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{{Coexpression_clusters
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|full_id=C4597_putamen_caudate_nucleus_left_insula_heart_temporal
|id=C4597
|ontology_enrichment_celltype=CL:0002139!7.99e-19!24;CL:0000115!1.52e-17!35;CL:0000071!1.45e-16!18;CL:0002546!1.45e-16!18;CL:0002078!5.13e-13!44;CL:0000213!1.92e-09!57;CL:0000215!1.92e-09!57;CL:1000413!3.58e-09!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!9.20e-61!115;UBERON:0001049!1.54e-38!57;UBERON:0005068!1.54e-38!57;UBERON:0006241!1.54e-38!57;UBERON:0007135!1.54e-38!57;UBERON:0001017!1.30e-34!82;UBERON:0005743!1.49e-33!86;UBERON:0003080!1.73e-32!42;UBERON:0000955!6.70e-32!69;UBERON:0006238!6.70e-32!69;UBERON:0002780!8.05e-32!41;UBERON:0001890!8.05e-32!41;UBERON:0006240!8.05e-32!41;UBERON:0002616!1.64e-31!59;UBERON:0003075!2.51e-30!86;UBERON:0007284!2.51e-30!86;UBERON:0000073!1.88e-29!94;UBERON:0001016!1.88e-29!94;UBERON:0002346!4.87e-28!90;UBERON:0001893!1.40e-26!34;UBERON:0002020!2.85e-26!34;UBERON:0003528!2.85e-26!34;UBERON:0002791!1.94e-25!33;UBERON:0001869!4.69e-25!32;UBERON:0000025!8.14e-23!194;UBERON:0003056!2.11e-22!61;UBERON:0004111!7.14e-22!241;UBERON:0001950!2.97e-21!20;UBERON:0002619!7.17e-21!22;UBERON:0000477!7.84e-19!286;UBERON:0000956!1.71e-17!25;UBERON:0000203!1.71e-17!25;UBERON:0000153!2.22e-17!129;UBERON:0007811!2.22e-17!129;UBERON:0001986!1.45e-16!18;UBERON:0004638!1.45e-16!18;UBERON:0004852!1.45e-16!18;UBERON:0000033!3.32e-16!123;UBERON:0004121!5.53e-15!169;UBERON:0000924!3.88e-14!173;UBERON:0006601!3.88e-14!173;UBERON:0000483!1.42e-13!309;UBERON:0000119!3.77e-13!312;UBERON:0000487!1.99e-12!22;UBERON:0006914!1.97e-11!25;UBERON:0002420!8.74e-11!9;UBERON:0007245!8.74e-11!9;UBERON:0010009!8.74e-11!9;UBERON:0010011!8.74e-11!9;UBERON:0000454!8.74e-11!9;UBERON:0000468!1.05e-10!659;UBERON:0002308!1.67e-10!9;UBERON:0000125!1.67e-10!9;UBERON:0003915!3.58e-09!9;UBERON:0004700!3.58e-09!9;UBERON:0001917!3.58e-09!9;UBERON:0009663!7.35e-09!7;UBERON:0000467!7.43e-09!625;UBERON:0000480!9.06e-09!626;UBERON:0000200!4.67e-08!6;UBERON:0003076!1.55e-07!15;UBERON:0003057!1.55e-07!15;UBERON:0001871!1.59e-07!7;UBERON:0002298!1.98e-07!8;UBERON:0000064!3.91e-07!219;UBERON:0000922!4.71e-07!612;UBERON:0001872!5.16e-07!5;UBERON:0000475!6.14e-07!365;UBERON:0002021!8.76e-07!5
}}

Latest revision as of 14:16, 17 September 2013


Full id: C4597_putamen_caudate_nucleus_left_insula_heart_temporal



Phase1 CAGE Peaks

Hg19::chr6:36807213..36807231,-p3@CPNE5
Hg19::chr6:36807240..36807269,-p4@CPNE5
Hg19::chr6:36807270..36807282,-p7@CPNE5


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

No GOStat results

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
adult organism6.70e-52114
neural tube2.33e-4256
neural rod2.33e-4256
future spinal cord2.33e-4256
neural keel2.33e-4256
telencephalon5.40e-4134
regional part of nervous system1.04e-4053
regional part of brain1.04e-4053
brain grey matter1.99e-4034
gray matter1.99e-4034
cerebral hemisphere1.53e-3832
regional part of telencephalon7.11e-3832
regional part of forebrain1.25e-3741
forebrain1.25e-3741
anterior neural tube1.25e-3741
future forebrain1.25e-3741
central nervous system4.69e-3581
brain2.90e-3468
future brain2.90e-3468
neocortex1.13e-3120
regional part of cerebral cortex1.87e-3122
neural plate2.16e-3182
presumptive neural plate2.16e-3182
nervous system3.93e-3089
neurectoderm2.80e-2986
cerebral cortex5.34e-2725
pallium5.34e-2725
tube3.09e-26192
ecto-epithelium3.51e-24104
pre-chordal neural plate1.28e-2361
anatomical conduit1.30e-21240
structure with developmental contribution from neural crest1.20e-20132
blood vessel endothelium1.94e-1918
endothelium1.94e-1918
cardiovascular system endothelium1.94e-1918
anatomical cluster1.03e-18373
basal ganglion1.20e-159
nuclear complex of neuraxis1.20e-159
aggregate regional part of brain1.20e-159
collection of basal ganglia1.20e-159
cerebral subcortex1.20e-159
simple squamous epithelium4.38e-1522
neural nucleus4.42e-159
nucleus of brain4.42e-159
squamous epithelium1.96e-1425
ectoderm-derived structure2.00e-14171
ectoderm2.00e-14171
presumptive ectoderm2.00e-14171
epithelium8.73e-14306
cell layer1.87e-13309
endothelial tube1.93e-139
arterial system endothelium1.93e-139
endothelium of artery1.93e-139
telencephalic nucleus1.18e-127
organ system subdivision5.00e-12223
gyrus1.97e-116
organ part4.18e-11218
multi-cellular organism2.55e-10656
parietal lobe6.30e-105
anatomical system1.37e-09624
anatomical group1.57e-09625
occipital lobe2.53e-095
temporal lobe2.54e-096
corpus striatum7.06e-094
striatum7.06e-094
ventral part of telencephalon7.06e-094
future corpus striatum7.06e-094
embryo8.09e-09592
vessel3.46e-0868
developing anatomical structure4.56e-08581
embryonic structure1.02e-07564
epithelial tube open at both ends1.24e-0759
blood vessel1.24e-0759
blood vasculature1.24e-0759
vascular cord1.24e-0759
germ layer1.74e-07560
germ layer / neural crest1.74e-07560
embryonic tissue1.74e-07560
presumptive structure1.74e-07560
germ layer / neural crest derived structure1.74e-07560
epiblast (generic)1.74e-07560
splanchnic layer of lateral plate mesoderm2.72e-0783
caudate-putamen4.69e-073
dorsal striatum4.69e-073
posterior neural tube7.41e-0715
chordal neural plate7.41e-0715


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
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
MA0073.13.33427
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0105.10.31555
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
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.21.39232
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
MA0159.14.68786
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.17.47293
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.211.5899
MA0102.21.88331
MA0258.11.29138
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
EGR1#195834.988179094810140.008056488137383440.0322244098111979



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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