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Coexpression cluster:C3729: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.027549189648299,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.297691787557545,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.165493755864807,0,0,0,0,0,0,0,0,0,0,0,0.236431101238142,0,0.191142455090553,0.20169617591284,0.404097490429746,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0517780703133839,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.204234048342335,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.696893327800144,0.320068822863804,0,0,0,0,0,0.0727088341078527,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.216539256609758,0.145102450696258,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.731826034356456,0.376047495482148,0,0,0.0261639379934246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.377048286893918,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0765267314685607,0,0.214455838206723,0.149290789502833,0.0976291981890722,0.0290415862703977,0.294213484466631,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0550246232064646,0,0.350271434513732,0.0756372526246955,0,0,0,0,0,0.18630690345421,0.125898678133584,0,0,0,0,0,0.0553551885028491,0.0782096278833456,0,0,0,0.288404295914723,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.15309981666883,0,0,0,0,0,0,0,0,0,0,0,0.148586905529929,0,0,0,0,0,0,0,0,0,0,0,0,0.0317229404497622,0,0.262253936867136,0.0816590494793475,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C3729_medial_hippocampus_cerebral_middle_parietal_globus_olfactory|gostat_on_coexpression_clusters=GO:0007026!negative regulation of microtubule depolymerization!0.0169474033792886!4134$GO:0031114!regulation of microtubule depolymerization!0.0169474033792886!4134$GO:0007019!microtubule depolymerization!0.0169474033792886!4134$GO:0031111!negative regulation of microtubule polymerization or depolymerization!0.0169474033792886!4134$GO:0031110!regulation of microtubule polymerization or depolymerization!0.0169474033792886!4134$GO:0031109!microtubule polymerization or depolymerization!0.0169474033792886!4134$GO:0051261!protein depolymerization!0.0206485650106885!4134$GO:0051129!negative regulation of cellular component organization and biogenesis!0.0206485650106885!4134$GO:0051128!regulation of cellular component organization and biogenesis!0.0300112721168847!4134$GO:0000226!microtubule cytoskeleton organization and biogenesis!0.0300112721168847!4134$GO:0051248!negative regulation of protein metabolic process!0.0300112721168847!4134$GO:0005875!microtubule associated 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7.1;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;0.440097,MA0140.1;0.894983,MA0141.1;1.6959,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;1.98824,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.0526989,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;2.23118,MA0112.2;0.731309,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;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.00160703,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3729_medial_hippocampus_cerebral_middle_parietal_globus_olfactory
|id=C3729
}}

Latest revision as of 12:31, 17 September 2013


Full id: C3729_medial_hippocampus_cerebral_middle_parietal_globus_olfactory



Phase1 CAGE Peaks

Hg19::chr18:55030190..55030203,+p@chr18:55030190..55030203
+
Hg19::chr3:48016734..48016748,-p49@MAP4
Hg19::chr7:98460933..98460941,-p19@TMEM130


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:0007026negative regulation of microtubule depolymerization0.0169474033792886
GO:0031114regulation of microtubule depolymerization0.0169474033792886
GO:0007019microtubule depolymerization0.0169474033792886
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0169474033792886
GO:0031110regulation of microtubule polymerization or depolymerization0.0169474033792886
GO:0031109microtubule polymerization or depolymerization0.0169474033792886
GO:0051261protein depolymerization0.0206485650106885
GO:0051129negative regulation of cellular component organization and biogenesis0.0206485650106885
GO:0051128regulation of cellular component organization and biogenesis0.0300112721168847
GO:0000226microtubule cytoskeleton organization and biogenesis0.0300112721168847
GO:0051248negative regulation of protein metabolic process0.0300112721168847
GO:0005875microtubule associated complex0.0475606955091801



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 tube6.19e-9256
neural rod6.19e-9256
future spinal cord6.19e-9256
neural keel6.19e-9256
regional part of nervous system4.20e-9153
regional part of brain4.20e-9153
regional part of forebrain3.07e-7641
forebrain3.07e-7641
anterior neural tube3.07e-7641
future forebrain3.07e-7641
brain9.38e-7468
future brain9.38e-7468
brain grey matter2.64e-7134
gray matter2.64e-7134
central nervous system5.71e-7081
cerebral hemisphere9.61e-6932
telencephalon1.49e-6434
nervous system1.61e-6289
regional part of telencephalon2.43e-6232
neural plate3.04e-6182
presumptive neural plate3.04e-6182
neurectoderm3.80e-5886
regional part of cerebral cortex8.71e-5822
cerebral cortex1.02e-5025
pallium1.02e-5025
pre-chordal neural plate6.11e-5061
neocortex4.84e-4820
ecto-epithelium3.95e-47104
adult organism5.28e-46114
structure with developmental contribution from neural crest1.41e-38132
ectoderm-derived structure4.34e-30171
ectoderm4.34e-30171
presumptive ectoderm4.34e-30171
organ system subdivision3.12e-23223
gyrus3.35e-236
tube8.42e-23192
regional part of diencephalon4.37e-224
neural nucleus1.32e-219
nucleus of brain1.32e-219
limbic system2.33e-185
occipital lobe2.07e-175
anatomical conduit5.33e-17240
pons7.92e-173
posterior neural tube9.05e-1715
chordal neural plate9.05e-1715
segmental subdivision of hindbrain1.18e-1512
hindbrain1.18e-1512
presumptive hindbrain1.18e-1512
basal ganglion2.37e-159
nuclear complex of neuraxis2.37e-159
aggregate regional part of brain2.37e-159
collection of basal ganglia2.37e-159
cerebral subcortex2.37e-159
regional part of metencephalon5.30e-159
metencephalon5.30e-159
future metencephalon5.30e-159
segmental subdivision of nervous system2.07e-1413
brainstem2.11e-146
temporal lobe2.73e-136
corpus striatum4.66e-134
striatum4.66e-134
ventral part of telencephalon4.66e-134
future corpus striatum4.66e-134
telencephalic nucleus6.95e-137
middle temporal gyrus9.14e-132
diencephalon1.07e-127
future diencephalon1.07e-127
Ammon's horn1.15e-122
lobe parts of cerebral cortex1.15e-122
hippocampal formation1.15e-122
limbic lobe1.15e-122
organ part1.55e-12218
locus ceruleus5.23e-122
brainstem nucleus5.23e-122
hindbrain nucleus5.23e-122
dorsal plus ventral thalamus5.53e-122
thalamic complex5.53e-122
epithelium5.70e-12306
pineal body7.28e-122
regional part of epithalamus7.28e-122
secretory circumventricular organ7.28e-122
circumventricular organ7.28e-122
epithalamus7.28e-122
cell layer8.59e-12309
anatomical cluster2.36e-11373
parietal lobe2.24e-105
multi-tissue structure5.16e-10342
caudate-putamen1.64e-083
dorsal striatum1.64e-083
frontal cortex2.95e-083
olfactory region4.69e-071
primary subdivision of skull4.69e-071
cranium4.69e-071
neurocranium4.69e-071
chondrocranium4.69e-071
cartilaginous neurocranium4.69e-071
head paraxial mesoderm4.69e-071
putamen4.97e-071


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
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
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
MA0139.10.440097
MA0140.10.894983
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.11.98824
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.22.23118
MA0112.20.731309
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
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
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

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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