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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.055712496781182,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0534545700183436,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.074127477864629,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0477396614475454,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0635969392553137,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0495511575604446,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0400762477245316,0,0,0,0,0,0,0.0370406554214911,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0571597974145305,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.591954359268079,0.192179422446085,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.157991613466995,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0549201943193819,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.213014895508784,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0874873383132558,0,0,0,0,0,0,0,0,0,0.0554560868715733,0,0,0,0,0,0.237793656955104,0,0.0329432353726146,0.0433265804049448,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0998759650431728,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.172633593304824,0.176312323189237,0,0,0.0741905798248643,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.228218641027579,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.120950855450194,0.383270498593678,0,0.208266392091069,0,0.309067516716086,0.216404126670406,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.303857532566742,0,0.150256972842231,0.229828692485782,0,0,0,0,0,0.18630690345421,0,0,0,0,0,0,0.148546636415814,0.25267667713979,0,0,0,0.0633767449113307,0,0,0,0,0.0299826682885844,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0778431765528363,0,0,0,0,0,0,0,0,0,0,0,0,0,0.225287282578643,0,0,0,0,0,0,0,0,0,0,0,0,0.0317229404497622,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C3331_brain_occipital_paracentral_parietal_insula_postcentral_pons|gostat_on_coexpression_clusters=GO:0030955!potassium ion binding!0.00539806025887904!476;3747$GO:0031420!alkali metal ion binding!0.00585347486191332!476;3747$GO:0006813!potassium ion transport!0.00585347486191332!476;3747$GO:0005890!sodium:potassium-exchanging ATPase complex!0.0148899497119923!476$GO:0015672!monovalent inorganic cation transport!0.0148899497119923!476;3747$GO:0030641!cellular hydrogen ion homeostasis!0.0153004158396385!476$GO:0030001!metal ion transport!0.0153004158396385!476;3747$GO:0055067!monovalent inorganic cation homeostasis!0.0153004158396385!476$GO:0030004!cellular monovalent inorganic cation homeostasis!0.0153004158396385!476$GO:0005391!sodium:potassium-exchanging ATPase activity!0.01548990470091!476$GO:0030317!sperm motility!0.01548990470091!476$GO:0006812!cation transport!0.01548990470091!476;3747$GO:0008324!cation transmembrane transporter activity!0.01548990470091!476;3747$GO:0015075!ion transmembrane transporter activity!0.0287753110400164!476;3747$GO:0005887!integral to plasma 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|full_id=C3331_brain_occipital_paracentral_parietal_insula_postcentral_pons
|gostat_on_coexpression_clusters=GO:0030955!potassium ion binding!0.00539806025887904!476;3747$GO:0031420!alkali metal ion binding!0.00585347486191332!476;3747$GO:0006813!potassium ion transport!0.00585347486191332!476;3747$GO:0005890!sodium:potassium-exchanging ATPase complex!0.0148899497119923!476$GO:0015672!monovalent inorganic cation transport!0.0148899497119923!476;3747$GO:0030641!cellular hydrogen ion homeostasis!0.0153004158396385!476$GO:0030001!metal ion transport!0.0153004158396385!476;3747$GO:0055067!monovalent inorganic cation homeostasis!0.0153004158396385!476$GO:0030004!cellular monovalent inorganic cation homeostasis!0.0153004158396385!476$GO:0005391!sodium:potassium-exchanging ATPase activity!0.01548990470091!476$GO:0030317!sperm motility!0.01548990470091!476$GO:0006812!cation transport!0.01548990470091!476;3747$GO:0008324!cation transmembrane transporter activity!0.01548990470091!476;3747$GO:0015075!ion transmembrane transporter activity!0.0287753110400164!476;3747$GO:0005887!integral to plasma membrane!0.0287753110400164!476;3747$GO:0031226!intrinsic to plasma membrane!0.0287753110400164!476;3747$GO:0006811!ion transport!0.0287753110400164!476;3747$GO:0022891!substrate-specific transmembrane transporter activity!0.0336885223102745!476;3747$GO:0022857!transmembrane transporter activity!0.0362112514340256!476;3747$GO:0048770!pigment granule!0.0362112514340256!476$GO:0042470!melanosome!0.0362112514340256!476$GO:0022892!substrate-specific transporter activity!0.0369774297685521!476;3747$GO:0031402!sodium ion binding!0.0382262584592676!476$GO:0008076!voltage-gated potassium channel complex!0.0468993386301315!3747
|id=C3331
}}

