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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0.0787106646522085,0,0,0,0,0,0,0,0.0934726072708047,0,0.0592075530067425,0,0.0304928680006475,0,0,0,0,0,0,0,0,0,0,0.0453761270468853,0.178921998059593,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0259870263648859,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.111449348043638,0.115825018491817,0,0,0,0,0,0.0196147905178636,0.0434875120355909,0.104065219852414,0.11091642773236,0,0,0,0,0,0,0,0,0,0,0.06470644667023,0,0.0760676121854375,0,0,0,0,0,0,0,0,0,0,0,0,0.0231717684481141,0,0,0.073058801099379,0,0,0,0,0,0,0,0,0,0,0.0478753273256649,0.0588362978411115,0.144233573286801,0.165636020373816,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.042030159414282,0,0,0,0,0,0,0,0,0,0,0.0659711848606685,0.0208447609871159,0,0,0,0,0.147870352938202,0.154078645521249,0.167421761054727,0.154453994595894,0.200176167530276,0.119017367774156,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0938778219198735,0.00986889761507705,0,0.0343837153039546,0,0,0,0,0,0,0,0.0476371106609188,0.0241060230789031,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0292357798753831,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.154822999768582,0,0,0,0,0,0,0,0,0,0,0.227669247532428,0,0,0,0,0,0,0,0,0,0,0,0.0213493283291655,0,0,0.0983303062134256,0.361991832974167,0.467995605038548,0.295986698712246,0.644039281222353,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0114829428752784,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0406884221662749,0,0,0,0,0,0.0200381238622658,0,0,0,0,0,0,0.146311944286978,0,0,0,0,0,0,0,0.104229702589419,0,0,0,0.054662655644364,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0555694062070307,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0283084336801597,0,0,0,0.0374607828862372,0,0,0,0,0,0,0,0,0,0,0,0,0,0.146402603716833,0,0,0,0.0149234925142461,0.0978087148759722,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0296885786825552,0.0248726312013101,0,0,0.084762123621365,0.101234535406224,0.103995002545457,0.475423511109794,0.462459818002952,0.0436452879209715,0,0.0764880958447485,0,0,0,0.0361271691077303,0,0,0.0358925453903706,0,0,0.0204283766509788,0,0,0.147159551208692,0.537786955839366,0.997063024884645,0,0,0,0,0.123096710672199,0,0,0,0.155770852860924,0,0.357172813387332,0,0.327592573208029,0.464983958560785,0.436908998860573,0,0.0203420053388399,0.0451027018107718,0.063848128494866,0,0,0,0,0.107578525216293,0.092776003344243,0,0,0,0,0,0,0,0,0,0,0,0,0,0.035372572826539,0,0,0.0505977919678937,0,0.638979381573095,0,0.61076855344186,0.094796295901329,0,0,0,0.0446392630615396,0.556105294789393,0.0376931284480336,0,0.0409213382341519,0,0,0,0,0.054385572482455,0.0281998304782202,0,0,0,0.0349684140344003,0,0,0,0,0,0.640770486702401,0.193366048861236,0,0,0.443509311118913,0,0,0,0.167100528319899,0,0,0,0,0,0,0,0.0216030789840009,0,0,0.626895066921086,0.431882555804485,0,0,0.0506823072663195,0.053483212730439,0.0819265422366715,0,0.0395325284566706,0.0521497100718105,0,0.128383119724414,0,0,0.0164670836994265,0.00298354409390225,0.0090971463119099,0,0,0.206688393303695,0.395276592247434,0.22110537096969,0.187867861032557,0.288030341589708,0,0,0.514534635206082,0,0.0460825052702691,0.0679131845393035,0.0416080517422001,0.0665417579397175,0.038122678605483,0,0,0,0,0,0,0,0,0,0,0,0,0.435562153134484,0.464880360796257,0,0,0.107517828351886,0.161154120326771,0.0752614132322225,0,0,0.0249562850978746,0,0,0,0,0,0.059315561406254,0.275557388108753,0.628610928148045,0.33508934494851,0.434605240679025,0.275120039821865,0.503723757799459,0.0753852644113325,0,0,0,0,0,0.0587755320721174,0,0,0,0,0,0,0,0,0,0.056253955557224,0,0.080654513839309,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0421883161150136,0,0,0,0,0,0,0,0,0,0,0.0495365713353616,0,0,0.418320292765251,0,0,0,0,0.0477194411199613,0,0,0,0,0,0,0,0,0.141036640960701,0,0,0.123076702386819,0,0.0418542907017061,0,0,0,0.191863837255831,0.207581988767781,0,0,0.344856951832498,0.483457425382718,0.437340972615449,0.614600071642566,0.603897414193262,0.452380352467278,0.536390186958299,1.15135155736358,0,0.0459985967800308,0,0,0,0,0,0.0441798658901723,0,0,0,0,0.0562542693604755,0.414475097689672,0.329644282741866,0.388097