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{{Coexpression_clusters
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vesicle exocytosis!0.0196401586040074!22999$GO:0042734!presynaptic membrane!0.0196401586040074!22999$GO:0017156!calcium ion-dependent exocytosis!0.0196401586040074!22999$GO:0048489!synaptic vesicle transport!0.0203940481014304!22999$GO:0017137!Rab GTPase binding!0.0244696150905867!22999$GO:0006944!membrane fusion!0.0258888161799637!22999$GO:0007269!neurotransmitter secretion!0.0258888161799637!22999$GO:0045055!regulated secretory pathway!0.0274886381140926!22999$GO:0003001!generation of a signal involved in cell-cell signaling!0.0274886381140926!22999$GO:0017016!Ras GTPase binding!0.0274886381140926!22999$GO:0006836!neurotransmitter transport!0.0274886381140926!22999$GO:0001505!regulation of neurotransmitter levels!0.0274886381140926!22999$GO:0005200!structural constituent of cytoskeleton!0.0274886381140926!287$GO:0031267!small GTPase binding!0.0274886381140926!22999$GO:0051020!GTPase binding!0.0292729170215506!22999$GO:0006887!exocytosis!0.031397776726905!22999$GO:0044456!synapse 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|full_id=C2770_melanoma_pons_cerebellum_medial_pituitary_parietal_locus
|id=C2770
}}

Latest revision as of 12:12, 17 September 2013


Full id: C2770_melanoma_pons_cerebellum_medial_pituitary_parietal_locus



Phase1 CAGE Peaks

Hg19::chr4:114037833..114037852,+p12@ANK2
Hg19::chr4:114037991..114038015,+p8@ANK2
Hg19::chr4:114038031..114038042,+p22@ANK2
Hg19::chr6:72926217..72926229,+p15@RIMS1


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:0016079synaptic vesicle exocytosis0.0196401586040074
GO:0042734presynaptic membrane0.0196401586040074
GO:0017156calcium ion-dependent exocytosis0.0196401586040074
GO:0048489synaptic vesicle transport0.0203940481014304
GO:0017137Rab GTPase binding0.0244696150905867
GO:0006944membrane fusion0.0258888161799637
GO:0007269neurotransmitter secretion0.0258888161799637
GO:0045055regulated secretory pathway0.0274886381140926
GO:0003001generation of a signal involved in cell-cell signaling0.0274886381140926
GO:0017016Ras GTPase binding0.0274886381140926
GO:0006836neurotransmitter transport0.0274886381140926
GO:0001505regulation of neurotransmitter levels0.0274886381140926
GO:0005200structural constituent of cytoskeleton0.0274886381140926
GO:0031267small GTPase binding0.0274886381140926
GO:0051020GTPase binding0.0292729170215506
GO:0006887exocytosis0.031397776726905
GO:0044456synapse part0.0428304475215015



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 tube5.35e-9856
neural rod5.35e-9856
future spinal cord5.35e-9856
neural keel5.35e-9856
regional part of nervous system2.02e-9053
regional part of brain2.02e-9053
central nervous system4.56e-7681
brain5.58e-7468
future brain5.58e-7468
regional part of forebrain2.49e-7141
forebrain2.49e-7141
anterior neural tube2.49e-7141
future forebrain2.49e-7141
nervous system3.70e-7089
neural plate1.18e-6682
presumptive neural plate1.18e-6682
adult organism7.16e-64114
neurectoderm5.23e-6386
ecto-epithelium4.29e-55104
brain grey matter1.73e-5434
gray matter1.73e-5434
telencephalon3.90e-5434
cerebral hemisphere1.24e-4932
regional part of telencephalon4.22e-4932
pre-chordal neural plate2.56e-4861
regional part of cerebral cortex1.01e-4222
structure with developmental contribution from neural crest1.35e-42132
ectoderm-derived structure4.80e-39171
ectoderm4.80e-39171
presumptive ectoderm4.80e-39171
neocortex1.58e-3720
cerebral cortex3.72e-3725
pallium3.72e-3725
organ system subdivision1.99e-34223
posterior neural tube2.77e-2615
chordal neural plate2.77e-2615
tube7.27e-24192
segmental subdivision of hindbrain2.71e-1912
hindbrain2.71e-1912
presumptive hindbrain2.71e-1912
diencephalon7.98e-197
future diencephalon7.98e-197
neural nucleus9.40e-199
nucleus of brain9.40e-199
anatomical conduit1.42e-18240
anatomical cluster1.94e-18373
gyrus2.90e-186
basal ganglion3.00e-189
nuclear complex of neuraxis3.00e-189
aggregate regional part of brain3.00e-189
collection of basal ganglia3.00e-189
cerebral subcortex3.00e-189
brainstem4.49e-186
segmental subdivision of nervous system1.17e-1713
epithelium2.67e-15306
cell layer5.06e-15309
limbic system1.33e-145
multi-tissue structure2.54e-14342
telencephalic nucleus2.49e-137
organ part9.52e-13218
regional part of metencephalon4.03e-129
metencephalon4.03e-129
future metencephalon4.03e-129
gland of diencephalon6.45e-124
neuroendocrine gland6.45e-124
organ2.57e-11503
regional part of diencephalon3.43e-114
corpus striatum3.52e-114
striatum3.52e-114
ventral part of telencephalon3.52e-114
future corpus striatum3.52e-114
pons2.67e-103
temporal lobe3.05e-106
parietal lobe3.18e-105
occipital lobe4.71e-105
frontal cortex6.51e-103
medulla oblongata1.70e-093
myelencephalon1.70e-093
future myelencephalon1.70e-093
embryo4.71e-09592
spinal cord6.23e-093
dorsal region element6.23e-093
dorsum6.23e-093
caudate-putamen1.27e-083
dorsal striatum1.27e-083
developing anatomical structure2.88e-08581
germ layer6.09e-08560
germ layer / neural crest6.09e-08560
embryonic tissue6.09e-08560
presumptive structure6.09e-08560
germ layer / neural crest derived structure6.09e-08560
epiblast (generic)6.09e-08560
embryonic structure8.87e-08564
middle frontal gyrus1.93e-072
locus ceruleus2.39e-072
brainstem nucleus2.39e-072
hindbrain nucleus2.39e-072
anatomical system3.25e-07624
anatomical group3.54e-07625
pituitary gland5.19e-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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.114.9996
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.11.32557
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
TRIM28#10155313.94289378394690.0005972858184258420.00499599019626594
ZNF263#1012736.166381227758010.006539814347975980.0279865466375031



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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