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{{Coexpression_clusters
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recognition!0.01320504727344!8851$GO:0030295!protein kinase activator activity!0.013504565630361!8851$GO:0045296!cadherin binding!0.0137687530116964!8851$GO:0050839!cell adhesion molecule binding!0.0140034979185793!8851$GO:0030426!growth cone!0.0162011855987303!8851$GO:0019209!kinase activator activity!0.0162011855987303!8851$GO:0030427!site of polarized growth!0.0162861869441539!8851$GO:0007215!glutamate signaling pathway!0.0171807993626783!8851$GO:0007399!nervous system development!0.0172130658216937!8851;6252$GO:0043523!regulation of neuron apoptosis!0.0187147571999021!8851$GO:0045664!regulation of neuron differentiation!0.0187147571999021!8851$GO:0051402!neuron apoptosis!0.0207597465600854!8851$GO:0030424!axon!0.0213659970292782!8851$GO:0043025!cell soma!0.0213659970292782!8851$GO:0001764!neuron migration!0.0213659970292782!8851$GO:0008037!cell recognition!0.0213659970292782!8851$GO:0030425!dendrite!0.0213659970292782!8851$GO:0022610!biological adhesion!0.0213659970292782!8851;57526$GO:0007155!cell adhesion!0.0213659970292782!8851;57526$GO:0044463!cell projection part!0.0248523245329768!8851$GO:0000079!regulation of cyclin-dependent protein kinase activity!0.0251673650516551!8851$GO:0030176!integral to endoplasmic reticulum membrane!0.0264610062785568!6252$GO:0007411!axon guidance!0.0271995516014897!8851$GO:0031227!intrinsic to endoplasmic reticulum membrane!0.028842026336961!6252$GO:0043292!contractile fiber!0.0291797408887818!8851$GO:0048468!cell development!0.0291797408887818!8851;6252$GO:0043005!neuron projection!0.0354647600560195!8851$GO:0005509!calcium ion binding!0.0379224089843669!8851;57526$GO:0003755!peptidyl-prolyl cis-trans isomerase activity!0.0379224089843669!285755$GO:0016859!cis-trans isomerase activity!0.0379224089843669!285755$GO:0019887!protein kinase regulator activity!0.041766460181213!8851$GO:0048731!system 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|full_id=C1395_temporal_occipital_duodenum_parietal_medial_cerebellum_brain
|id=C1395
}}

Latest revision as of 11:44, 17 September 2013


Full id: C1395_temporal_occipital_duodenum_parietal_medial_cerebellum_brain



Phase1 CAGE Peaks

Hg19::chr14:60074147..60074162,-p12@RTN1
Hg19::chr16:56390504..56390515,+p@chr16:56390504..56390515
+
Hg19::chr17:30814707..30814718,+p17@CDK5R1
Hg19::chr19:42471082..42471122,-p@chr19:42471082..42471122
-
Hg19::chr6:109761966..109761979,-p4@PPIL6
Hg19::chrX:99665097..99665125,-p2@PCDH19


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:0030182neuron differentiation0.00720561611857918
GO:0016533cyclin-dependent protein kinase 5 activator complex0.00720561611857918
GO:0043539protein serine/threonine kinase activator activity0.00720561611857918
GO:0035235ionotropic glutamate receptor signaling pathway0.00720561611857918
GO:0016534cyclin-dependent protein kinase 5 activator activity0.00720561611857918
GO:0048699generation of neurons0.00765940106601726
GO:0022008neurogenesis0.00769157031996023
GO:0007413axonal fasciculation0.00969772650622996
GO:0016337cell-cell adhesion0.00969772650622996
GO:0031594neuromuscular junction0.00969772650622996
GO:0043197dendritic spine0.00969772650622996
GO:0007213acetylcholine receptor signaling, muscarinic pathway0.00969772650622996
GO:0007158neuron adhesion0.00969772650622996
GO:0043525positive regulation of neuron apoptosis0.011576875510383
GO:0008038neuron recognition0.01320504727344
GO:0030295protein kinase activator activity0.013504565630361
GO:0045296cadherin binding0.0137687530116964
GO:0050839cell adhesion molecule binding0.0140034979185793
GO:0030426growth cone0.0162011855987303
GO:0019209kinase activator activity0.0162011855987303
GO:0030427site of polarized growth0.0162861869441539
GO:0007215glutamate signaling pathway0.0171807993626783
GO:0007399nervous system development0.0172130658216937
GO:0043523regulation of neuron apoptosis0.0187147571999021
GO:0045664regulation of neuron differentiation0.0187147571999021
GO:0051402neuron apoptosis0.0207597465600854
GO:0030424axon0.0213659970292782
GO:0043025cell soma0.0213659970292782
GO:0001764neuron migration0.0213659970292782
GO:0008037cell recognition0.0213659970292782
GO:0030425dendrite0.0213659970292782
GO:0022610biological adhesion0.0213659970292782
GO:0007155cell adhesion0.0213659970292782
GO:0044463cell projection part0.0248523245329768
GO:0000079regulation of cyclin-dependent protein kinase activity0.0251673650516551
GO:0030176integral to endoplasmic reticulum membrane0.0264610062785568
GO:0007411axon guidance0.0271995516014897
GO:0031227intrinsic to endoplasmic reticulum membrane0.028842026336961
GO:0043292contractile fiber0.0291797408887818
GO:0048468cell development0.0291797408887818
GO:0043005neuron projection0.0354647600560195
GO:0005509calcium ion binding0.0379224089843669
GO:0003755peptidyl-prolyl cis-trans isomerase activity0.0379224089843669
GO:0016859cis-trans isomerase activity0.0379224089843669
GO:0019887protein kinase regulator activity0.041766460181213
GO:0048731system development0.041766460181213
GO:0007409axonogenesis0.0434780166963583
GO:0048667neuron morphogenesis during differentiation0.0437219029656972
GO:0048812neurite morphogenesis0.0437219029656972
GO:0019207kinase regulator activity0.0437219029656972
GO:0000904cellular morphogenesis during differentiation0.0442621846464368
GO:0031175neurite development0.0444436574628336
GO:0048869cellular developmental process0.0444436574628336
GO:0030154cell differentiation0.0444436574628336
GO:0007420brain development0.0444436574628336
GO:0031301integral to organelle membrane0.0444436574628336
GO:0045595regulation of cell differentiation0.0452245969787288
GO:0031300intrinsic to organelle membrane0.0467050532889091
GO:0048666neuron development0.0467050532889091
GO:0048856anatomical structure development0.0491735817345141



