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{{Coexpression_clusters
{
|full_id=C599_medial_neuroectodermal_hippocampus_amygdala_parietal_middle_cerebellum
 

Latest revision as of 11:26, 17 September 2013


Full id: C599_medial_neuroectodermal_hippocampus_amygdala_parietal_middle_cerebellum



Phase1 CAGE Peaks

Hg19::chr17:7080883..7080903,-p6@ASGR1
Hg19::chr19:51162984..51163013,-p@chr19:51162984..51163013
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Hg19::chr19:51163812..51163823,-p@chr19:51163812..51163823
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Hg19::chr19:51163865..51163880,-p@chr19:51163865..51163880
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Hg19::chr19:51164142..51164155,-p@chr19:51164142..51164155
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Hg19::chr19:51164317..51164344,-p@chr19:51164317..51164344
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Hg19::chr19:51164347..51164387,-p@chr19:51164347..51164387
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Hg19::chr19:51164405..51164431,-p@chr19:51164405..51164431
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Hg19::chr19:51164492..51164503,-p@chr19:51164492..51164503
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Hg19::chr19:51164648..51164677,-p@chr19:51164648..51164677
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Hg19::chr19:51164729..51164740,-p@chr19:51164729..51164740
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Hg19::chr19:51164762..51164787,-p@chr19:51164762..51164787
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Hg19::chr19:51189524..51189535,-p@chr19:51189524..51189535
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Hg19::chr19:57159011..57159029,+p@chr19:57159011..57159029
+
Hg19::chr6:110423382..110423428,-p4@AK056044


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:0004873asialoglycoprotein receptor activity0.00264924055104203
GO:0006898receptor-mediated endocytosis0.0181031437654539
GO:0010324membrane invagination0.0434916990462734
GO:0006897endocytosis0.0434916990462734



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
neural tube7.81e-8656
neural rod7.81e-8656
future spinal cord7.81e-8656
neural keel7.81e-8656
regional part of nervous system2.48e-7953
regional part of brain2.48e-7953
nervous system1.23e-7689
central nervous system1.62e-6881
brain2.45e-6768
future brain2.45e-6768
regional part of forebrain6.32e-6541
forebrain6.32e-6541
anterior neural tube6.32e-6541
future forebrain6.32e-6541
neurectoderm1.72e-6486
neural plate1.52e-5982
presumptive neural plate1.52e-5982
brain grey matter6.08e-5534
gray matter6.08e-5534
telencephalon1.08e-5434
cerebral hemisphere5.16e-5132
regional part of cerebral cortex5.55e-5122
regional part of telencephalon1.28e-5032
neocortex6.10e-4620
pre-chordal neural plate2.21e-4561
cerebral cortex2.73e-4425
pallium2.73e-4425
ecto-epithelium4.14e-44104
ectoderm-derived structure2.96e-39171
ectoderm2.96e-39171
presumptive ectoderm2.96e-39171
adult organism1.80e-37114
structure with developmental contribution from neural crest2.70e-35132
organ system subdivision4.03e-25223
posterior neural tube6.15e-2115
chordal neural plate6.15e-2115
tube7.60e-18192
gyrus7.39e-166
segmental subdivision of hindbrain4.59e-1512
hindbrain4.59e-1512
presumptive hindbrain4.59e-1512
brainstem8.59e-146
segmental subdivision of nervous system9.30e-1413
temporal lobe1.29e-136
limbic system1.34e-135
occipital lobe3.23e-135
parietal lobe3.65e-135
basal ganglion1.63e-129
nuclear complex of neuraxis1.63e-129
aggregate regional part of brain1.63e-129
collection of basal ganglia1.63e-129
cerebral subcortex1.63e-129
neural nucleus4.34e-129
nucleus of brain4.34e-129
anatomical conduit9.28e-12240
diencephalon2.47e-117
future diencephalon2.47e-117
anatomical cluster8.60e-11373
regional part of diencephalon9.98e-104
regional part of metencephalon1.17e-099
metencephalon1.17e-099
future metencephalon1.17e-099
frontal cortex1.03e-083
peripheral nervous system1.56e-088
epithelium3.05e-08306
telencephalic nucleus3.57e-087
cell layer4.80e-08309
pons6.03e-083
spinal cord7.12e-083
dorsal region element7.12e-083
dorsum7.12e-083
organ part1.25e-07218
medulla oblongata1.62e-073
myelencephalon1.62e-073
future myelencephalon1.62e-073
sympathetic nervous system2.08e-075
autonomic nervous system2.08e-075
Disease
Ontology termp-valuen
neuroectodermal tumor9.69e-1110


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)
MA0003.10.0289908
MA0004.10.256222
MA0006.10.137644
MA0007.10.241375
MA0009.10.669377
MA0014.10.533948
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.11.43794
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.687159
MA0043.10.669676
MA0046.10.659066
MA0048.10.23222
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.00246981
MA0056.10
MA0057.17.42637
MA0058.10.182945
MA0059.10.182001
MA0060.10.51173
MA0061.11.64561
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.12.37487
MA0069.10.655419
MA0070.11.55511
MA0071.10.308534
MA0072.10.640598
MA0073.19.2367
MA0074.10.337035
MA0076.10.567195
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.244241
MA0089.10
MA0090.10.205547
MA0091.10.258318
MA0092.10.228476
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.141917
MA0103.10.411001
MA0105.10.929586
MA0106.10.37688
MA0107.10.315431
MA0108.20.515791
MA0109.10
MA0111.10.617603
MA0113.10.39123
MA0114.10.30732
MA0115.10.900969
MA0116.10.320986
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.406749
MA0140.10.30631
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.0838502
MA0145.10.135956
MA0146.10.0580435
MA0147.10.0991954
MA0148.10.276339
MA0149.10.298252
MA0062.20.0512998
MA0035.20.305721
MA0039.20.0182366
MA0138.20.425279
MA0002.20.0612545
MA0137.20.153033
MA0104.20.236755
MA0047.20.366327
MA0112.20.124752
MA0065.25.65748
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.0723831
MA0155.11.6461
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.11.64059
MA0160.10.288813
MA0161.10
MA0162.10.000900738
MA0163.11.26578
MA0164.10.402162
MA0080.20.139746
MA0018.20.378086
MA0099.20.312108
MA0079.214.5961
MA0102.21.1957
MA0258.10.0785319
MA0259.10.104286
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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