0414590676224523
GO:0019725cellular homeostasis0.0447891739188977
GO:0046903secretion0.0449588284627961
GO:0005261cation channel activity0.0482023710215125



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
neuronal stem cell2.29e-098
neuron1.19e-076
neuroblast1.19e-076
electrically signaling cell1.19e-076
Uber Anatomy
Ontology termp-valuen
central nervous system5.05e-5081
nervous system9.66e-4889
neural tube6.79e-4456
neural rod6.79e-4456
future spinal cord6.79e-4456
neural keel6.79e-4456
regional part of nervous system1.13e-4053
regional part of brain1.13e-4053
neural plate8.94e-3982
presumptive neural plate8.94e-3982
brain2.44e-3768
future brain2.44e-3768
neurectoderm3.70e-3786
regional part of forebrain5.27e-3341
forebrain5.27e-3341
anterior neural tube5.27e-3341
future forebrain5.27e-3341
telencephalon1.22e-3034
brain grey matter1.46e-3034
gray matter1.46e-3034
adult organism6.03e-30114
pre-chordal neural plate9.24e-3061
regional part of telencephalon2.16e-2832
cerebral hemisphere2.82e-2832
structure with developmental contribution from neural crest2.53e-27132
ectoderm-derived structure3.16e-27171
ectoderm3.16e-27171
presumptive ectoderm3.16e-27171
ecto-epithelium7.49e-27104
organ system subdivision8.45e-26223
regional part of cerebral cortex1.18e-2522
neocortex1.07e-2320
cerebral cortex3.09e-2325
pallium3.09e-2325
anatomical cluster1.01e-17373
tube1.76e-17192
anatomical conduit2.22e-12240
posterior neural tube9.48e-1215
chordal neural plate9.48e-1215
organ part4.20e-10218
multi-tissue structure6.30e-10342
segmental subdivision of nervous system6.53e-1013
embryo8.50e-09592
segmental subdivision of hindbrain8.71e-0912
hindbrain8.71e-0912
presumptive hindbrain8.71e-0912
basal ganglion9.33e-099
nuclear complex of neuraxis9.33e-099
aggregate regional part of brain9.33e-099
collection of basal ganglia9.33e-099
cerebral subcortex9.33e-099
temporal lobe9.36e-096
neural nucleus1.01e-089
nucleus of brain1.01e-089
epithelium2.81e-08306
cell layer5.72e-08309
brainstem7.60e-086
gyrus7.87e-086
organ8.22e-08503
multi-cellular organism2.18e-07656
occipital lobe3.36e-075
germ layer4.31e-07560
germ layer / neural crest4.31e-07560
embryonic tissue4.31e-07560
presumptive structure4.31e-07560
germ layer / neural crest derived structure4.31e-07560
epiblast (generic)4.31e-07560
parietal lobe7.65e-075
developing anatomical structure7.81e-07581
embryonic structure8.75e-07564
anatomical system8.87e-07624


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)
MA0003.14.63763
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.13.10532
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.808182
MA0056.10
MA0057.11.41984
MA0058.10.458909
MA0059.10.457555
MA0060.10.737586
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.17.1651
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.11.34409
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.811435
MA0145.11.16614
MA0146.11.44958
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.22.74691
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.680553
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.12.84974
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.14.94781
MA0163.14.41596
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.211.8119
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
EGR1#195854.156815912341780.001617966818864440.0101312330832414
ZBTB7A#5134144.901272871917260.004079628118843750.0194847158322551
ZNF263#1012745.481227758007120.002675609380607230.0147429549488888



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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