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{{Coexpression_clusters
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domain specific binding!0.0265630519251148!50649$GO:0005089!Rho guanyl-nucleotide exchange factor activity!0.0265630519251148!50649$GO:0035023!regulation of Rho protein signal transduction!0.0265630519251148!50649$GO:0005088!Ras guanyl-nucleotide exchange factor activity!0.0265630519251148!50649$GO:0007266!Rho protein signal transduction!0.0265630519251148!50649$GO:0005085!guanyl-nucleotide exchange factor activity!0.0334864005651713!50649$GO:0046578!regulation of Ras protein signal transduction!0.0334864005651713!50649$GO:0007265!Ras protein signal transduction!0.0334864005651713!50649$GO:0005083!small GTPase regulator activity!0.0334864005651713!50649$GO:0051056!regulation of small GTPase mediated signal transduction!0.0334864005651713!50649$GO:0030695!GTPase regulator activity!0.0449568093510163!50649$GO:0009966!regulation of signal transduction!0.0470976097963028!50649$GO:0007264!small GTPase mediated signal 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|full_id=C1818_brain_temporal_occipital_diencephalon_cerebellum_olfactory_cerebral
|gostat_on_coexpression_clusters=GO:0019904!protein domain specific binding!0.0265630519251148!50649$GO:0005089!Rho guanyl-nucleotide exchange factor activity!0.0265630519251148!50649$GO:0035023!regulation of Rho protein signal transduction!0.0265630519251148!50649$GO:0005088!Ras guanyl-nucleotide exchange factor activity!0.0265630519251148!50649$GO:0007266!Rho protein signal transduction!0.0265630519251148!50649$GO:0005085!guanyl-nucleotide exchange factor activity!0.0334864005651713!50649$GO:0046578!regulation of Ras protein signal transduction!0.0334864005651713!50649$GO:0007265!Ras protein signal transduction!0.0334864005651713!50649$GO:0005083!small GTPase regulator activity!0.0334864005651713!50649$GO:0051056!regulation of small GTPase mediated signal transduction!0.0334864005651713!50649$GO:0030695!GTPase regulator activity!0.0449568093510163!50649$GO:0009966!regulation of signal transduction!0.0470976097963028!50649$GO:0007264!small GTPase mediated signal transduction!0.0474961280330408!50649
|id=C1818
|ontology_enrichment_celltype=CL:0002319!6.81e-08!25;CL:0000540!1.33e-07!6;CL:0000031!1.33e-07!6;CL:0000404!1.33e-07!6;CL:0000047!5.26e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!1.68e-56!86;UBERON:0001017!6.08e-55!82;UBERON:0000073!6.77e-54!94;UBERON:0001016!6.77e-54!94;UBERON:0001049!1.58e-47!57;UBERON:0005068!1.58e-47!57;UBERON:0006241!1.58e-47!57;UBERON:0007135!1.58e-47!57;UBERON:0000955!8.96e-44!69;UBERON:0006238!8.96e-44!69;UBERON:0002616!1.55e-42!59;UBERON:0002780!1.31e-39!41;UBERON:0001890!1.31e-39!41;UBERON:0006240!1.31e-39!41;UBERON:0003080!2.58e-38!42;UBERON:0001893!4.00e-37!34;UBERON:0002020!7.29e-37!34;UBERON:0003528!7.29e-37!34;UBERON:0002791!7.75e-36!33;UBERON:0001869!9.00e-35!32;UBERON:0003075!1.72e-34!86;UBERON:0007284!1.72e-34!86;UBERON:0002346!2.24e-33!90;UBERON:0003056!1.65e-27!61;UBERON:0004121!4.82e-27!169;UBERON:0000956!5.29e-27!25;UBERON:0000203!5.29e-27!25;UBERON:0000924!1.02e-26!173;UBERON:0006601!1.02e-26!173;UBERON:0007023!1.55e-25!115;UBERON:0002619!3.15e-25!22;UBERON:0000033!5.65e-24!123;UBERON:0000153!1.75e-23!129;UBERON:0007811!1.75e-23!129;UBERON:0001950!6.11e-23!20;UBERON:0000025!3.43e-13!194;UBERON:0002308!3.30e-11!9;UBERON:0000125!3.30e-11!9;UBERON:0002420!4.29e-11!9;UBERON:0007245!4.29e-11!9;UBERON:0010009!4.29e-11!9;UBERON:0010011!4.29e-11!9;UBERON:0000454!4.29e-11!9;UBERON:0003076!2.74e-10!15;UBERON:0003057!2.74e-10!15;UBERON:0000475!4.15e-10!365;UBERON:0000119!1.31e-09!312;UBERON:0000483!1.73e-09!309;UBERON:0004111!3.33e-09!241;UBERON:0009663!4.32e-09!7;UBERON:0000200!1.13e-08!6;UBERON:0000922!3.66e-08!612;UBERON:0001871!4.67e-08!7;UBERON:0002021!2.10e-07!5;UBERON:0001872!2.36e-07!5;UBERON:0004733!2.36e-07!12;UBERON:0002028!2.36e-07!12;UBERON:0007277!2.36e-07!12;UBERON:0000468!2.79e-07!659;UBERON:0000477!4.20e-07!286;UBERON:0000349!4.67e-07!5;UBERON:0000467!6.14e-07!625;UBERON:0000480!7.27e-07!626
}}

