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Coexpression cluster:C993: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.57e-74!57;UBERON:0005068!1.57e-74!57;UBERON:0006241!1.57e-74!57;UBERON:0007135!1.57e-74!57;UBERON:0001017!1.87e-65!82;UBERON:0005743!1.15e-64!86;UBERON:0000073!1.45e-64!94;UBERON:0001016!1.45e-64!94;UBERON:0002616!9.34e-61!59;UBERON:0000955!7.99e-58!69;UBERON:0006238!7.99e-58!69;UBERON:0002780!1.46e-52!41;UBERON:0001890!1.46e-52!41;UBERON:0006240!1.46e-52!41;UBERON:0003075!2.90e-52!86;UBERON:0007284!2.90e-52!86;UBERON:0002346!8.77e-52!90;UBERON:0003080!4.17e-51!42;UBERON:0002020!2.61e-43!34;UBERON:0003528!2.61e-43!34;UBERON:0001893!1.41e-42!34;UBERON:0007023!1.80e-41!115;UBERON:0002791!1.40e-40!33;UBERON:0001869!5.32e-39!32;UBERON:0003056!7.77e-35!61;UBERON:0002619!3.20e-33!22;UBERON:0001950!5.20e-33!20;UBERON:0000924!9.12e-33!173;UBERON:0006601!9.12e-33!173;UBERON:0004121!2.12e-32!169;UBERON:0000033!2.08e-30!123;UBERON:0000153!8.35e-30!129;UBERON:0007811!8.35e-30!129;UBERON:0000956!9.67e-29!25;UBERON:0000203!9.67e-29!25;UBERON:0003076!9.80e-24!15;UBERON:0003057!9.80e-24!15;UBERON:0000025!1.07e-19!194;UBERON:0004733!6.88e-17!12;UBERON:0002028!6.88e-17!12;UBERON:0007277!6.88e-17!12;UBERON:0002308!3.01e-16!9;UBERON:0000125!3.01e-16!9;UBERON:0002420!4.53e-16!9;UBERON:0007245!4.53e-16!9;UBERON:0010009!4.53e-16!9;UBERON:0010011!4.53e-16!9;UBERON:0000454!4.53e-16!9;UBERON:0002298!1.48e-15!8;UBERON:0004732!2.01e-15!13;UBERON:0000200!1.19e-14!6;UBERON:0001871!3.08e-14!7;UBERON:0004111!3.15e-13!241;UBERON:0001872!2.26e-12!5;UBERON:0009663!1.38e-11!7;UBERON:0001894!3.19e-11!7;UBERON:0006222!3.19e-11!7;UBERON:0000477!5.36e-11!286;UBERON:0002680!2.48e-10!9;UBERON:0001895!2.48e-10!9;UBERON:0010092!2.48e-10!9;UBERON:0000064!4.48e-10!219;UBERON:0000483!7.87e-10!309;UBERON:0000119!1.32e-09!312;UBERON:0000475!1.73e-09!365;UBERON:0001896!5.64e-09!3;UBERON:0005290!5.64e-09!3;UBERON:0010096!5.64e-09!3;UBERON:0000988!5.94e-09!3;UBERON:0002240!5.94e-09!3;UBERON:0002771!2.39e-08!3;UBERON:0006331!2.63e-08!3;UBERON:0000349!4.19e-08!5;UBERON:0000922!3.26e-07!612
|ontology_enrichment_uberon=UBERON:0001049!1.57e-74!57;UBERON:0005068!1.57e-74!57;UBERON:0006241!1.57e-74!57;UBERON:0007135!1.57e-74!57;UBERON:0001017!1.87e-65!82;UBERON:0005743!1.15e-64!86;UBERON:0000073!1.45e-64!94;UBERON:0001016!1.45e-64!94;UBERON:0002616!9.34e-61!59;UBERON:0000955!7.99e-58!69;UBERON:0006238!7.99e-58!69;UBERON:0002780!1.46e-52!41;UBERON:0001890!1.46e-52!41;UBERON:0006240!1.46e-52!41;UBERON:0003075!2.90e-52!86;UBERON:0007284!2.90e-52!86;UBERON:0002346!8.77e-52!90;UBERON:0003080!4.17e-51!42;UBERON:0002020!2.61e-43!34;UBERON:0003528!2.61e-43!34;UBERON:0001893!1.41e-42!34;UBERON:0007023!1.80e-41!115;UBERON:0002791!1.40e-40!33;UBERON:0001869!5.32e-39!32;UBERON:0003056!7.77e-35!61;UBERON:0002619!3.20e-33!22;UBERON:0001950!5.20e-33!20;UBERON:0000924!9.12e-33!173;UBERON:0006601!9.12e-33!173;UBERON:0004121!2.12e-32!169;UBERON:0000033!2.08e-30!123;UBERON:0000153!8.35e-30!129;UBERON:0007811!8.35e-30!129;UBERON:0000956!9.67e-29!25;UBERON:0000203!9.67e-29!25;UBERON:0003076!9.80e-24!15;UBERON:0003057!9.80e-24!15;UBERON:0000025!1.07e-19!194;UBERON:0004733!6.88e-17!12;UBERON:0002028!6.88e-17!12;UBERON:0007277!6.88e-17!12;UBERON:0002308!3.01e-16!9;UBERON:0000125!3.01e-16!9;UBERON:0002420!4.53e-16!9;UBERON:0007245!4.53e-16!9;UBERON:0010009!4.53e-16!9;UBERON:0010011!4.53e-16!9;UBERON:0000454!4.53e-16!9;UBERON:0002298!1.48e-15!8;UBERON:0004732!2.01e-15!13;UBERON:0000200!1.19e-14!6;UBERON:0001871!3.08e-14!7;UBERON:0004111!3.15e-13!241;UBERON:0001872!2.26e-12!5;UBERON:0009663!1.38e-11!7;UBERON:0001894!3.19e-11!7;UBERON:0006222!3.19e-11!7;UBERON:0000477!5.36e-11!286;UBERON:0002680!2.48e-10!9;UBERON:0001895!2.48e-10!9;UBERON:0010092!2.48e-10!9;UBERON:0000064!4.48e-10!219;UBERON:0000483!7.87e-10!309;UBERON:0000119!1.32e-09!312;UBERON:0000475!1.73e-09!365;UBERON:0001896!5.64e-09!3;UBERON:0005290!5.64e-09!3;UBERON:0010096!5.64e-09!3;UBERON:0000988!5.94e-09!3;UBERON:0002240!5.94e-09!3;UBERON:0002771!2.39e-08!3;UBERON:0006331!2.63e-08!3;UBERON:0000349!4.19e-08!5;UBERON:0000922!3.26e-07!612
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}}
}}

