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{{Coexpression_clusters
{
|full_id=C711_cerebellum_Pericytes_Fibroblast_Meningeal_spinal_Astrocyte_Hair
 

Latest revision as of 11:29, 17 September 2013


Full id: C711_cerebellum_Pericytes_Fibroblast_Meningeal_spinal_Astrocyte_Hair



Phase1 CAGE Peaks

Hg19::chr3:147114993..147115013,-p5@ZIC4
Hg19::chr3:147115338..147115349,+p@chr3:147115338..147115349
+
Hg19::chr3:147115400..147115411,+p@chr3:147115400..147115411
+
Hg19::chr3:147126815..147126825,-p@chr3:147126815..147126825
-
Hg19::chr3:147127177..147127194,+p2@ZIC1
Hg19::chr3:147129975..147129992,+p@chr3:147129975..147129992
+
Hg19::chr3:147130332..147130352,+p@chr3:147130332..147130352
+
Hg19::chr3:147131290..147131301,+p@chr3:147131290..147131301
+
Hg19::chr3:147137194..147137222,+p1@FLJ30375
Hg19::chr3:147139053..147139112,+p5@ZIC1
Hg19::chr3:147139152..147139163,+p15@ZIC1
Hg19::chr3:147139238..147139247,+p26@ZIC1


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:0008589regulation of smoothened signaling pathway0.0197690591558547
GO:0007224smoothened signaling pathway0.0197690591558547
GO:0042472inner ear morphogenesis0.0197690591558547
GO:0042471ear morphogenesis0.0197690591558547
GO:0048839inner ear development0.0197690591558547
GO:0043583ear development0.0197690591558547
GO:0007423sensory organ development0.0328060999854834
GO:0048598embryonic morphogenesis0.0328060999854834
GO:0007389pattern specification process0.0388635391999214
GO:0007420brain development0.0391996244308409
GO:0003677DNA binding0.0464642615688377



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>

Uber Anatomy
Ontology termp-valuen
central nervous system2.68e-6881
neural tube1.83e-6556
neural rod1.83e-6556
future spinal cord1.83e-6556
neural keel1.83e-6556
brain7.75e-6368
future brain7.75e-6368
nervous system3.21e-6089
neural plate1.77e-5982
presumptive neural plate1.77e-5982
regional part of nervous system8.89e-5953
regional part of brain8.89e-5953
neurectoderm4.07e-5686
ecto-epithelium9.33e-54104
ectoderm-derived structure1.79e-42171
ectoderm1.79e-42171
presumptive ectoderm1.79e-42171
structure with developmental contribution from neural crest3.42e-41132
posterior neural tube1.21e-3615
chordal neural plate1.21e-3615
pre-chordal neural plate1.07e-3561
regional part of forebrain1.09e-3341
forebrain1.09e-3341
anterior neural tube1.09e-3341
future forebrain1.09e-3341
segmental subdivision of hindbrain1.39e-2912
hindbrain1.39e-2912
presumptive hindbrain1.39e-2912
segmental subdivision of nervous system4.56e-2713
telencephalon3.63e-2634
brain grey matter4.07e-2634
gray matter4.07e-2634
adult organism2.12e-23114
regional part of metencephalon7.36e-239
metencephalon7.36e-239
future metencephalon7.36e-239
regional part of telencephalon8.17e-2332
cerebral hemisphere1.33e-2232
cell layer2.79e-20309
organ system subdivision3.83e-20223
vasculature of organ2.50e-1811
epithelium1.22e-17306
cerebellum6.03e-176
rhombic lip6.03e-176
cerebral cortex4.27e-1625
pallium4.27e-1625
brainstem2.19e-146
regional part of cerebral cortex7.43e-1422
brain vasculature2.80e-135
neocortex5.56e-1320
multi-tissue structure2.23e-12342
neural nucleus3.33e-129
nucleus of brain3.33e-129
anatomical cluster1.13e-11373
tube2.25e-11192
atypical epithelium2.77e-114
regional part of diencephalon4.87e-114
organ part2.53e-10218
diencephalon4.19e-097
future diencephalon4.19e-097
hair follicle4.34e-095
hair follicle placode4.34e-095
blood-cerebrospinal fluid barrier4.35e-093
basal ganglion4.69e-099
nuclear complex of neuraxis4.69e-099
aggregate regional part of brain4.69e-099
collection of basal ganglia4.69e-099
cerebral subcortex4.69e-099
ciliary epithelium4.84e-093
ciliary body4.84e-093
spinal cord1.06e-083
dorsal region element1.06e-083
dorsum1.06e-083
telencephalic nucleus1.50e-087
medulla oblongata2.10e-083
myelencephalon2.10e-083
future myelencephalon2.10e-083
pigment epithelium of eye3.78e-0811
ectodermal placode5.52e-0831
occipital lobe7.49e-085
pons1.15e-073
vasculature of eye1.73e-076
uvea1.73e-076
vasculature of head1.73e-076
germ layer2.35e-07560
germ layer / neural crest2.35e-07560
embryonic tissue2.35e-07560


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)
MA0003.10.371182
MA0004.12.3599
MA0006.10.552945
MA0007.10.825205
MA0009.10.756202
MA0014.10.455267
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.583404
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.835565
MA0043.10.756508
MA0046.10.745626
MA0048.10.0399193
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.10.0371476
MA0056.10
MA0057.11.38004
MA0058.11.25545
MA0059.10.673606
MA0060.12.27824
MA0061.10.605357
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.12.34618
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.16.71936
MA0074.10.40963
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.20556
MA0089.10
MA0090.10.734839
MA0091.10.324543
MA0092.10.291716
MA0093.11.67662
MA0095.10
MA0098.10
MA0100.11.91612
MA0101.10.19375
MA0103.10.181541
MA0105.10.563165
MA0106.10.452066
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.11.39265
MA0113.10.467266
MA0114.11.34132
MA0115.10.992167
MA0116.11.37961
MA0117.10.792789
MA0119.11.20117
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.961223
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.39221
MA0145.10.232227
MA0146.10.79336
MA0147.12.01107
MA0148.10.344198
MA0149.10.367947
MA0062.20.0823902
MA0035.20.376007
MA0039.20.59101
MA0138.20.503176
MA0002.20.316618
MA0137.20.20663
MA0104.21.66831
MA0047.20.440861
MA0112.20.216805
MA0065.21.92393
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.875403
MA0155.12.21597
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.441451
MA0160.10.357736
MA0161.10
MA0162.10.63904
MA0163.10.478611
MA0164.12.09064
MA0080.20.191221
MA0018.20.453345
MA0099.20.382887
MA0079.25.08071
MA0102.21.28978
MA0258.10.117513
MA0259.11.43272
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
CTBP2#1488420.9056667797762.88227050924922e-050.000603733352818851
SUZ12#23512937.58683568329721.0350112335066e-131.620622761862e-11



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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