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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:35, 17 September 2013


Full id: C993_locus_medulla_spinal_pons_small_cerebellum_amygdala



Phase1 CAGE Peaks

Hg19::chr11:20621148..20621166,+p1@SLC6A5
Hg19::chr11:20621167..20621170,+p6@SLC6A5
Hg19::chr5:151304337..151304405,-p1@GLRA1
Hg19::chr5:151304407..151304416,-p2@GLRA1
Hg19::chr5:151304948..151304984,-p@chr5:151304948..151304984
-
Hg19::chr5:151304987..151304998,-p@chr5:151304987..151304998
-
Hg19::chrX:2502363..2502375,-p@chrX:2502363..2502375
-
Hg19::chrX:2502646..2502657,-p@chrX:2502646..2502657
-


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:0060081membrane hyperpolarization0.00135405628164371
GO:0002087neurological control of breathing0.00135405628164371
GO:0060004reflex0.00135405628164371
GO:0060012synaptic transmission, glycinergic0.00135405628164371
GO:0060013righting reflex0.00135405628164371
GO:0060080regulation of inhibitory postsynaptic membrane potential0.00135405628164371
GO:0030977taurine binding0.00135405628164371
GO:0007268synaptic transmission0.00146151165470533
GO:0019226transmission of nerve impulse0.00157970907739466
GO:0043576regulation of respiratory gaseous exchange0.00157970907739466
GO:0015375glycine:sodium symporter activity0.00157970907739466
GO:0003016respiratory system process0.00157970907739466
GO:0051970negative regulation of transmission of nerve impulse0.00189559509001838
GO:0005294neutral L-amino acid secondary active transmembrane transporter activity0.00189559509001838
GO:0016594glycine binding0.00189559509001838
GO:0050884neuromuscular process controlling posture0.00189559509001838
GO:0016934extracellular-glycine-gated chloride channel activity0.00189559509001838
GO:0015187glycine transmembrane transporter activity0.00189559509001838
GO:0060078regulation of postsynaptic membrane potential0.00189559509001838
GO:0001964startle response0.00189559509001838
GO:0016933extracellular-glycine-gated ion channel activity0.00215405362339861
GO:0016855racemase and epimerase activity, acting on amino acids and derivatives0.00215405362339861
GO:0007267cell-cell signaling0.00248055822458995
GO:0031645negative regulation of neurological process0.00276428743753103
GO:0007628adult walking behavior0.00291612843739686
GO:0051291protein heterooligomerization0.00291612843739686
GO:0007340acrosome reaction0.00315909263813393
GO:0005283sodium:amino acid symporter activity0.00406151116842331
GO:0017156calcium ion-dependent exocytosis0.00410657861720154
GO:0005416cation:amino acid symporter activity0.00410657861720154
GO:0008344adult locomotory behavior0.00427974597748268
GO:0015175neutral amino acid transmembrane transporter activity0.00503421098668936
GO:0051969regulation of transmission of nerve impulse0.00516873946372341
GO:0007270nerve-nerve synaptic transmission0.0052953462946297
GO:0016597amino acid binding0.00541471047764775
GO:0050905neuromuscular process0.00594927216790162
GO:0050877neurological system process0.00594927216790162
GO:0016854racemase and epimerase activity0.00594927216790162
GO:0031644regulation of neurological process0.00594927216790162
GO:0015075ion transmembrane transporter activity0.00594927216790162
GO:0005887integral to plasma membrane0.00594927216790162
GO:0031226intrinsic to plasma membrane0.00594927216790162
GO:0030534adult behavior0.00594927216790162
GO:0005275amine transmembrane transporter activity0.00610578100839108
GO:0007585respiratory gaseous exchange0.00610578100839108
GO:0042391regulation of membrane potential0.00638479285822445
GO:0022891substrate-specific transmembrane transporter activity0.00686232643694342
GO:0003008system process0.00687939342854417
GO:0005343organic acid:sodium symporter activity0.00728688707163315
GO:0004890GABA-A receptor activity0.00728688707163315
