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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:29, 17 September 2013


Full id: C734_brain_occipital_parietal_middle_medial_frontal_hippocampus



Phase1 CAGE Peaks

Hg19::chr11:133110104..133110106,-p@chr11:133110104..133110106
-
Hg19::chr11:35280774..35280791,-p18@SLC1A2
Hg19::chr11:35428629..35428633,-p@chr11:35428629..35428633
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Hg19::chr11:64490531..64490542,-p15@NRXN2
Hg19::chr12:6806552..6806592,-p@chr12:6806552..6806592
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Hg19::chr16:24228379..24228398,+p11@PRKCB
Hg19::chr17:36689327..36689331,-p@chr17:36689327..36689331
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Hg19::chr5:11385202..11385207,-p32@CTNND2
Hg19::chr5:11385208..11385211,-p31@CTNND2
Hg19::chr8:133460745..133460750,-p@chr8:133460745..133460750
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Hg19::chr9:138053475..138053498,-p@chr9:138053475..138053498
-


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:0007268synaptic transmission0.012004234792766
GO:0019226transmission of nerve impulse0.012004234792766
GO:0007158neuron adhesion0.012004234792766
GO:0005313L-glutamate transmembrane transporter activity0.012004234792766
GO:0015172acidic amino acid transmembrane transporter activity0.012004234792766
GO:0005246calcium channel regulator activity0.012004234792766
GO:0007267cell-cell signaling0.012004234792766
GO:0015813L-glutamate transport0.012004234792766
GO:0015800acidic amino acid transport0.012004234792766
GO:0017153sodium:dicarboxylate symporter activity0.012004234792766
GO:0032501multicellular organismal process0.012004234792766
GO:0005310dicarboxylic acid transmembrane transporter activity0.012004234792766
GO:0006835dicarboxylic acid transport0.012004234792766
GO:0007416synaptogenesis0.015263430192972
GO:0022610biological adhesion0.015263430192972
GO:0007155cell adhesion0.015263430192972
GO:0015179L-amino acid transmembrane transporter activity0.0166790804028058
GO:0016247channel regulator activity0.0166790804028058
GO:0005343organic acid:sodium symporter activity0.0166790804028058
GO:0015296anion:cation symporter activity0.0166790804028058
GO:0050808synapse organization and biogenesis0.0166790804028058
GO:0007269neurotransmitter secretion0.0166790804028058
GO:0050877neurological system process0.0184434811931709
GO:0007154cell communication0.0189883449215195
GO:0045055regulated secretory pathway0.0194403635047792
GO:0015171amino acid transmembrane transporter activity0.0221233606276199
GO:0003008system process0.0221233606276199
GO:0006865amino acid transport0.0221233606276199
GO:0003001generation of a signal involved in cell-cell signaling0.0221233606276199
GO:0001505regulation of neurotransmitter levels0.0238244046128343
GO:0015837amine transport0.0240492340692788
GO:0043062extracellular structure organization and biogenesis0.0240492340692788
GO:0015370solute:sodium symporter activity0.0244280890003623
GO:0046943carboxylic acid transmembrane transporter activity0.0245026736589769
GO:0046942carboxylic acid transport0.0245026736589769
GO:0015849organic acid transport0.0245026736589769
GO:0005342organic acid transmembrane transporter activity0.0245026736589769
GO:0015294solute:cation symporter activity0.0274605540620924
GO:0044425membrane part0.0313573386065829
GO:0007275multicellular organismal development0.0340974263283226
GO:0008509anion transmembrane transporter activity0.0465301057857495