Latest revision as of 11:52, 17 September 2013


Full id: C1818_brain_temporal_occipital_diencephalon_cerebellum_olfactory_cerebral



Phase1 CAGE Peaks

Hg19::chr19:36367501..36367512,-p@chr19:36367501..36367512
-
Hg19::chr19:42470973..42470984,+p4@CU679344
Hg19::chr2:131769317..131769328,+p13@ARHGEF4
Hg19::chr9:120173722..120173724,-p@chr9:120173722..120173724
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Hg19::chr9:34523008..34523018,-p5@ENHO


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:0019904protein domain specific binding0.0265630519251148
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0265630519251148
GO:0035023regulation of Rho protein signal transduction0.0265630519251148
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0265630519251148
GO:0007266Rho protein signal transduction0.0265630519251148
GO:0005085guanyl-nucleotide exchange factor activity0.0334864005651713
GO:0046578regulation of Ras protein signal transduction0.0334864005651713
GO:0007265Ras protein signal transduction0.0334864005651713
GO:0005083small GTPase regulator activity0.0334864005651713
GO:0051056regulation of small GTPase mediated signal transduction0.0334864005651713
GO:0030695GTPase regulator activity0.0449568093510163
GO:0009966regulation of signal transduction0.0470976097963028
GO:0007264small GTPase mediated signal transduction0.0474961280330408



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
central nervous system5.73e-7281
neural tube3.20e-7156
neural rod3.20e-7156
future spinal cord3.20e-7156
neural keel3.20e-7156
regional part of nervous system7.33e-6653
regional part of brain7.33e-6653
brain8.42e-6568
future brain8.42e-6568
nervous system4.05e-6489
telencephalon7.65e-6134
brain grey matter2.26e-6034
gray matter2.26e-6034
regional part of forebrain2.78e-5941
forebrain2.78e-5941
anterior neural tube2.78e-5941
future forebrain2.78e-5941
regional part of cerebral cortex8.96e-5822
cerebral hemisphere1.17e-5332
regional part of telencephalon1.35e-5332
neural plate6.11e-5382
presumptive neural plate6.11e-5382
cerebral cortex1.34e-5025
pallium1.34e-5025
neocortex3.65e-5020
neurectoderm3.75e-5086
pre-chordal neural plate8.66e-4561
ecto-epithelium6.41e-43104
ectoderm-derived structure1.06e-33171
ectoderm1.06e-33171
presumptive ectoderm1.06e-33171
structure with developmental contribution from neural crest2.47e-32132
adult organism7.28e-32114
organ system subdivision5.67e-24223
gyrus1.59e-186
tube8.03e-16192
temporal lobe2.30e-156
parietal lobe9.86e-155
occipital lobe1.78e-145
limbic system8.05e-145
posterior neural tube3.29e-1315
chordal neural plate3.29e-1315
pons4.44e-133
anatomical cluster8.22e-12373
neural nucleus1.43e-119
nucleus of brain1.43e-119
brainstem2.10e-116
anatomical conduit3.17e-11240
organ part6.97e-11218
middle temporal gyrus1.05e-092
Ammon's horn1.36e-092
lobe parts of cerebral cortex1.36e-092
hippocampal formation1.36e-092
limbic lobe1.36e-092
epithelium1.56e-09306
cell layer2.29e-09309
locus ceruleus3.81e-092
brainstem nucleus3.81e-092
hindbrain nucleus3.81e-092
segmental subdivision of hindbrain9.44e-0912
hindbrain9.44e-0912
presumptive hindbrain9.44e-0912
segmental subdivision of nervous system4.69e-0813
regional part of metencephalon8.68e-089
metencephalon8.68e-089
future metencephalon8.68e-089
basal ganglion1.02e-079
nuclear complex of neuraxis1.02e-079
aggregate regional part of brain1.02e-079
collection of basal ganglia1.02e-079
cerebral subcortex1.02e-079
multi-tissue structure5.10e-07342
frontal cortex7.80e-073
spinal cord9.02e-073
dorsal region element9.02e-073
dorsum9.02e-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)
MA0003.10.737422
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.369468
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
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.860776
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0469445
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.11.52322
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
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
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.81299
MA0163.11.49262
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.475695
MA0102.21.66336
MA0258.10.914277
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

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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