Latest revision as of 12:24, 17 September 2013


Full id: C3331_brain_occipital_paracentral_parietal_insula_postcentral_pons



Phase1 CAGE Peaks

Hg19::chr12:75603643..75603652,-p19@KCNC2
Hg19::chr1:116915494..116915499,+p52@ATP1A1
Hg19::chr7:152456920..152456929,+p4@ACTR3B


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:0030955potassium ion binding0.00539806025887904
GO:0031420alkali metal ion binding0.00585347486191332
GO:0006813potassium ion transport0.00585347486191332
GO:0005890sodium:potassium-exchanging ATPase complex0.0148899497119923
GO:0015672monovalent inorganic cation transport0.0148899497119923
GO:0030641cellular hydrogen ion homeostasis0.0153004158396385
GO:0030001metal ion transport0.0153004158396385
GO:0055067monovalent inorganic cation homeostasis0.0153004158396385
GO:0030004cellular monovalent inorganic cation homeostasis0.0153004158396385
GO:0005391sodium:potassium-exchanging ATPase activity0.01548990470091
GO:0030317sperm motility0.01548990470091
GO:0006812cation transport0.01548990470091
GO:0008324cation transmembrane transporter activity0.01548990470091
GO:0015075ion transmembrane transporter activity0.0287753110400164
GO:0005887integral to plasma membrane0.0287753110400164
GO:0031226intrinsic to plasma membrane0.0287753110400164
GO:0006811ion transport0.0287753110400164
GO:0022891substrate-specific transmembrane transporter activity0.0336885223102745
GO:0022857transmembrane transporter activity0.0362112514340256
GO:0048770pigment granule0.0362112514340256
GO:0042470melanosome0.0362112514340256
GO:0022892substrate-specific transporter activity0.0369774297685521
GO:0031402sodium ion binding0.0382262584592676
GO:0008076voltage-gated potassium channel complex0.0468993386301315



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
telencephalon3.97e-4934
cerebral hemisphere5.42e-4732
neural tube9.82e-4756
neural rod9.82e-4756
future spinal cord9.82e-4756
neural keel9.82e-4756
regional part of nervous system2.14e-4553
regional part of brain2.14e-4553
regional part of forebrain8.40e-4541
forebrain8.40e-4541
anterior neural tube8.40e-4541
future forebrain8.40e-4541
brain grey matter7.06e-4434
gray matter7.06e-4434
cerebral cortex7.70e-4225
pallium7.70e-4225
regional part of cerebral cortex1.20e-4122
regional part of telencephalon1.31e-4132
brain1.13e-4068
future brain1.13e-4068
neocortex1.06e-3920
central nervous system1.62e-3981
nervous system4.57e-3589
adult organism3.70e-34114
neural plate4.25e-3382
presumptive neural plate4.25e-3382
pre-chordal neural plate6.96e-3261
neurectoderm2.56e-3186
ecto-epithelium5.52e-25104
gyrus4.93e-226
structure with developmental contribution from neural crest2.29e-20132
ectoderm-derived structure4.09e-17171
ectoderm4.09e-17171
presumptive ectoderm4.09e-17171
organ system subdivision7.25e-13223
temporal lobe4.43e-126
middle temporal gyrus1.53e-112
occipital lobe2.61e-105
parietal lobe3.90e-105
tube5.24e-10192
limbic system1.65e-095
brainstem3.80e-086
frontal cortex6.14e-083
anatomical conduit8.60e-08240
pons9.88e-083
anatomical cluster3.14e-07373
epithelium5.93e-07306
multi-tissue structure6.51e-07342
cell layer7.89e-07309
occipital pole8.34e-071
pole of cerebral hemisphere8.34e-071
paracentral gyrus8.81e-071
postcentral gyrus9.30e-071
insula9.81e-071


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.15.1975
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.90288
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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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