GO:0022857transmembrane transporter activity0.00728688707163315
GO:0001508regulation of action potential0.00728688707163315
GO:0051260protein homooligomerization0.00732802568161109
GO:0043176amine binding0.00771824791187268
GO:0022892substrate-specific transporter activity0.00790622462079804
GO:0016917GABA receptor activity0.00794969468264957
GO:0005328neurotransmitter:sodium symporter activity0.00816513631184729
GO:0009897external side of plasma membrane0.00816513631184729
GO:0005326neurotransmitter transporter activity0.00850797286131233
GO:0007338single fertilization0.00883933967365377
GO:0009566fertilization0.0090046826188368
GO:0031404chloride ion binding0.00901920290510728
GO:0043168anion binding0.00901920290510728
GO:0051259protein oligomerization0.0091739501599589
GO:0015171amino acid transmembrane transporter activity0.00917836777421169
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0103292606887706
GO:0044459plasma membrane part0.0108599536750957
GO:0006836neurotransmitter transport0.0108599536750957
GO:0005254chloride channel activity0.0112507492645326
GO:0006821chloride transport0.0117328253921666
GO:0015370solute:sodium symporter activity0.0117328253921666
GO:0046943carboxylic acid transmembrane transporter activity0.0127514600662058
GO:0005342organic acid transmembrane transporter activity0.0127899767092456
GO:0005253anion channel activity0.0127899767092456
GO:0006887exocytosis0.0140053113157588
GO:0015294solute:cation symporter activity0.0141939444973642
GO:0005230extracellular ligand-gated ion channel activity0.0160947247234644
GO:0030594neurotransmitter receptor activity0.0170987138343306
GO:0042165neurotransmitter binding0.0173601799598286
GO:0009986cell surface0.017397583831441
GO:0045211postsynaptic membrane0.017397583831441
GO:0044456synapse part0.0181413946760884
GO:0015276ligand-gated ion channel activity0.0181413946760884
GO:0022834ligand-gated channel activity0.0181413946760884
GO:0003012muscle system process0.0181413946760884
GO:0006936muscle contraction0.0181413946760884
GO:0007218neuropeptide signaling pathway0.0182581169534328
GO:0007626locomotory behavior0.0194436837077933
GO:0008509anion transmembrane transporter activity0.0221901088285466
GO:0005886plasma membrane0.0223883845240826
GO:0032501multicellular organismal process0.0223883845240826
GO:0007601visual perception0.0226534990889344
GO:0050953sensory perception of light stimulus0.0226534990889344
GO:0055082cellular chemical homeostasis0.0233228061816399
GO:0006873cellular ion homeostasis0.0233228061816399
GO:0045045secretory pathway0.0233228061816399
GO:0006810transport0.0233228061816399
GO:0015293symporter activity0.0233228061816399
GO:0051234establishment of localization0.024088359323175
GO:0015698inorganic anion transport0.0245498802191714
GO:0050801ion homeostasis0.024958644697381
GO:0051239regulation of multicellular organismal process0.0256357797097164
GO:0007610behavior0.0266935110287568
GO:0051179localization0.0266935110287568
GO:0032940secretion by cell0.0266935110287568
GO:0048878chemical homeostasis0.0268848443540973
GO:0022414reproductive process0.0268969631726346
GO:0016853isomerase activity0.0272650958715835
GO:0019953sexual reproduction0.0272650958715835
GO:0006820anion transport0.0277001061218117
GO:0006461protein complex assembly0.0288880572755278
GO:0015291secondary active transmembrane transporter activity0.0303052850645014
GO:0019725cellular homeostasis0.0312816979044878
GO:0046903secretion0.0317472429057463
GO:0030054cell junction0.0351357898186916
GO:0007154cell communication0.0371714845023831
GO:0042592homeostatic process0.0386115694457162
GO:0022836gated channel activity0.0402634033800093
GO:0016192vesicle-mediated transport0.0478383129808364
GO:0009605response to external stimulus0.0495334393029555



