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Coexpression cluster:C1255: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0779013103271332,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.475423511109794,0.265764802378901,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.591954359268079,0.395202216134025,0,0,0,0,0,0,0,0,0,0,0,0.0938392746630608,0,0.275227040110799,0.875179816376311,0.321583308753707,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0549201943193819,0,0.287142576021595,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0884836478019413,0,0,0.471678101506004,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.204234048342335,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.413376786607389,0.0554560868715733,0,0,0,0,0,0.379711479994828,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0998759650431728,0.101906882599192,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.275557388108753,0.34640435295189,0.243322253338365,0.196841684047034,0.124760798356953,0.137537165784479,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.150687471629542,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.35880722631943,0,0.214455838206723,0.306549790733434,0,0.424844746016102,0.257049046425766,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.471084778244776,0.250682963288844,0.308230077159195,0.367678635496266,0,0,0,0,0,0,0,0,0,0,0,0,0.442042598277176,0.560015596847598,0,0,0,0.251778814110724,0,0,0,0,0.0299826682885844,0.0637136642840507,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0778431765528363,0,0,0,0,0,0,0,0,0,0,0,0,0,0.408884867260008,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C1255_cerebellum_postcentral_brain_paracentral_frontal_temporal_pons|gostat_on_coexpression_clusters=GO:0004890!GABA-A receptor activity!0.0185673269389271!2563$GO:0016917!GABA receptor activity!0.0185673269389271!2563$GO:0043168!anion binding!0.0185673269389271!2563$GO:0031404!chloride ion binding!0.0185673269389271!2563$GO:0005254!chloride channel activity!0.0185673269389271!2563$GO:0005253!anion channel activity!0.0185673269389271!2563$GO:0005230!extracellular ligand-gated ion channel activity!0.0185673269389271!2563$GO:0030594!neurotransmitter receptor activity!0.0185673269389271!2563$GO:0042165!neurotransmitter binding!0.0185673269389271!2563$GO:0045211!postsynaptic membrane!0.0185673269389271!2563$GO:0044456!synapse part!0.0185673269389271!2563$GO:0015276!ligand-gated ion channel activity!0.0185673269389271!2563$GO:0022834!ligand-gated channel activity!0.0185673269389271!2563$GO:0008509!anion transmembrane transporter activity!0.0219718759987216!2563$GO:0007268!synaptic transmission!0.0284548059185996!2563$GO:0019226!transmission of nerve impulse!0.0303558813140233!2563$GO:0030054!cell 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0,MA0057.1;0.115382,MA0058.1;1.04727,MA0059.1;1.84146,MA0060.1;0.224688,MA0061.1;0.575931,MA0063.1;0,MA0066.1;1.47685,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;4.03024,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;1.67751,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.252594,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.9112,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.695228,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.547495,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.708913,MA0145.1;0.0807715,MA0146.1;0.162729,MA0147.1;0.768766,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.60756,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;1.70023,MA0104.2;0.636673,MA0047.2;0.636643,MA0112.2;0.944394,MA0065.2;0.282161,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.335384,MA0155.1;0.250175,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.106355,MA0163.1;0.382702,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.478894,MA0102.2;1.51913,MA0258.1;0.687127,MA0259.1;0.289405,MA0442.1;0}}
|full_id=C1255_cerebellum_postcentral_brain_paracentral_frontal_temporal_pons
|id=C1255
}}

Latest revision as of 11:41, 17 September 2013


Full id: C1255_cerebellum_postcentral_brain_paracentral_frontal_temporal_pons



Phase1 CAGE Peaks

Hg19::chr1:1950743..1950748,+p3@GABRD
Hg19::chr20:10273831..10273842,-p@chr20:10273831..10273842
-
Hg19::chr20:10286834..10286851,-p1@CU679782
Hg19::chr20:10287450..10287493,-p@chr20:10287450..10287493
-
Hg19::chr20:10287525..10287552,-p@chr20:10287525..10287552
-
Hg19::chr3:184103946..184103949,+p@chr3:184103946..184103949
+
Hg19::chr7:100244171..100244173,-p@chr7:100244171..100244173
-


