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Coexpression cluster:C3136: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.0471418,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;1.67416,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;1.36698,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;1.96087,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.432958,MA0138.2;1.04628,MA0002.2;1.20011,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.455568,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.481578,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:09, 22 January 2013


Full id: C3136_medial_pons_parietal_amygdala_paracentral_brain_frontal



Phase1 CAGE Peaks

Hg19::chr11:26353753..26353767,+p7@ANO3
Hg19::chr1:236917218..236917230,+p8@ACTN2
Hg19::chr5:126984919..126984976,+p3@CTXN3


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:0051370ZASP binding0.00256093253267397
GO:0051374FATZ 1 binding0.00256093253267397
GO:0051373FATZ binding0.00341452645300212
GO:0031143pseudopodium0.00512163890781363
GO:0043197dendritic spine0.00614578576334893
GO:0030175filopodium0.00658447968675831
GO:0051289protein homotetramerization0.00658447968675831
GO:0048041focal adhesion formation0.00832156070721741
GO:0051262protein tetramerization0.00967235568457086
GO:0030035microspike biogenesis0.0116364904660761
GO:0005884actin filament0.0116364904660761
GO:0005925focal adhesion0.0119438065733289
GO:0005924cell-substrate adherens junction0.0119438065733289
GO:0030425dendrite0.0119438065733289
GO:0030055cell-matrix junction0.0119438065733289
GO:0005178integrin binding0.0119438065733289
GO:0051260protein homooligomerization0.0119438065733289
GO:0008307structural constituent of muscle0.0119438065733289
GO:0044463cell projection part0.0126612986249979
GO:0030031cell projection biogenesis0.0127954278973855
GO:0005912adherens junction0.0131602361543361
GO:0051259protein oligomerization0.0144213874903024
GO:0043005neuron projection0.0180166334790902
GO:0016323basolateral plasma membrane0.0181175114842883
GO:0007160cell-matrix adhesion0.0195096332609514
GO:0032403protein complex binding0.0195096332609514
GO:0031589cell-substrate adhesion0.0195096332609514
GO:0032990cell part morphogenesis0.0347246198242458
GO:0030030cell projection organization and biogenesis0.0347246198242458
GO:0048858cell projection morphogenesis0.0347246198242458
GO:0015629actin cytoskeleton0.0486932053992805
GO:0042995cell projection0.0498681839186583



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
regional part of nervous system3.93e-8053
regional part of brain3.93e-8053
regional part of cerebral cortex1.57e-7622
neural tube1.17e-7556
neural rod1.17e-7556
future spinal cord1.17e-7556
neural keel1.17e-7556
telencephalon1.34e-7534
neocortex1.11e-7420
cerebral hemisphere4.95e-7332
brain grey matter2.08e-6834
gray matter2.08e-6834
regional part of forebrain2.15e-6841
forebrain2.15e-6841
anterior neural tube2.15e-6841
future forebrain2.15e-6841
cerebral cortex2.63e-6725
pallium2.63e-6725
brain1.20e-6568
future brain1.20e-6568
regional part of telencephalon1.34e-6532
central nervous system9.92e-5981
neural plate2.00e-5482
presumptive neural plate2.00e-5482
nervous system1.72e-5289
neurectoderm1.08e-5186
pre-chordal neural plate6.24e-4561
adult organism1.67e-44114
ecto-epithelium5.70e-42104
gyrus3.32e-386
structure with developmental contribution from neural crest1.02e-34132
ectoderm-derived structure2.26e-27171
ectoderm2.26e-27171
presumptive ectoderm2.26e-27171
brainstem5.21e-266
temporal lobe1.04e-226
parietal lobe6.30e-215
tube1.72e-20192
limbic system2.02e-205
frontal cortex3.36e-203
organ system subdivision8.75e-20223
medulla oblongata4.26e-193
myelencephalon4.26e-193
future myelencephalon4.26e-193
anatomical conduit2.31e-15240
organ part1.38e-14218
middle frontal gyrus3.99e-142
middle temporal gyrus5.52e-142
amygdala8.12e-142
segmental subdivision of hindbrain6.21e-1312
hindbrain6.21e-1312
presumptive hindbrain6.21e-1312
occipital lobe4.33e-125
segmental subdivision of nervous system6.35e-1213
basal ganglion1.89e-119
nuclear complex of neuraxis1.89e-119
aggregate regional part of brain1.89e-119
collection of basal ganglia1.89e-119
cerebral subcortex1.89e-119
epithelium6.46e-11306
cell layer9.29e-11309
anatomical cluster1.04e-10373
posterior neural tube2.63e-1015
chordal neural plate2.63e-1015
multi-tissue structure3.78e-10342
pons1.40e-093
paracentral gyrus6.37e-081
nucleus accumbens8.84e-081
ventral striatum8.84e-081
occipital pole1.01e-071
pole of cerebral hemisphere1.01e-071
olfactory region1.07e-071
primary subdivision of skull1.07e-071
cranium1.07e-071
neurocranium1.07e-071
chondrocranium1.07e-071
cartilaginous neurocranium1.07e-071
head paraxial mesoderm1.07e-071
insula1.22e-071
postcentral gyrus1.91e-071
mitral valve2.31e-071
corpus callosum3.17e-071
central nervous system cell part cluster3.17e-071
axon tract3.17e-071
intercerebral commissure3.17e-071
dorsal telencephalic commissure3.17e-071
brain white matter3.17e-071
brain commissure3.17e-071
white matter3.17e-071
nervous system commissure3.17e-071
cerebral hemisphere white matter3.17e-071
corpus striatum3.60e-074
striatum3.60e-074
ventral part of telencephalon3.60e-074
future corpus striatum3.60e-074
neural nucleus9.27e-079
nucleus of brain9.27e-079


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0055.11.67416
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
MA0073.11.36698
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
MA0093.10.642957
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
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.21.20011
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
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.481578
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
SMC3#9126210.02995522995520.0126656379767470.0457126365778581



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3136&oldid=2571647"