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 tube2.53e-7756
neural rod2.53e-7756
future spinal cord2.53e-7756
neural keel2.53e-7756
regional part of nervous system1.05e-6453
regional part of brain1.05e-6453
central nervous system4.49e-5981
brain7.07e-5768
future brain7.07e-5768
nervous system2.09e-5689
neural plate3.61e-5582
presumptive neural plate3.61e-5582
posterior neural tube4.83e-5415
chordal neural plate4.83e-5415
neurectoderm2.29e-5286
ecto-epithelium2.17e-42104
brain grey matter8.47e-4234
gray matter8.47e-4234
cerebral hemisphere7.69e-3932
adult organism2.24e-38114
segmental subdivision of hindbrain3.41e-3812
hindbrain3.41e-3812
presumptive hindbrain3.41e-3812
regional part of cerebral cortex2.05e-3722
telencephalon1.99e-3634
brainstem3.73e-356
segmental subdivision of nervous system3.86e-3513
neocortex4.48e-3520
structure with developmental contribution from neural crest1.06e-34132
regional part of telencephalon5.38e-3432
regional part of forebrain6.98e-3441
forebrain6.98e-3441
anterior neural tube6.98e-3441
future forebrain6.98e-3441
cerebral cortex8.46e-3325
pallium8.46e-3325
ectoderm-derived structure5.31e-29171
ectoderm5.31e-29171
presumptive ectoderm5.31e-29171
pre-chordal neural plate1.26e-2461
regional part of metencephalon6.45e-239
metencephalon6.45e-239
future metencephalon6.45e-239
gyrus1.38e-226
organ system subdivision8.68e-21223
tube9.24e-19192
medulla oblongata1.54e-183
myelencephalon1.54e-183
future myelencephalon1.54e-183
pons2.06e-183
spinal cord2.18e-183
dorsal region element2.18e-183
dorsum2.18e-183
anatomical conduit7.52e-14240
temporal lobe4.32e-136
locus ceruleus5.89e-132
brainstem nucleus5.89e-132
hindbrain nucleus5.89e-132
amygdala1.58e-122
middle temporal gyrus5.19e-122
organ part7.31e-12218
anatomical cluster6.16e-11373
limbic system9.79e-115
epithelium1.46e-10306
cell layer2.12e-10309
parietal lobe2.23e-105
neural nucleus2.28e-109
nucleus of brain2.28e-109
basal ganglion3.45e-109
nuclear complex of neuraxis3.45e-109
aggregate regional part of brain3.45e-109
collection of basal ganglia3.45e-109
cerebral subcortex3.45e-109
cerebellum2.98e-096
rhombic lip2.98e-096
caudate-putamen2.91e-083
dorsal striatum2.91e-083
frontal cortex3.76e-083
multi-tissue structure4.80e-07342
putamen5.69e-071
olfactory region8.02e-071
primary subdivision of skull8.02e-071
cranium8.02e-071
neurocranium8.02e-071
chondrocranium8.02e-071
cartilaginous neurocranium8.02e-071
head paraxial mesoderm8.02e-071
paracentral gyrus8.98e-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)
MA0003.12.40022
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.134069
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.11.12793
MA0051.10.553205
MA0052.10.842664
MA0055.10.283474
MA0056.10
MA0057.12.14064
MA0058.10.362328
MA0059.10.361075
MA0060.11.67203
MA0061.10.961853
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.14.95701
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.634172
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.11.40058
MA0101.10.30624
MA0103.10.291333
MA0105.10.988431
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.11.49247
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.913661
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.470675
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.480646
MA0146.10.00761723
MA0147.10.243042
MA0148.11.20731
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.164269
MA0138.25.16991
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.208783
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.197713
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.93331
MA0163.15.02939
MA0164.11.51849
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.21.5021
MA0102.21.46209
MA0258.10.603127
MA0259.10.25092
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
REST#597844.825014358064010.005720735398269540.0257896095420155



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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