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

Latest revision as of 11:22, 17 September 2013


Full id: C402_parietal_occipital_temporal_thalamus_optic_globus_brain



Phase1 CAGE Peaks

Hg19::chr12:123319068..123319080,+p6@HIP1R
Hg19::chr14:32799950..32799951,+p@chr14:32799950..32799951
+
Hg19::chr19:11562361..11562386,-p@chr19:11562361..11562386
-
Hg19::chr19:13134043..13134054,+p@chr19:13134043..13134054
+
Hg19::chr19:47142400..47142423,-p1@uc002pez.1
Hg19::chr19:55946892..55946910,-p@chr19:55946892..55946910
-
Hg19::chr1:172051480..172051484,+p@chr1:172051480..172051484
+
Hg19::chr20:58279639..58279642,+p@chr20:58279639..58279642
+
Hg19::chr21:41551108..41551112,-p@chr21:41551108..41551112
-
Hg19::chr22:18503369..18503380,-p@chr22:18503369..18503380
-
Hg19::chr3:181442608..181442615,+p@chr3:181442608..181442615
+
Hg19::chr4:113994134..113994138,+p@chr4:113994134..113994138
+
Hg19::chr4:114286837..114286840,+p@chr4:114286837..114286840
+
Hg19::chr4:164928140..164928142,-p@chr4:164928140..164928142
-
Hg19::chr4:164948511..164948515,-p@chr4:164948511..164948515
-
Hg19::chr4:165244747..165244750,-p@chr4:165244747..165244750
-
Hg19::chr5:146146606..146146609,-p@chr5:146146606..146146609
-
Hg19::chr5:146243956..146243960,-p@chr5:146243956..146243960
-
Hg19::chr7:86415034..86415036,+p@chr7:86415034..86415036
+
Hg19::chr9:103281957..103281962,+p@chr9:103281957..103281962
+
Hg19::chr9:8463305..8463309,-p@chr9:8463305..8463309
-
Hg19::chr9:8491655..8491659,-p@chr9:8491655..8491659
-
Hg19::chr9:8500547..8500558,-p@chr9:8500547..8500558
-
Hg19::chr9:8576629..8576632,-p@chr9:8576629..8576632
-
Hg19::chr9:8858623..8858638,-p@chr9:8858623..8858638
-
Hg19::chrX:13904834..13904839,-p@chrX:13904834..13904839
-


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:0005905coated pit0.0316437065818909
GO:0030136clathrin-coated vesicle0.0358138074492719
GO:0030135coated vesicle0.0358138074492719
GO:0005543phospholipid binding0.0358138074492719
GO:0016023cytoplasmic membrane-bound vesicle0.0358138074492719
GO:0031988membrane-bound vesicle0.0358138074492719
GO:0031410cytoplasmic vesicle0.0358138074492719
GO:0031982vesicle0.0358138074492719
GO:0003779actin binding0.0358138074492719
GO:0008289lipid binding0.0403407083908673
GO:0008092cytoskeletal protein binding0.0403407083908673



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 cell3.24e-078
Uber Anatomy
Ontology termp-valuen
central nervous system3.92e-9281
neural tube2.07e-9156
neural rod2.07e-9156
future spinal cord2.07e-9156
neural keel2.07e-9156
nervous system4.70e-8889
regional part of nervous system4.10e-8453
regional part of brain4.10e-8453
brain5.55e-7568
future brain5.55e-7568
regional part of forebrain4.78e-7341
forebrain4.78e-7341
anterior neural tube4.78e-7341
future forebrain4.78e-7341
neural plate1.04e-7282
presumptive neural plate1.04e-7282
neurectoderm1.60e-7186
brain grey matter4.41e-7034
gray matter4.41e-7034
telencephalon7.23e-7034
regional part of telencephalon3.97e-6532
cerebral hemisphere7.82e-6532
pre-chordal neural plate1.78e-5761
ecto-epithelium1.98e-54104
regional part of cerebral cortex4.35e-5122
adult organism3.66e-50114
cerebral cortex2.12e-4825
pallium2.12e-4825
ectoderm-derived structure3.00e-47171
ectoderm3.00e-47171
presumptive ectoderm3.00e-47171
neocortex2.71e-4620
structure with developmental contribution from neural crest2.21e-45132
organ system subdivision1.16e-32223
tube7.15e-23192
neural nucleus7.18e-239
nucleus of brain7.18e-239
basal ganglion8.80e-239
nuclear complex of neuraxis8.80e-239
aggregate regional part of brain8.80e-239
collection of basal ganglia8.80e-239
cerebral subcortex8.80e-239
posterior neural tube7.93e-1915
chordal neural plate7.93e-1915
anatomical cluster1.59e-18373
telencephalic nucleus4.50e-187
anatomical conduit1.32e-15240
gyrus2.20e-156
brainstem3.36e-156
segmental subdivision of nervous system9.40e-1513
organ part2.18e-14218
occipital lobe1.34e-135
parietal lobe1.52e-135
temporal lobe2.23e-136
limbic system2.73e-135
segmental subdivision of hindbrain1.45e-1212
hindbrain1.45e-1212
presumptive hindbrain1.45e-1212
epithelium3.94e-12306
cell layer7.01e-12309
corpus striatum1.37e-104
striatum1.37e-104
ventral part of telencephalon1.37e-104
future corpus striatum1.37e-104
multi-tissue structure2.41e-09342
embryo4.40e-09592
spinal cord1.00e-083
dorsal region element1.00e-083
dorsum1.00e-083
pons1.06e-083
frontal cortex1.06e-083
caudate-putamen2.10e-083
dorsal striatum2.10e-083
germ layer2.82e-08560
germ layer / neural crest2.82e-08560
embryonic tissue2.82e-08560
presumptive structure2.82e-08560
germ layer / neural crest derived structure2.82e-08560
epiblast (generic)2.82e-08560
medulla oblongata3.47e-083
myelencephalon3.47e-083
future myelencephalon3.47e-083
embryonic structure4.28e-08564
developing anatomical structure7.18e-08581
regional part of metencephalon4.26e-079
metencephalon4.26e-079
future metencephalon4.26e-079
dorsal plus ventral thalamus8.22e-072
thalamic complex8.22e-072