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:0004890GABA-A receptor activity0.0185673269389271
GO:0016917GABA receptor activity0.0185673269389271
GO:0043168anion binding0.0185673269389271
GO:0031404chloride ion binding0.0185673269389271
GO:0005254chloride channel activity0.0185673269389271
GO:0005253anion channel activity0.0185673269389271
GO:0005230extracellular ligand-gated ion channel activity0.0185673269389271
GO:0030594neurotransmitter receptor activity0.0185673269389271
GO:0042165neurotransmitter binding0.0185673269389271
GO:0045211postsynaptic membrane0.0185673269389271
GO:0044456synapse part0.0185673269389271
GO:0015276ligand-gated ion channel activity0.0185673269389271
GO:0022834ligand-gated channel activity0.0185673269389271
GO:0008509anion transmembrane transporter activity0.0219718759987216
GO:0007268synaptic transmission0.0284548059185996
GO:0019226transmission of nerve impulse0.0303558813140233
GO:0030054cell junction0.0371413136077462
GO:0022836gated channel activity0.0412921752554391
GO:0007267cell-cell signaling0.044665939725298
GO:0005216ion channel activity0.044665939725298
GO:0022838substrate specific channel activity0.044665939725298
GO:0015267channel activity0.044665939725298
GO:0022803passive transmembrane transporter activity0.044665939725298



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 tube2.51e-9156
neural rod2.51e-9156
future spinal cord2.51e-9156
neural keel2.51e-9156
regional part of nervous system4.24e-9153
regional part of brain4.24e-9153
brain6.66e-8368
future brain6.66e-8368
central nervous system3.26e-7781
telencephalon8.07e-7534
brain grey matter1.57e-7434
gray matter1.57e-7434
cerebral hemisphere2.89e-7332
nervous system6.07e-6989
neural plate3.59e-6882
presumptive neural plate3.59e-6882
regional part of forebrain6.27e-6741
forebrain6.27e-6741
anterior neural tube6.27e-6741
future forebrain6.27e-6741
regional part of telencephalon1.27e-6632
regional part of cerebral cortex3.43e-6522
neurectoderm1.05e-6486
cerebral cortex3.48e-5725
pallium3.48e-5725
neocortex1.24e-5620
adult organism3.22e-54114
ecto-epithelium2.25e-52104
pre-chordal neural plate6.30e-5161
structure with developmental contribution from neural crest2.15e-42132
ectoderm-derived structure5.82e-35171
ectoderm5.82e-35171
presumptive ectoderm5.82e-35171
gyrus3.56e-296
brainstem8.55e-286
organ system subdivision4.26e-25223
limbic system1.73e-245
segmental subdivision of hindbrain2.20e-2412
hindbrain2.20e-2412
presumptive hindbrain2.20e-2412
posterior neural tube3.53e-2415
chordal neural plate3.53e-2415
segmental subdivision of nervous system2.05e-2213
tube5.85e-22192
basal ganglion6.82e-199
nuclear complex of neuraxis6.82e-199
aggregate regional part of brain6.82e-199
collection of basal ganglia6.82e-199
cerebral subcortex6.82e-199
neural nucleus2.47e-189
nucleus of brain2.47e-189
temporal lobe1.48e-176
organ part4.14e-17218
parietal lobe3.26e-165
anatomical conduit3.78e-16240
frontal cortex1.87e-153
pons5.70e-153
medulla oblongata1.35e-143
myelencephalon1.35e-143
future myelencephalon1.35e-143
regional part of metencephalon1.99e-139
metencephalon1.99e-139
future metencephalon1.99e-139
epithelium4.78e-13306
anatomical cluster5.71e-13373
cell layer7.56e-13309
corpus striatum2.27e-114
striatum2.27e-114
ventral part of telencephalon2.27e-114
future corpus striatum2.27e-114
telencephalic nucleus4.17e-117
amygdala4.72e-112
multi-tissue structure7.22e-11342
middle temporal gyrus1.20e-102
middle frontal gyrus1.26e-102
Ammon's horn1.46e-102
lobe parts of cerebral cortex1.46e-102
hippocampal formation1.46e-102
limbic lobe1.46e-102
locus ceruleus3.45e-102
brainstem nucleus3.45e-102
hindbrain nucleus3.45e-102
occipital lobe1.94e-095
organ1.44e-07503
caudate-putamen3.53e-073
dorsal striatum3.53e-073


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)
MA0003.10.110456
MA0004.10.502801
MA0006.10.341337
MA0007.12.10741
MA0009.10.973289
MA0014.10.367415
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.12.12821
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.11.04727
MA0059.11.84146
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.11.47685
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.14.03024
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.11.67751
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.9112
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.695228
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.708913
MA0145.10.0807715
MA0146.10.162729
MA0147.10.768766
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.60756
MA0138.20.704862
MA0002.20.213296
MA0137.21.70023
MA0104.20.636673
MA0047.20.636643
MA0112.20.944394
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.106355
MA0163.10.382702
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.478894
MA0102.21.51913
MA0258.10.687127
MA0259.10.289405
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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