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{{Coexpression_clusters
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|full_id=C1062_extraskeletal_pineal_amygdala_middle_medial_parietal_hippocampus
|id=C1062
}}

Latest revision as of 11:36, 17 September 2013


Full id: C1062_extraskeletal_pineal_amygdala_middle_medial_parietal_hippocampus



Phase1 CAGE Peaks

Hg19::chr19:49149202..49149212,-p11@CA11
Hg19::chr19:49149234..49149251,-p9@CA11
Hg19::chr8:107282339..107282351,+p6@OXR1
Hg19::chr8:107440851..107440855,+p@chr8:107440851..107440855
+
Hg19::chrX:33357425..33357435,-p23@DMD
Hg19::chrX:33357482..33357512,-p6@DMD
Hg19::chrX:33357525..33357536,-p13@DMD
Hg19::chrX:33357642..33357657,-p16@DMD


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:0043034costamere0.0154520836096565
GO:0043043peptide biosynthetic process0.0154520836096565
GO:0016998cell wall catabolic process0.0194157566529812
GO:0010382cell wall metabolic process0.0194157566529812
GO:0007047cell wall organization and biogenesis0.0194157566529812
GO:0016010dystrophin-associated glycoprotein complex0.0194157566529812
GO:0045229external encapsulating structure organization and biogenesis0.0194157566529812
GO:0006518peptide metabolic process0.0216182731161402
GO:0005605basal lamina0.0246949599187639
GO:0008307structural constituent of muscle0.0246949599187639
GO:0004089carbonate dehydratase activity0.0246949599187639
GO:0030016myofibril0.0272601251068618
GO:0044449contractile fiber part0.0282061916009638
GO:0043292contractile fiber0.0282061916009638
GO:0005604basement membrane0.0304302166801092
GO:0005200structural constituent of cytoskeleton0.0326402487061384
GO:0016836hydro-lyase activity0.0326402487061384
GO:0016835carbon-oxygen lyase activity0.0345834233518151
GO:0006979response to oxidative stress0.0389048363651696
GO:0044420extracellular matrix part0.040334478647165
GO:0006730one-carbon compound metabolic process0.0440785620807245
GO:0003012muscle system process0.0440785620807245
GO:0006936muscle contraction0.0440785620807245
GO:0007517muscle development0.0440785620807245



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 tube7.31e-8456
neural rod7.31e-8456
future spinal cord7.31e-8456
neural keel7.31e-8456
regional part of nervous system2.56e-7653
regional part of brain2.56e-7653
central nervous system3.16e-6981
regional part of forebrain1.44e-6641
forebrain1.44e-6641
anterior neural tube1.44e-6641
future forebrain1.44e-6641
brain5.95e-6368
future brain5.95e-6368
brain grey matter1.23e-6134
gray matter1.23e-6134
telencephalon1.85e-6134
nervous system3.09e-6189
neural plate8.64e-5782
presumptive neural plate8.64e-5782
cerebral hemisphere1.39e-5632
regional part of telencephalon2.28e-5632
adult organism1.05e-53114
neurectoderm1.22e-5386
regional part of cerebral cortex2.40e-4922
pre-chordal neural plate5.96e-4561
neocortex1.23e-4320
cerebral cortex5.59e-4325
pallium5.59e-4325
ecto-epithelium1.89e-42104
structure with developmental contribution from neural crest2.11e-36132
ectoderm-derived structure5.36e-28171
ectoderm5.36e-28171
presumptive ectoderm5.36e-28171
organ system subdivision4.44e-23223
tube3.06e-21192
basal ganglion3.04e-209
nuclear complex of neuraxis3.04e-209
aggregate regional part of brain3.04e-209
collection of basal ganglia3.04e-209
cerebral subcortex3.04e-209
neural nucleus7.05e-209
nucleus of brain7.05e-209
gyrus1.06e-186
posterior neural tube8.79e-1815
chordal neural plate8.79e-1815
limbic system6.54e-165
temporal lobe9.53e-166
anatomical conduit1.41e-15240
telencephalic nucleus1.09e-147
epithelium1.22e-12306
cell layer2.12e-12309
corpus striatum2.79e-124
striatum2.79e-124
ventral part of telencephalon2.79e-124
future corpus striatum2.79e-124
anatomical cluster3.37e-12373
brainstem3.82e-126
segmental subdivision of hindbrain2.42e-1112
hindbrain2.42e-1112
presumptive hindbrain2.42e-1112
segmental subdivision of nervous system2.20e-1013
frontal cortex2.46e-103
parietal lobe2.80e-105
organ part5.85e-10218
occipital lobe8.00e-105
caudate-putamen1.52e-093
dorsal striatum1.52e-093
pons1.57e-093
multi-tissue structure2.55e-09342
spinal cord3.13e-093
dorsal region element3.13e-093
dorsum3.13e-093
regional part of metencephalon3.08e-089
metencephalon3.08e-089
future metencephalon3.08e-089
regional part of diencephalon1.20e-074
middle temporal gyrus1.29e-072
pineal body1.41e-072
regional part of epithalamus1.41e-072
secretory circumventricular organ1.41e-072
circumventricular organ1.41e-072
epithalamus1.41e-072
Ammon's horn1.93e-072
lobe parts of cerebral cortex1.93e-072
hippocampal formation1.93e-072
limbic lobe1.93e-072
amygdala2.05e-072
middle frontal gyrus2.18e-072
diencephalon3.34e-077
future diencephalon3.34e-077
locus ceruleus5.56e-072
brainstem nucleus5.56e-072
hindbrain nucleus5.56e-072
meninx7.25e-072
membrane organ7.25e-072
meningeal cluster7.25e-072
caudate nucleus7.92e-072
future caudate nucleus7.92e-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)
MA0003.10.393486
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.0484929
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.11.08711
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.835832
MA0056.10
MA0057.10.632427
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.0041831
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
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
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.11.60834
MA0132.10
MA0133.10
MA0135.12.18252
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.11.17059
MA0145.10.220937
MA0146.10.00761723
MA0147.10.243042
MA0148.11.20731
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.0325944
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.55506
MA0047.20.586412
MA0112.20.0572179
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.197713
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.0104024
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.916243
MA0102.21.46209
MA0258.10.209744
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

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

TF#promotersEnrichmentp-valueq-value
CTCF#1066453.350160233171890.007643853146021220.0314905281336953



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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