950995,0.397270546795426,0.631631332975976,0,0,0,0.0704561921623045,0,0,0.103003290575171,0.0445394404812913,0,0.0236829981957466,0,0.341895139159622,0.419801660052259,0,0,0.0316640867750834,0.362145940249622,0,0.140875500847939,0,0,0.0836188439410081,0.0318568321420254,0.412896102144333,0.155150087075562,0,0,0,0,0,0,0,0.076661505174214,0,0,0,0,0,0.0249805434194815,0,0,0,0,0.161103533194574,0.0394006764057046,0,0.080951051966903,0,0,0.0311684368993006,0.0858467613960337,0,0,0.0919048039302623,0.554478955382104,0.276723497112124,0.392744800955133,0,0.0195054688671048,0.0135642422894877,0,0,0,0.0732511233153285,0.119065270453924,0,0.607546460905772,0,0.565648548666583,0.62746376193649,0.092207554539194,0,0,0,0.189001763341664,0.243996403498899,0,0.0403092142030732,0.051425564666458,0.0190904186583736,0,0.0603432234981887,0,0.483562797577298,0.575967143909379,0,0.0463716234329315,0,0.0481592864582769,0,0,0,0,0,0.0141538448872959,0.0150411145536097,0,0,0,0,0,0,0.0250431515419316,0,0.110805794051404,0.0398210014092477,0
|full_id=C1367_optic_extraskeletal_brain_rhabdomyosarcoma_substantia_corpus_thalamus
|full_id=C1367_optic_extraskeletal_brain_rhabdomyosarcoma_substantia_corpus_thalamus
|gostat_on_coexpression_clusters=GO:0016342!catenin complex!0.00600494524902861!10297$GO:0019228!generation of action potential!0.0108076287272309!27345$GO:0005513!detection of calcium ion!0.0108076287272309!27345$GO:0019229!regulation of vasoconstriction!0.0108076287272309!27345$GO:0008013!beta-catenin binding!0.0108076287272309!10297$GO:0046928!regulation of neurotransmitter secretion!0.0120079460631646!27345$GO:0042310!vasoconstriction!0.0135077461451033!27345$GO:0009593!detection of chemical stimulus!0.0135077461451033!27345$GO:0042391!regulation of membrane potential!0.015179589722366!27345$GO:0015269!calcium-activated potassium channel activity!0.015179589722366!27345$GO:0022839!ion gated channel activity!0.015179589722366!27345$GO:0005227!calcium activated cation channel activity!0.015179589722366!27345$GO:0001508!regulation of action potential!0.015179589722366!27345$GO:0007269!neurotransmitter secretion!0.015179589722366!27345$GO:0035150!regulation of tube size!0.015179589722366!27345$GO:0050880!regulation of blood vessel size!0.015179589722366!27345$GO:0003018!vascular process in circulatory system!0.015179589722366!27345$GO:0008017!microtubule binding!0.0157910906900584!10297$GO:0019897!extrinsic to plasma membrane!0.0157910906900584!10297$GO:0045055!regulated secretory pathway!0.0159009256768253!27345$GO:0051046!regulation of secretion!0.0168566343658797!27345$GO:0015631!tubulin binding!0.0182573598082459!10297$GO:0003001!generation of a signal involved in cell-cell signaling!0.0182573598082459!27345$GO:0044459!plasma membrane part!0.0184552706464487!10297;27345$GO:0001505!regulation of neurotransmitter levels!0.0184552706464487!27345$GO:0051606!detection of stimulus!0.0184552706464487!27345$GO:0035239!tube morphogenesis!0.0186592293268234!27345$GO:0019898!extrinsic to membrane!0.0229116677526957!10297$GO:0035295!tube development!0.0237832898150614!27345$GO:0043234!protein complex!0.0237832898150614!10297;27345$GO:0008076!voltage-gated potassium channel complex!0.0237832898150614!27345$GO:0016055!Wnt receptor signaling pathway!0.027152237988412!10297$GO:0016043!cellular component organization and biogenesis!0.0273869361726116!10297;27345$GO:0008015!blood circulation!0.0273869361726116!27345$GO:0003013!circulatory system process!0.0273869361726116!27345$GO:0005267!potassium channel activity!0.0347753819963962!27345$GO:0005886!plasma membrane!0.0347753819963962!10297;27345$GO:0032991!macromolecular complex!0.0350272484805176!10297;27345$GO:0055082!cellular chemical homeostasis!0.0350272484805176!27345$GO:0006873!cellular ion homeostasis!0.0350272484805176!27345$GO:0045045!secretory pathway!0.0350272484805176!27345$GO:0006813!potassium ion transport!0.0364641979791503!27345$GO:0050801!ion homeostasis!0.0371405398920149!27345$GO:0051239!regulation of multicellular organismal process!0.0376502896809556!27345$GO:0007268!synaptic transmission!0.0384140263190828!27345$GO:0032940!secretion by cell!0.0384140263190828!27345$GO:0048878!chemical homeostasis!0.0384140263190828!27345$GO:0019226!transmission of nerve impulse!0.0410840863746678!27345$GO:0006461!protein complex assembly!0.0414590676224523!10297$GO:0019725!cellular homeostasis!0.0447891739188977!27345$GO:0046903!secretion!0.0449588284627961!27345$GO:0005261!cation channel activity!0.0482023710215125!27345
