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{{Coexpression_clusters
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receptor protein phosphatase activity!0.0250990844682031!5800$GO:0005001!transmembrane receptor protein tyrosine phosphatase activity!0.0250990844682031!5800$GO:0005887!integral to plasma membrane!0.0250990844682031!5800;2066$GO:0031226!intrinsic to plasma membrane!0.0250990844682031!5800;2066$GO:0006793!phosphorus metabolic process!0.0266015515049223!5800;2066$GO:0006796!phosphate metabolic process!0.0266015515049223!5800;2066$GO:0004888!transmembrane receptor activity!0.0321580955874543!5800;2066$GO:0043687!post-translational protein modification!0.0321580955874543!5800;2066$GO:0044459!plasma membrane part!0.0321580955874543!5800;2066$GO:0046982!protein heterodimerization activity!0.033791670924434!2066$GO:0006464!protein modification process!0.033791670924434!5800;2066$GO:0004714!transmembrane receptor protein tyrosine kinase activity!0.033791670924434!2066$GO:0043412!biopolymer modification!0.033791670924434!5800;2066$GO:0019199!transmembrane receptor protein kinase 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|full_id=C1665_kidney_occipital_duodenum_temporal_parietal_Neural_brain
|gostat_on_coexpression_clusters=GO:0019198!transmembrane receptor protein phosphatase activity!0.0250990844682031!5800$GO:0005001!transmembrane receptor protein tyrosine phosphatase activity!0.0250990844682031!5800$GO:0005887!integral to plasma membrane!0.0250990844682031!5800;2066$GO:0031226!intrinsic to plasma membrane!0.0250990844682031!5800;2066$GO:0006793!phosphorus metabolic process!0.0266015515049223!5800;2066$GO:0006796!phosphate metabolic process!0.0266015515049223!5800;2066$GO:0004888!transmembrane receptor activity!0.0321580955874543!5800;2066$GO:0043687!post-translational protein modification!0.0321580955874543!5800;2066$GO:0044459!plasma membrane part!0.0321580955874543!5800;2066$GO:0046982!protein heterodimerization activity!0.033791670924434!2066$GO:0006464!protein modification process!0.033791670924434!5800;2066$GO:0004714!transmembrane receptor protein tyrosine kinase activity!0.033791670924434!2066$GO:0043412!biopolymer modification!0.033791670924434!5800;2066$GO:0019199!transmembrane receptor protein kinase activity!0.0341160217542822!2066$GO:0004872!receptor activity!0.0352430259229253!5800;2066$GO:0060089!molecular transducer activity!0.0409379450656799!5800;2066$GO:0004871!signal transducer activity!0.0409379450656799!5800;2066$GO:0007169!transmembrane receptor protein tyrosine kinase signaling pathway!0.0409379450656799!2066$GO:0005886!plasma membrane!0.0409379450656799!5800;2066$GO:0004725!protein tyrosine phosphatase activity!0.0409379450656799!5800$GO:0006470!protein amino acid dephosphorylation!0.044156149366298!5800$GO:0016311!dephosphorylation!0.0469563405358217!5800$GO:0007167!enzyme linked receptor protein signaling pathway!0.0469563405358217!2066$GO:0004713!protein-tyrosine kinase activity!0.0469563405358217!2066$GO:0004721!phosphoprotein phosphatase activity!0.0469563405358217!5800
|id=C1665
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!3.08e-43!94;UBERON:0001016!3.08e-43!94;UBERON:0005743!3.41e-41!86;UBERON:0001017!9.56e-41!82;UBERON:0001049!2.22e-39!57;UBERON:0005068!2.22e-39!57;UBERON:0006241!2.22e-39!57;UBERON:0007135!2.22e-39!57;UBERON:0007023!3.89e-34!115;UBERON:0002616!3.79e-33!59;UBERON:0002346!6.66e-33!90;UBERON:0003080!8.96e-33!42;UBERON:0002780!2.77e-32!41;UBERON:0001890!2.77e-32!41;UBERON:0006240!2.77e-32!41;UBERON:0000955!6.52e-32!69;UBERON:0006238!6.52e-32!69;UBERON:0003075!8.14e-32!86;UBERON:0007284!8.14e-32!86;UBERON:0000924!8.45e-30!173;UBERON:0006601!8.45e-30!173;UBERON:0004121!1.26e-28!169;UBERON:0001893!1.84e-27!34;UBERON:0002020!2.08e-27!34;UBERON:0003528!2.08e-27!34;UBERON:0002791!1.48e-26!33;UBERON:0001869!5.24e-26!32;UBERON:0003056!1.65e-25!61;UBERON:0000153!1.70e-24!129;UBERON:0007811!1.70e-24!129;UBERON:0000033!3.93e-24!123;UBERON:0000956!6.22e-20!25;UBERON:0000203!6.22e-20!25;UBERON:0002619!1.11e-19!22;UBERON:0001950!6.72e-18!20;UBERON:0000477!2.86e-15!286;UBERON:0000064!1.16e-12!219;UBERON:0004111!2.06e-12!241;UBERON:0000481!4.43e-12!347;UBERON:0000475!6.02e-12!365;UBERON:0000025!8.29e-12!194;UBERON:0000922!4.74e-11!612;UBERON:0000468!1.48e-10!659;UBERON:0000483!1.47e-09!309;UBERON:0002420!3.03e-09!9;UBERON:0007245!3.03e-09!9;UBERON:0010009!3.03e-09!9;UBERON:0010011!3.03e-09!9;UBERON:0000454!3.03e-09!9;UBERON:0000119!3.80e-09!312;UBERON:0002050!5.71e-09!605;UBERON:0005423!5.71e-09!605;UBERON:0002308!6.44e-09!9;UBERON:0000125!6.44e-09!9;UBERON:0000923!1.13e-08!604;UBERON:0005291!1.13e-08!604;UBERON:0006598!1.13e-08!604;UBERON:0002532!1.13e-08!604;UBERON:0003076!5.53e-08!15;UBERON:0003057!5.53e-08!15;UBERON:0000467!8.82e-08!625;UBERON:0000480!1.12e-07!626;UBERON:0009663!2.23e-07!7;UBERON:0002298!3.96e-07!8;UBERON:0000062!4.54e-07!511;UBERON:0000200!8.61e-07!6
}}

