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{{Coexpression_clusters
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|full_id=C3363_pineal_pituitary_cerebellum_medial_occipital_parietal_middle
|gostat_on_coexpression_clusters=GO:0004089!carbonate dehydratase activity!0.0109011342674359!377677$GO:0016836!hydro-lyase activity!0.0109011342674359!377677$GO:0016835!carbon-oxygen lyase activity!0.0109011342674359!377677$GO:0006730!one-carbon compound metabolic process!0.0125470976097963!377677$GO:0016829!lyase activity!0.0180030613446368!377677
|id=C3363
}}

Latest revision as of 12:24, 17 September 2013


Full id: C3363_pineal_pituitary_cerebellum_medial_occipital_parietal_middle



Phase1 CAGE Peaks

Hg19::chr13:29394461..29394487,+p@chr13:29394461..29394487
+
Hg19::chr6:166401568..166401573,-p4@LINC00473
Hg19::chr8:86133055..86133142,+p5@CA13


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:0004089carbonate dehydratase activity0.0109011342674359
GO:0016836hydro-lyase activity0.0109011342674359
GO:0016835carbon-oxygen lyase activity0.0109011342674359
GO:0006730one-carbon compound metabolic process0.0125470976097963
GO:0016829lyase activity0.0180030613446368



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 tube9.97e-6956
neural rod9.97e-6956
future spinal cord9.97e-6956
neural keel9.97e-6956
adult organism2.38e-68114
regional part of nervous system8.73e-6453
regional part of brain8.73e-6453
regional part of forebrain6.92e-5341
forebrain6.92e-5341
anterior neural tube6.92e-5341
future forebrain6.92e-5341
neural plate1.34e-5082
presumptive neural plate1.34e-5082
central nervous system2.54e-5081
brain3.46e-5068
future brain3.46e-5068
neurectoderm1.69e-4786
nervous system9.59e-4689
telencephalon2.42e-4034
brain grey matter3.83e-4034
gray matter3.83e-4034
ecto-epithelium3.76e-38104
cerebral hemisphere6.50e-3832
regional part of telencephalon1.80e-3732
pre-chordal neural plate5.94e-3661
structure with developmental contribution from neural crest5.83e-35132
regional part of cerebral cortex2.54e-3122
cerebral cortex1.64e-2925
pallium1.64e-2925
neocortex8.70e-2820
ectoderm-derived structure2.21e-24171
ectoderm2.21e-24171
presumptive ectoderm2.21e-24171
organ system subdivision6.63e-23223
posterior neural tube2.58e-1615
chordal neural plate2.58e-1615
tube4.48e-16192
anatomical conduit5.14e-15240
diencephalon3.45e-147
future diencephalon3.45e-147
anatomical cluster3.91e-14373
basal ganglion1.21e-129
nuclear complex of neuraxis1.21e-129
aggregate regional part of brain1.21e-129
collection of basal ganglia1.21e-129
cerebral subcortex1.21e-129
gyrus1.99e-126
neural nucleus6.10e-129
nucleus of brain6.10e-129
segmental subdivision of hindbrain7.10e-1212
hindbrain7.10e-1212
presumptive hindbrain7.10e-1212
brainstem7.45e-116
segmental subdivision of nervous system8.48e-1113
limbic system2.01e-105
multi-tissue structure2.06e-10342
temporal lobe9.86e-106
gland of diencephalon1.82e-094
neuroendocrine gland1.82e-094
telencephalic nucleus2.33e-097
organ part4.66e-09218
regional part of diencephalon8.34e-094
organ1.07e-08503
epithelium5.62e-08306
cell layer9.34e-08309
regional part of metencephalon2.11e-079
metencephalon2.11e-079
future metencephalon2.11e-079
frontal cortex3.22e-073
occipital lobe4.09e-075
parietal lobe4.84e-075


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
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
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.16.1256
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.22771
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

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

TF#promotersEnrichmentp-valueq-value
CTCF#1066435.360256373075030.0064925092527670.0278731933181129
SMC3#9126210.02995522995520.0126656379767470.0457189563700094



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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