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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:34, 17 September 2013


Full id: C939_neuroblastoma_argyrophil_small_cerebellum_retinoblastoma_pineal_medulloblastoma



Phase1 CAGE Peaks

Hg19::chr2:182543057..182543068,-p1@GQ904713
Hg19::chr2:182543197..182543218,-p4@NEUROD1
Hg19::chr2:182543249..182543261,-p5@NEUROD1
Hg19::chr2:182543547..182543559,-p9@NEUROD1
Hg19::chr2:182545234..182545252,-p1@NEUROD1
Hg19::chr2:182545296..182545307,-p3@NEUROD1
Hg19::chr2:182545330..182545341,-p2@CERKL
Hg19::chr2:182545363..182545372,-p3@CERKL
Hg19::chr6:66194027..66194031,-p@chr6:66194027..66194031
-


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:0030902hindbrain development0.0428039440196433
GO:0004143diacylglycerol kinase activity0.0428039440196433
GO:0043010camera-type eye development0.0428039440196433
GO:0007205protein kinase C activation0.0428039440196433
GO:0001654eye development0.0428039440196433
GO:0009952anterior/posterior pattern formation0.0428039440196433
GO:0032147activation of protein kinase activity0.0428039440196433
GO:0045165cell fate commitment0.0428039440196433
GO:0007423sensory organ development0.0428039440196433
GO:0003002regionalization0.0428039440196433
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0428039440196433
GO:0007389pattern specification process0.0436576993985432
GO:0048015phosphoinositide-mediated signaling0.0436576993985432
GO:0007420brain development0.0436576993985432
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0436576993985432
GO:0045860positive regulation of protein kinase activity0.0436576993985432
GO:0033674positive regulation of kinase activity0.0436576993985432
GO:0051347positive regulation of transferase activity0.0436576993985432
GO:0032501multicellular organismal process0.0496195203628137
GO:0007601visual perception0.0496195203628137
GO:0050953sensory perception of light stimulus0.0496195203628137
GO:0045893positive regulation of transcription, DNA-dependent0.0496195203628137
GO:0007417central nervous system development0.0496195203628137
GO:0045859regulation of protein kinase activity0.0496195203628137
GO:0043549regulation of kinase activity0.0496195203628137
GO:0051338regulation of transferase activity0.0496195203628137
GO:0043085positive regulation of catalytic activity0.0496195203628137
GO:0019932second-messenger-mediated signaling0.0496195203628137
GO:0003702RNA polymerase II transcription factor activity0.0496195203628137
GO:0045941positive regulation of transcription0.0496195203628137
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0497326468379995



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
neuron3.93e-076
neuroblast3.93e-076
electrically signaling cell3.93e-076
Uber Anatomy
Ontology termp-valuen
central nervous system1.86e-4181
nervous system1.51e-3989
regional part of nervous system1.94e-3853
regional part of brain1.94e-3853
brain4.39e-3768
future brain4.39e-3768
regional part of cerebral cortex2.13e-3622
neural tube4.14e-3656
neural rod4.14e-3656
future spinal cord4.14e-3656
neural keel4.14e-3656
neocortex7.52e-3520
cerebral cortex8.39e-3225
pallium8.39e-3225
cerebral hemisphere1.53e-3132
regional part of forebrain1.26e-3041
forebrain1.26e-3041
anterior neural tube1.26e-3041
future forebrain1.26e-3041
telencephalon1.63e-2934
regional part of telencephalon8.26e-2832
neural plate1.22e-2782
presumptive neural plate1.22e-2782
neurectoderm4.39e-2686
brain grey matter5.22e-2634
gray matter5.22e-2634
pre-chordal neural plate3.39e-2461
ecto-epithelium1.97e-22104
ectoderm-derived structure2.99e-20171
ectoderm2.99e-20171
presumptive ectoderm2.99e-20171
organ system subdivision2.74e-17223
adult organism1.11e-16114
structure with developmental contribution from neural crest2.39e-16132
occipital lobe1.84e-135
parietal lobe2.92e-135
gyrus4.89e-116
pineal body7.90e-102
regional part of epithalamus7.90e-102
secretory circumventricular organ7.90e-102
circumventricular organ7.90e-102
epithalamus7.90e-102
segmental subdivision of hindbrain6.61e-0912
hindbrain6.61e-0912
presumptive hindbrain6.61e-0912
segmental subdivision of nervous system3.39e-0813
small intestine4.10e-084
regional part of metencephalon4.68e-089
metencephalon4.68e-089
future metencephalon4.68e-089
limbic system5.12e-085
anatomical cluster7.34e-08373
tube1.24e-07192
cerebellum1.76e-076
rhombic lip1.76e-076
posterior neural tube4.66e-0715
chordal neural plate4.66e-0715
organ part7.76e-07218


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)
MA0003.10.0913842
MA0004.11.87712
MA0006.11.34805
MA0007.10.397529
MA0009.10.870971
MA0014.11.50001
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.0199484
MA0056.10
MA0057.11.9083
MA0058.14.25461
MA0059.15.28745
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.13.05635
MA0074.13.23534
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.865814
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.363555
MA0089.10
MA0090.10.353576
MA0091.13.8401
MA0092.10.381858
MA0093.12.91169
MA0095.10
MA0098.10
MA0100.11.30927
MA0101.10.271368
MA0103.10.257174
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.599942
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.046841
MA0146.10.0045741
MA0147.13.33389
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.323611
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.25.40426
MA0047.20.542971
MA0112.20.0433683
MA0065.20.182082
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.156896
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.11.15068
MA0161.10
MA0162.12.3084
MA0163.10.101664
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.22.91533
MA0102.21.41188
MA0258.10.532421
MA0259.10.218904
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
ATF3#46749.983633122670560.0004127843277241880.00393203050010822
NRF1#489945.426790865649290.004046698912068520.0193681860445225
REST#597844.288901651612450.009457025945962830.0356705671122255
SUZ12#23512211.13684020245840.01305435313902310.0463121569172334
TCF12#693844.726428845416190.006680355302603970.0284202870768119
USF2#739245.774309948919820.003223241005374920.016701332970845
ZNF263#1012787.308303677342823.84008362723504e-071.8758395413695e-05



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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