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{{Coexpression_clusters
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|full_id=C2113_brain_medial_hippocampus_diencephalon_amygdala_substantia_olfactory
|id=C2113
}}

Latest revision as of 11:59, 17 September 2013


Full id: C2113_brain_medial_hippocampus_diencephalon_amygdala_substantia_olfactory



Phase1 CAGE Peaks

Hg19::chr11:134281749..134281759,-p5@B3GAT1
Hg19::chr15:30248510..30248535,-p32@TJP1
Hg19::chr20:58349377..58349415,+p@chr20:58349377..58349415
+
Hg19::chr3:58551422..58551434,-p@chr3:58551422..58551434
-


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:0005918septate junction0.00423878488166725
GO:0015018galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity0.00953487963183759
GO:0008499UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity0.00953487963183759
GO:0048531beta-1,3-galactosyltransferase activity0.00953487963183759
GO:0005913cell-cell adherens junction0.00953487963183759
GO:0007043intercellular junction assembly0.00953487963183759
GO:0035250UDP-galactosyltransferase activity0.00953487963183759
GO:0045216intercellular junction assembly and maintenance0.00953487963183759
GO:0007028cytoplasm organization and biogenesis0.0112995998696127
GO:0015020glucuronosyltransferase activity0.014404868632055
GO:0008378galactosyltransferase activity0.015404915412871
GO:0005912adherens junction0.0190596523614523
GO:0016323basolateral plasma membrane0.026911659244122
GO:0005923tight junction0.026911659244122
GO:0043296apical junction complex0.027774445781206
GO:0016327apicolateral plasma membrane0.027774445781206
GO:0008194UDP-glycosyltransferase activity0.0343395765145704
GO:0030145manganese ion binding0.0345423555680781
GO:0005911intercellular junction0.0349728933440095
GO:0006486protein amino acid glycosylation0.0349728933440095
GO:0043413biopolymer glycosylation0.0349728933440095
GO:0009101glycoprotein biosynthetic process0.0349728933440095
GO:0009100glycoprotein metabolic process0.0382165680597289
GO:0016758transferase activity, transferring hexosyl groups0.0494245767274581



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
neural tube1.30e-9256
neural rod1.30e-9256
future spinal cord1.30e-9256
neural keel1.30e-9256
regional part of nervous system8.57e-8353
regional part of brain8.57e-8353
nervous system4.44e-7789
central nervous system3.92e-7581
brain8.96e-7068
future brain8.96e-7068
regional part of forebrain3.15e-6941
forebrain3.15e-6941
anterior neural tube3.15e-6941
future forebrain3.15e-6941
brain grey matter5.07e-6734
gray matter5.07e-6734
telencephalon6.88e-6734
neural plate4.31e-6482
presumptive neural plate4.31e-6482
neurectoderm6.38e-6486
regional part of telencephalon1.94e-6032
cerebral hemisphere4.37e-6032
adult organism7.33e-52114
ecto-epithelium1.14e-48104
pre-chordal neural plate8.14e-4861
regional part of cerebral cortex1.32e-4322
structure with developmental contribution from neural crest1.06e-38132
cerebral cortex4.49e-3825
pallium4.49e-3825
ectoderm-derived structure9.10e-38171
ectoderm9.10e-38171
presumptive ectoderm9.10e-38171
neocortex5.61e-3720
neural nucleus6.10e-339
nucleus of brain6.10e-339
organ system subdivision3.84e-31223
basal ganglion2.56e-269
nuclear complex of neuraxis2.56e-269
aggregate regional part of brain2.56e-269
collection of basal ganglia2.56e-269
cerebral subcortex2.56e-269
telencephalic nucleus4.54e-267
posterior neural tube3.32e-2315
chordal neural plate3.32e-2315
tube4.13e-22192
segmental subdivision of nervous system3.59e-1713
gyrus4.41e-166
anatomical conduit7.84e-16240
corpus striatum1.10e-154
striatum1.10e-154
ventral part of telencephalon1.10e-154
future corpus striatum1.10e-154
anatomical cluster2.23e-15373
brainstem3.25e-156
segmental subdivision of hindbrain1.97e-1412
hindbrain1.97e-1412
presumptive hindbrain1.97e-1412
temporal lobe1.05e-136
limbic system8.05e-135
organ part1.46e-12218
caudate-putamen2.67e-123
dorsal striatum2.67e-123
occipital lobe3.55e-125
spinal cord4.21e-123
dorsal region element4.21e-123
dorsum4.21e-123
pons1.07e-113
epithelium2.92e-11306
cell layer4.63e-11309
regional part of metencephalon2.44e-109
metencephalon2.44e-109
future metencephalon2.44e-109
multi-tissue structure1.06e-09342
middle temporal gyrus3.31e-092
Ammon's horn6.68e-092
lobe parts of cerebral cortex6.68e-092
hippocampal formation6.68e-092
limbic lobe6.68e-092
dorsal plus ventral thalamus9.44e-092
thalamic complex9.44e-092
caudate nucleus1.06e-082
future caudate nucleus1.06e-082
locus ceruleus1.38e-082
brainstem nucleus1.38e-082
hindbrain nucleus1.38e-082
multi cell component structure1.87e-082
neuron projection bundle1.87e-082
globus pallidus2.17e-082
pallidum2.17e-082
parietal lobe2.35e-075
germ layer3.41e-07560
germ layer / neural crest3.41e-07560
embryonic tissue3.41e-07560
presumptive structure3.41e-07560
germ layer / neural crest derived structure3.41e-07560
epiblast (generic)3.41e-07560
developing anatomical structure3.97e-07581
embryonic structure4.60e-07564
embryo8.71e-07592


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)
MA0003.11.45381
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.12.83685
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.88496
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.13.14178
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.24.43857
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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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