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 tube2.35e-8856
neural rod2.35e-8856
future spinal cord2.35e-8856
neural keel2.35e-8856
central nervous system5.03e-8781
regional part of nervous system7.63e-8553
regional part of brain7.63e-8553
nervous system1.98e-8089
brain grey matter7.39e-7734
gray matter7.39e-7734
telencephalon1.13e-7634
regional part of forebrain4.09e-7641
forebrain4.09e-7641
anterior neural tube4.09e-7641
future forebrain4.09e-7641
brain1.09e-7368
future brain1.09e-7368
cerebral hemisphere1.07e-7132
regional part of telencephalon1.92e-7132
neural plate9.65e-6382
presumptive neural plate9.65e-6382
regional part of cerebral cortex3.04e-6122
neurectoderm2.61e-5986
cerebral cortex4.06e-5825
pallium4.06e-5825
neocortex1.90e-5520
pre-chordal neural plate1.85e-5461
ecto-epithelium2.19e-49104
adult organism3.80e-42114
ectoderm-derived structure2.62e-41171
ectoderm2.62e-41171
presumptive ectoderm2.62e-41171
structure with developmental contribution from neural crest2.42e-40132
organ system subdivision5.61e-33223
tube1.24e-22192
basal ganglion3.94e-209
nuclear complex of neuraxis3.94e-209
aggregate regional part of brain3.94e-209
collection of basal ganglia3.94e-209
cerebral subcortex3.94e-209
neural nucleus1.18e-199
nucleus of brain1.18e-199
gyrus1.32e-186
anatomical cluster1.19e-17373
temporal lobe3.59e-166
occipital lobe8.09e-165
anatomical conduit8.79e-16240
limbic system9.41e-165
parietal lobe1.06e-155
telencephalic nucleus1.61e-147
posterior neural tube3.66e-1415
chordal neural plate3.66e-1415
organ part1.97e-13218
epithelium4.69e-12306
cell layer7.99e-12309
brainstem8.43e-126
segmental subdivision of hindbrain5.57e-1112
hindbrain5.57e-1112
presumptive hindbrain5.57e-1112
frontal cortex3.30e-103
segmental subdivision of nervous system4.69e-1013
multi-tissue structure1.28e-09342
pons2.10e-093
germ layer4.10e-08560
germ layer / neural crest4.10e-08560
embryonic tissue4.10e-08560
presumptive structure4.10e-08560
germ layer / neural crest derived structure4.10e-08560
epiblast (generic)4.10e-08560
regional part of metencephalon4.78e-089
metencephalon4.78e-089
future metencephalon4.78e-089
embryo4.98e-08592
embryonic structure5.93e-08564
middle frontal gyrus1.62e-072
amygdala1.72e-072
middle temporal gyrus1.89e-072
corpus striatum2.26e-074
striatum2.26e-074
ventral part of telencephalon2.26e-074
future corpus striatum2.26e-074
Ammon's horn2.28e-072
lobe parts of cerebral cortex2.28e-072
hippocampal formation2.28e-072
limbic lobe2.28e-072
developing anatomical structure2.70e-07581
dorsal plus ventral thalamus5.33e-072
thalamic complex5.33e-072
organ6.04e-07503
locus ceruleus6.38e-072
brainstem nucleus6.38e-072
hindbrain nucleus6.38e-072


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)
MA0003.13.05245
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.11.149
MA0017.11.10421
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.11.3446
MA0043.11.03713
MA0046.11.02569
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.12.26581
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.11.54633
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.11.52717
MA0115.11.28169
MA0116.12.36812
MA0117.11.07516
MA0119.11.12205
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.86787
MA0140.10.622527
MA0141.11.15452
MA0142.10.838805
MA0143.10.725558
MA0144.10.811435
MA0145.10.347815
MA0146.10.718193
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.35955
MA0138.20.765223
MA0002.22.02127
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.101413
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.819655
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.978497
MA0163.11.60684
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.62382
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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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