Latest revision as of 11:49, 17 September 2013


Full id: C1665_kidney_occipital_duodenum_temporal_parietal_Neural_brain



Phase1 CAGE Peaks

Hg19::chr12:15475214..15475223,+p9@PTPRO
Hg19::chr12:15475249..15475280,+p4@PTPRO
Hg19::chr12:15475292..15475303,+p7@PTPRO
Hg19::chr12:15475462..15475483,+p5@PTPRO
Hg19::chr2:213403858..213403879,-p2@ERBB4


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:0019198transmembrane receptor protein phosphatase activity0.0250990844682031
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.0250990844682031
GO:0005887integral to plasma membrane0.0250990844682031
GO:0031226intrinsic to plasma membrane0.0250990844682031
GO:0006793phosphorus metabolic process0.0266015515049223
GO:0006796phosphate metabolic process0.0266015515049223
GO:0004888transmembrane receptor activity0.0321580955874543
GO:0043687post-translational protein modification0.0321580955874543
GO:0044459plasma membrane part0.0321580955874543
GO:0046982protein heterodimerization activity0.033791670924434
GO:0006464protein modification process0.033791670924434
GO:0004714transmembrane receptor protein tyrosine kinase activity0.033791670924434
GO:0043412biopolymer modification0.033791670924434
GO:0019199transmembrane receptor protein kinase activity0.0341160217542822
GO:0004872receptor activity0.0352430259229253
GO:0060089molecular transducer activity0.0409379450656799
GO:0004871signal transducer activity0.0409379450656799
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0409379450656799
GO:0005886plasma membrane0.0409379450656799
GO:0004725protein tyrosine phosphatase activity0.0409379450656799
GO:0006470protein amino acid dephosphorylation0.044156149366298
GO:0016311dephosphorylation0.0469563405358217
GO:0007167enzyme linked receptor protein signaling pathway0.0469563405358217
GO:0004713protein-tyrosine kinase activity0.0469563405358217
GO:0004721phosphoprotein phosphatase activity0.0469563405358217



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
neuronal stem cell3.20e-118
neuron7.14e-086
neuroblast7.14e-086
electrically signaling cell7.14e-086
Uber Anatomy
Ontology termp-valuen
central nervous system2.05e-6681
nervous system3.73e-6589
neural tube9.48e-6056
neural rod9.48e-6056
future spinal cord9.48e-6056
neural keel9.48e-6056
regional part of nervous system7.73e-5553
regional part of brain7.73e-5553
regional part of forebrain1.51e-5341
forebrain1.51e-5341
anterior neural tube1.51e-5341
future forebrain1.51e-5341
cerebral hemisphere5.62e-5232
telencephalon9.98e-5234
brain grey matter1.45e-5134
gray matter1.45e-5134
brain1.23e-4868
future brain1.23e-4868
regional part of telencephalon3.52e-4832
regional part of cerebral cortex2.58e-4122
neural plate2.47e-4082
presumptive neural plate2.47e-4082
ectoderm-derived structure3.71e-40171
ectoderm3.71e-40171
presumptive ectoderm3.71e-40171
neurectoderm6.76e-4086
cerebral cortex8.64e-3925
pallium8.64e-3925
neocortex1.98e-3720
pre-chordal neural plate1.42e-3661
ecto-epithelium3.67e-32104
adult organism3.58e-29114
organ system subdivision5.05e-27223
structure with developmental contribution from neural crest2.52e-23132
anatomical cluster2.91e-16373
basal ganglion1.23e-149
nuclear complex of neuraxis1.23e-149
aggregate regional part of brain1.23e-149
collection of basal ganglia1.23e-149
cerebral subcortex1.23e-149
neural nucleus5.79e-149
nucleus of brain5.79e-149
tube2.40e-13192
gyrus8.78e-136
limbic system1.84e-115
temporal lobe3.06e-116
parietal lobe4.65e-115
occipital lobe5.05e-115
anatomical conduit6.44e-11240
telencephalic nucleus1.00e-107
organ part2.37e-10218
corpus striatum1.93e-094
striatum1.93e-094
ventral part of telencephalon1.93e-094
future corpus striatum1.93e-094
embryo7.98e-09592
posterior neural tube9.45e-0915
chordal neural plate9.45e-0915
brainstem4.43e-086
caudate-putamen1.68e-073
dorsal striatum1.68e-073
multi-tissue structure2.03e-07342
frontal cortex3.46e-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)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.11.7452
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.13.99021
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.14.57459
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.111822
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.13.01153
MA0106.10.779931
MA0107.12.62998
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.21.12758
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.21.96224
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.53298
MA0102.21.66336
MA0258.11.63655
MA0259.10.395396
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
REST#597847.720022972902420.0005286363773650570.00457152062727741



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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