Revision as of 14:10, 5 September 2012


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
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Hg19::chr5:151304987..151304998,-p@chr5:151304987..151304998
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Hg19::chrX:2502363..2502375,-p@chrX:2502363..2502375
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Hg19::chrX:2502646..2502657,-p@chrX:2502646..2502657
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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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
embryonic stem cell2.73e-125
Uber Anatomy
Ontology termp-valuen
neural tube1.57e-7457
neural rod1.57e-7457
future spinal cord1.57e-7457
neural keel1.57e-7457
central nervous system1.87e-6582
regional part of nervous system1.45e-6494
nervous system1.45e-6494
regional part of brain9.34e-6159
brain7.99e-5869
future brain7.99e-5869
regional part of forebrain1.46e-5241
forebrain1.46e-5241
future forebrain1.46e-5241
neural plate2.90e-5286
presumptive neural plate2.90e-5286
neurectoderm8.77e-5290
anterior neural tube4.17e-5142
gray matter2.61e-4334
brain grey matter2.61e-4334
telencephalon1.41e-4234
adult organism1.80e-41115
regional part of telencephalon1.40e-4033
cerebral hemisphere5.32e-3932
pre-chordal neural plate7.77e-3561
regional part of cerebral cortex3.20e-3322
neocortex5.20e-3320
ectoderm9.12e-33173
presumptive ectoderm9.12e-33173
ectoderm-derived structure2.12e-32169
head2.08e-30123
anterior region of body8.35e-30129
craniocervical region8.35e-30129
cerebral cortex9.67e-2925
pallium9.67e-2925
posterior neural tube9.80e-2415
chordal neural plate9.80e-2415
tube1.07e-19194
segmental subdivision of hindbrain6.88e-1712
hindbrain6.88e-1712
presumptive hindbrain6.88e-1712
nucleus of brain3.01e-169
neural nucleus3.01e-169
basal ganglion4.53e-169
nuclear complex of neuraxis4.53e-169
aggregate regional part of brain4.53e-169
collection of basal ganglia4.53e-169
cerebral subcortex4.53e-169
brainstem1.48e-158
segmental subdivision of nervous system2.01e-1513
gyrus1.19e-146
temporal lobe3.08e-147
anatomical conduit3.15e-13241
parietal lobe2.26e-125
telencephalic nucleus1.38e-117
diencephalon3.19e-117
future diencephalon3.19e-117
anatomical cluster5.36e-11286
regional part of metencephalon2.48e-109
metencephalon2.48e-109
future metencephalon2.48e-109
organ part4.48e-10219
epithelium7.87e-10309
cell layer1.32e-09312
organism subdivision1.73e-09365
medulla oblongata5.64e-093
myelencephalon5.64e-093
future myelencephalon5.64e-093
pons5.94e-093
spinal cord5.94e-093
middle temporal gyrus2.39e-083
brainstem nucleus2.63e-083
limbic system4.19e-085
embryo3.26e-07612


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)

{{{tfbs_overrepresentation_jaspar}}}



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.