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 tube1.19e-10456
neural rod1.19e-10456
future spinal cord1.19e-10456
neural keel1.19e-10456
regional part of nervous system4.03e-9953
regional part of brain4.03e-9953
regional part of forebrain1.02e-8941
forebrain1.02e-8941
anterior neural tube1.02e-8941
future forebrain1.02e-8941
telencephalon6.55e-8834
brain grey matter1.67e-8734
gray matter1.67e-8734
central nervous system5.42e-8681
brain5.66e-8468
future brain5.66e-8468
cerebral hemisphere2.80e-8032
regional part of telencephalon8.63e-8032
nervous system8.99e-7789
neural plate3.28e-7382
presumptive neural plate3.28e-7382
neurectoderm1.79e-6986
regional part of cerebral cortex2.78e-6722
pre-chordal neural plate1.50e-6261
cerebral cortex5.58e-5925
pallium5.58e-5925
neocortex8.87e-5920
ecto-epithelium3.58e-56104
adult organism3.56e-51114
structure with developmental contribution from neural crest9.12e-48132
ectoderm-derived structure1.12e-38171
ectoderm1.12e-38171
presumptive ectoderm1.12e-38171
neural nucleus9.59e-309
nucleus of brain9.59e-309
organ system subdivision1.65e-29223
tube3.25e-25192
basal ganglion2.92e-239
nuclear complex of neuraxis2.92e-239
aggregate regional part of brain2.92e-239
collection of basal ganglia2.92e-239
cerebral subcortex2.92e-239
parietal lobe2.18e-225
telencephalic nucleus4.48e-227
gyrus7.07e-196
anatomical conduit1.46e-18240
brainstem2.05e-176
posterior neural tube9.26e-1715
chordal neural plate9.26e-1715
temporal lobe4.47e-166
anatomical cluster2.76e-15373
limbic system3.29e-155
occipital lobe4.39e-155
organ part1.05e-14218
epithelium8.94e-14306
cell layer1.46e-13309
pons2.38e-133
segmental subdivision of hindbrain4.87e-1212
hindbrain4.87e-1212
presumptive hindbrain4.87e-1212
multi-tissue structure1.77e-11342
segmental subdivision of nervous system4.54e-1113
corpus striatum8.10e-114
striatum8.10e-114
ventral part of telencephalon8.10e-114
future corpus striatum8.10e-114
Ammon's horn2.02e-102
lobe parts of cerebral cortex2.02e-102
hippocampal formation2.02e-102
limbic lobe2.02e-102
middle temporal gyrus4.39e-102
globus pallidus1.34e-092
pallidum1.34e-092
locus ceruleus1.66e-092
brainstem nucleus1.66e-092
hindbrain nucleus1.66e-092
meninx2.80e-092
membrane organ2.80e-092
meningeal cluster2.80e-092
organ2.77e-08503
regional part of metencephalon1.22e-079
metencephalon1.22e-079
future metencephalon1.22e-079
germ layer3.39e-07560
germ layer / neural crest3.39e-07560
embryonic tissue3.39e-07560
presumptive structure3.39e-07560
germ layer / neural crest derived structure3.39e-07560
epiblast (generic)3.39e-07560
embryonic structure4.43e-07564
frontal cortex4.46e-073
caudate-putamen6.01e-073
dorsal striatum6.01e-073


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)
MA0003.11.34363
MA0004.10.349539
MA0006.10.605586
MA0007.10.332734
MA0009.10.79061
MA0014.10.79286
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.729247
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.0496191
MA0056.10
MA0057.10.0465155
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.10.6764
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.140284
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.730303
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.755189
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.587485
MA0105.11.43099
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.481808
MA0117.10.827487
MA0119.10.698186
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.307853
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.515404
MA0146.10.0109959
MA0147.10.488526
MA0148.10.372124
MA0149.11.81263
MA0062.20.0969238
MA0035.21.84093
MA0039.20.0944823
MA0138.20.534556
MA0002.20.111226
MA0137.20.229531
MA0104.20.760822
MA0047.20.47109
MA0112.20.106997
MA0065.20.11899
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.153348
MA0155.10.099499
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.11.74876
MA0163.10.232847
MA0164.11.2703
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.20.311083
MA0102.21.32663
MA0258.10.135061
MA0259.10.168926
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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