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)
MA0003.12.56917e-07
MA0004.10.122847
MA0006.10.180714
MA0007.10.112494
MA0009.10.46676
MA0014.10.000721098
MA0017.10.226532
MA0019.10.619765
MA0024.10.378349
MA0025.10.584598
MA0027.12.02165
MA0028.10.0539336
MA0029.11.80508
MA0030.10.384823
MA0031.10.33249
MA0038.10.546283
MA0040.11.03187
MA0041.11.3364
MA0042.10.74466
MA0043.10.467032
MA0046.11.15807
MA0048.10.0142327
MA0050.10.115873
MA0051.11.6318
MA0052.10.402401
MA0055.15.54793e-05
MA0056.10
MA0057.10.103816
MA0058.10.0742284
MA0059.10.0736469
MA0060.10.0152409
MA0061.10.0105788
MA0063.10
MA0066.10.546967
MA0067.10.753856
MA0068.10.202094
MA0069.10.454067
MA0070.10.44448
MA0071.10.941189
MA0072.10.44064
MA0073.10.0162396
MA0074.10.538325
MA0076.10.0815705
MA0077.10.434073
MA0078.10.252504
MA0081.10.256536
MA0083.10.473254
MA0084.10.931415
MA0087.11.11745
MA0088.10.0379733
MA0089.10
MA0090.10.088522
MA0091.10.124326
MA0092.10.338625
MA0093.10.0490184
MA0095.10
MA0098.10
MA0100.10.195288
MA0101.10.0502397
MA0103.10.170494
MA0105.10.169587
MA0106.10.214057
MA0107.10.0266946
MA0108.20.330055
MA0109.10
MA0111.10.316029
MA0113.10.225587
MA0114.10.107626
MA0115.10.682809
MA0116.10.115411
MA0117.10.499451
MA0119.10.236164
MA0122.10.522217
MA0124.11.55472
MA0125.10.568516
MA0130.10
MA0131.10.26595
MA0132.10
MA0133.10
MA0135.10.493123
MA0136.10.190708
MA0139.10.0450422
MA0140.10.15932
MA0141.10.0728657
MA0142.12.28689
MA0143.11.19813
MA0144.10.0952058
MA0145.10.00059844
MA0146.10.0102995
MA0147.10.0285818
MA0148.10.137223
MA0149.10.153304
MA0062.20.00978787
MA0035.20.479916
MA0039.20.029627
MA0138.20.253407
MA0002.20.0625933
MA0137.20.0564642
MA0104.20.0150955
MA0047.20.205658
MA0112.20.0152311
MA0065.20.109893
MA0150.10.0856547
MA0151.10
MA0152.10.163454
MA0153.10.553438
MA0154.10.0812436
MA0155.10.155082
MA0156.10.0573678
MA0157.10.286356
MA0158.10
MA0159.10.119258
MA0160.10.146326
MA0161.10
MA0162.10.0026608
MA0163.10.000196937
MA0164.10.23445
MA0080.20.184213
MA0018.20.615632
MA0099.20.16368
MA0079.20.000429839
MA0102.20.967149
MA0258.10.21977
MA0259.10.300465
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

No analysis results for this cluster

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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