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{{Coexpression_clusters
{
|full_id=C978_skeletal_amygdala_insula_occipital_medial_frontal_cerebral
 

Latest revision as of 11:35, 17 September 2013


Full id: C978_skeletal_amygdala_insula_occipital_medial_frontal_cerebral



Phase1 CAGE Peaks

Hg19::chr10:3147130..3147141,+p14@PFKP
Hg19::chr12:49393148..49393164,-p1@DDN
Hg19::chr14:89757957..89757974,-p1@ENST00000557743
Hg19::chr1:162458011..162458031,-p@chr1:162458011..162458031
-
Hg19::chr1:162458051..162458067,-p@chr1:162458051..162458067
-
Hg19::chr1:40137922..40137962,-p2@NT5C1A
Hg19::chr6:17393807..17393833,+p2@CAP2
Hg19::chr6:17393888..17393954,+p1@CAP2


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:00082535'-nucleotidase activity0.0275670551604664
GO:0008252nucleotidase activity0.0275670551604664
GO:0000287magnesium ion binding0.0275670551604664
GO:0005829cytosol0.0275670551604664
GO:00059456-phosphofructokinase complex0.0275670551604664
GO:00038726-phosphofructokinase activity0.0275670551604664
GO:0007190adenylate cyclase activation0.0275670551604664
GO:0031281positive regulation of cyclase activity0.0275670551604664
GO:0051349positive regulation of lyase activity0.0275670551604664
GO:0045762positive regulation of adenylate cyclase activity0.0275670551604664
GO:0008443phosphofructokinase activity0.0275670551604664
GO:0007163establishment and/or maintenance of cell polarity0.0275670551604664
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.0281659660913172
GO:0030425dendrite0.0281659660913172
GO:0045761regulation of adenylate cyclase activity0.0281659660913172
GO:0031279regulation of cyclase activity0.0281659660913172
GO:0051339regulation of lyase activity0.0281659660913172
GO:0009116nucleoside metabolic process0.0329202640965178
GO:0019200carbohydrate kinase activity0.0353750131089477
GO:0043005neuron projection0.0449943136693105
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0449943136693105
GO:0019933cAMP-mediated signaling0.0449943136693105



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
adult organism4.77e-64114
regional part of nervous system2.40e-5453
regional part of brain2.40e-5453
telencephalon5.53e-5234
cerebral hemisphere7.66e-5232
regional part of forebrain3.44e-5141
forebrain3.44e-5141
anterior neural tube3.44e-5141
future forebrain3.44e-5141
neural tube7.32e-5156
neural rod7.32e-5156
future spinal cord7.32e-5156
neural keel7.32e-5156
brain grey matter5.95e-4834
gray matter5.95e-4834
regional part of telencephalon1.01e-4732
brain6.28e-4768
future brain6.28e-4768
regional part of cerebral cortex1.03e-4322
central nervous system5.97e-4281
neocortex2.01e-3920
nervous system2.16e-3889
cerebral cortex6.82e-3825
pallium6.82e-3825
neural plate3.24e-3782
presumptive neural plate3.24e-3782
neurectoderm6.14e-3586
pre-chordal neural plate1.54e-3361
ecto-epithelium2.23e-28104
structure with developmental contribution from neural crest4.01e-28132
ectoderm-derived structure9.86e-24171
ectoderm9.86e-24171
presumptive ectoderm9.86e-24171
organ system subdivision2.67e-19223
gyrus1.31e-156
basal ganglion2.79e-159
nuclear complex of neuraxis2.79e-159
aggregate regional part of brain2.79e-159
collection of basal ganglia2.79e-159
cerebral subcortex2.79e-159
multi-tissue structure4.16e-14342
anatomical conduit9.77e-14240
tube2.49e-13192
anatomical cluster2.70e-13373
organ part4.02e-13218
temporal lobe1.27e-126
occipital lobe1.55e-125
limbic system2.48e-125
neural nucleus2.04e-119
nucleus of brain2.04e-119
telencephalic nucleus3.77e-117
epithelium8.50e-10306
corpus striatum1.23e-094
striatum1.23e-094
ventral part of telencephalon1.23e-094
future corpus striatum1.23e-094
cell layer1.43e-09309
organ1.46e-09503
parietal lobe9.45e-095
frontal cortex1.83e-083
caudate-putamen1.76e-073
dorsal striatum1.76e-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)
MA0003.10.576745
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.134069
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.846854
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.11.3714
MA0040.10.838784
MA0041.11.19384
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.11.96448
MA0055.12.65641
MA0056.10
MA0057.10.632427
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.11.3723
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.12.91012
MA0074.10.552456
MA0076.10.985027
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.11.04489
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.480646
MA0146.10.00761723
MA0147.10.681318
MA0148.10.480298
MA0149.10.506665
MA0062.20.485915
MA0035.20.515566
MA0039.20.284736
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.55506
MA0047.20.586412
MA0112.20.79629
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.974997
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.194027
MA0163.11.06699
MA0164.10.627336
MA0080.20.818924
MA0018.20.599912
MA0099.20.523145
MA0079.23.40762
MA0102.21.46209
MA0258.10.603127
MA0259.10.25092
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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