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{{Coexpression_clusters
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|full_id=C3054_mature_locus_thalamus_pons_amygdala_diencephalon_hippocampus
|id=C3054
|ontology_enrichment_celltype=CL:0002139!6.15e-10!24;CL:0000115!1.14e-08!35;CL:0000071!8.38e-08!18;CL:0002546!8.38e-08!18;CL:0002078!2.66e-07!44;CL:0000222!5.29e-07!119
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000477!5.80e-37!286;UBERON:0004111!4.66e-34!241;UBERON:0007023!4.88e-33!115;UBERON:0000483!1.19e-27!309;UBERON:0000119!1.85e-27!312;UBERON:0000025!2.01e-27!194;UBERON:0001049!5.99e-24!57;UBERON:0005068!5.99e-24!57;UBERON:0006241!5.99e-24!57;UBERON:0007135!5.99e-24!57;UBERON:0000481!1.68e-23!347;UBERON:0003075!4.02e-22!86;UBERON:0007284!4.02e-22!86;UBERON:0000064!9.08e-21!219;UBERON:0000468!1.76e-20!659;UBERON:0002616!3.23e-20!59;UBERON:0002346!4.61e-20!90;UBERON:0000475!1.38e-19!365;UBERON:0000467!1.67e-19!625;UBERON:0000480!3.54e-19!626;UBERON:0000033!8.24e-19!123;UBERON:0000153!4.86e-18!129;UBERON:0007811!4.86e-18!129;UBERON:0000955!1.88e-17!69;UBERON:0006238!1.88e-17!69;UBERON:0003080!4.37e-17!42;UBERON:0005743!7.99e-17!86;UBERON:0002780!1.61e-16!41;UBERON:0001890!1.61e-16!41;UBERON:0006240!1.61e-16!41;UBERON:0001017!1.81e-16!82;UBERON:0000922!7.21e-16!612;UBERON:0002020!4.80e-15!34;UBERON:0003528!4.80e-15!34;UBERON:0003056!7.78e-15!61;UBERON:0002050!9.60e-15!605;UBERON:0005423!9.60e-15!605;UBERON:0001893!1.01e-14!34;UBERON:0000923!1.63e-14!604;UBERON:0005291!1.63e-14!604;UBERON:0006598!1.63e-14!604;UBERON:0002532!1.63e-14!604;UBERON:0000073!3.56e-14!94;UBERON:0001016!3.56e-14!94;UBERON:0002791!3.74e-14!33;UBERON:0001869!5.75e-14!32;UBERON:0004121!9.51e-14!169;UBERON:0000924!8.65e-13!173;UBERON:0006601!8.65e-13!173;UBERON:0002619!1.12e-11!22;UBERON:0000062!5.00e-11!511;UBERON:0001950!1.84e-10!20;UBERON:0000055!3.76e-10!69;UBERON:0000956!4.62e-10!25;UBERON:0000203!4.62e-10!25;UBERON:0002049!6.23e-10!79;UBERON:0007798!6.23e-10!79;UBERON:0003103!2.32e-09!69;UBERON:0000063!2.80e-09!97;UBERON:0004872!3.60e-09!84;UBERON:0003914!1.01e-08!118;UBERON:0001981!3.05e-08!60;UBERON:0007500!3.05e-08!60;UBERON:0004537!3.05e-08!60;UBERON:0006965!3.05e-08!60;UBERON:0003076!4.19e-08!15;UBERON:0003057!4.19e-08!15;UBERON:0001986!8.38e-08!18;UBERON:0004638!8.38e-08!18;UBERON:0004852!8.38e-08!18;UBERON:0000487!1.91e-07!22;UBERON:0006914!2.50e-07!25;UBERON:0001048!4.50e-07!168;UBERON:0001004!7.34e-07!72;UBERON:0004732!9.42e-07!13
}}

Latest revision as of 12:18, 17 September 2013


Full id: C3054_mature_locus_thalamus_pons_amygdala_diencephalon_hippocampus



Phase1 CAGE Peaks

Hg19::chr10:88718314..88718388,+p1@SNCG
Hg19::chr1:161101568..161101584,+p@chr1:161101568..161101584
+
Hg19::chr1:27120942..27120945,-p@chr1:27120942..27120945
-


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism3.57e-41114
neural tube7.91e-3456
neural rod7.91e-3456
future spinal cord7.91e-3456
neural keel7.91e-3456
regional part of nervous system3.47e-3253
regional part of brain3.47e-3253
regional part of forebrain9.27e-2741
forebrain9.27e-2741
anterior neural tube9.27e-2741
future forebrain9.27e-2741
neural plate9.41e-2582
presumptive neural plate9.41e-2582
brain grey matter6.58e-2434
gray matter6.58e-2434
telencephalon3.92e-2334
neurectoderm7.11e-2386
brain7.42e-2368
future brain7.42e-2368
central nervous system3.44e-2281
regional part of telencephalon2.12e-2132
ecto-epithelium3.72e-21104
cerebral hemisphere4.40e-2132
structure with developmental contribution from neural crest4.89e-21132
nervous system1.52e-1889
pre-chordal neural plate1.48e-1661
regional part of cerebral cortex7.27e-1622
anatomical conduit1.20e-15240
tube2.17e-15192
neocortex1.05e-1320
anatomical cluster1.36e-13373
neural nucleus1.68e-139
nucleus of brain1.68e-139
cerebral cortex2.36e-1325
pallium2.36e-1325
basal ganglion2.43e-139
nuclear complex of neuraxis2.43e-139
aggregate regional part of brain2.43e-139
collection of basal ganglia2.43e-139
cerebral subcortex2.43e-139
organ system subdivision3.40e-12223
organ part1.17e-11218
telencephalic nucleus9.28e-117
epithelium2.36e-10306
cell layer4.90e-10309
ectoderm-derived structure7.76e-10171
ectoderm7.76e-10171
presumptive ectoderm7.76e-10171
brainstem3.55e-096
multi-tissue structure7.66e-09342
gyrus1.74e-086
posterior neural tube3.05e-0815
chordal neural plate3.05e-0815
limbic system9.57e-085
organ4.28e-07503
corpus striatum8.69e-074
striatum8.69e-074
ventral part of telencephalon8.69e-074
future corpus striatum8.69e-074
segmental subdivision of hindbrain1.00e-0612
hindbrain1.00e-0612
presumptive hindbrain1.00e-0612


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0055.11.67416
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.12.15449
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
MA0105.10.846801
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.12.36034
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
MA0144.11.31729
MA0145.12.11725
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.14.84523
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
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
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.481578
MA0102.21.88331
MA0258.10.519674
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

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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