|gostat_on_coexpression_clusters=GO:0016342!catenin complex!0.00600494524902861!10297$GO:0019228!generation of action potential!0.0108076287272309!27345$GO:0005513!detection of calcium ion!0.0108076287272309!27345$GO:0019229!regulation of vasoconstriction!0.0108076287272309!27345$GO:0008013!beta-catenin binding!0.0108076287272309!10297$GO:0046928!regulation of neurotransmitter secretion!0.0120079460631646!27345$GO:0042310!vasoconstriction!0.0135077461451033!27345$GO:0009593!detection of chemical stimulus!0.0135077461451033!27345$GO:0042391!regulation of membrane potential!0.015179589722366!27345$GO:0015269!calcium-activated potassium channel activity!0.015179589722366!27345$GO:0022839!ion gated channel activity!0.015179589722366!27345$GO:0005227!calcium activated cation channel activity!0.015179589722366!27345$GO:0001508!regulation of action potential!0.015179589722366!27345$GO:0007269!neurotransmitter secretion!0.015179589722366!27345$GO:0035150!regulation of tube size!0.015179589722366!27345$GO:0050880!regulation of blood vessel size!0.015179589722366!27345$GO:0003018!vascular process in circulatory system!0.015179589722366!27345$GO:0008017!microtubule binding!0.0157910906900584!10297$GO:0019897!extrinsic to plasma membrane!0.0157910906900584!10297$GO:0045055!regulated secretory pathway!0.0159009256768253!27345$GO:0051046!regulation of secretion!0.0168566343658797!27345$GO:0015631!tubulin binding!0.0182573598082459!10297$GO:0003001!generation of a signal involved in cell-cell signaling!0.0182573598082459!27345$GO:0044459!plasma membrane part!0.0184552706464487!10297;27345$GO:0001505!regulation of neurotransmitter levels!0.0184552706464487!27345$GO:0051606!detection of stimulus!0.0184552706464487!27345$GO:0035239!tube morphogenesis!0.0186592293268234!27345$GO:0019898!extrinsic to membrane!0.0229116677526957!10297$GO:0035295!tube development!0.0237832898150614!27345$GO:0043234!protein complex!0.0237832898150614!10297;27345$GO:0008076!voltage-gated potassium channel complex!0.0237832898150614!27345$GO:0016055!Wnt receptor signaling pathway!0.027152237988412!10297$GO:0016043!cellular component organization and biogenesis!0.0273869361726116!10297;27345$GO:0008015!blood circulation!0.0273869361726116!27345$GO:0003013!circulatory system process!0.0273869361726116!27345$GO:0005267!potassium channel activity!0.0347753819963962!27345$GO:0005886!plasma membrane!0.0347753819963962!10297;27345$GO:0032991!macromolecular complex!0.0350272484805176!10297;27345$GO:0055082!cellular chemical homeostasis!0.0350272484805176!27345$GO:0006873!cellular ion homeostasis!0.0350272484805176!27345$GO:0045045!secretory pathway!0.0350272484805176!27345$GO:0006813!potassium ion transport!0.0364641979791503!27345$GO:0050801!ion homeostasis!0.0371405398920149!27345$GO:0051239!regulation of multicellular organismal process!0.0376502896809556!27345$GO:0007268!synaptic transmission!0.0384140263190828!27345$GO:0032940!secretion by cell!0.0384140263190828!27345$GO:0048878!chemical homeostasis!0.0384140263190828!27345$GO:0019226!transmission of nerve impulse!0.0410840863746678!27345$GO:0006461!protein complex assembly!0.0414590676224523!10297$GO:0019725!cellular homeostasis!0.0447891739188977!27345$GO:0046903!secretion!0.0449588284627961!27345$GO:0005261!cation channel activity!0.0482023710215125!27345

Revision as of 13:54, 12 September 2012


Full id: C1367_optic_extraskeletal_brain_rhabdomyosarcoma_substantia_corpus_thalamus



Phase1 CAGE Peaks

Hg19::chr12:70760058..70760085,+p1@KCNMB4
Hg19::chr12:70760380..70760395,+p6@KCNMB4
Hg19::chr12:70760508..70760600,+p4@KCNMB4
Hg19::chr17:36759531..36759542,+p@chr17:36759531..36759542
+
Hg19::chr19:1450095..1450102,+p4@APC2
Hg19::chr19:36370460..36370479,+p@chr19:36370460..36370479
+


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:0016342catenin complex0.00600494524902861
GO:0019228generation of action potential0.0108076287272309
GO:0005513detection of calcium ion0.0108076287272309
GO:0019229regulation of vasoconstriction0.0108076287272309
GO:0008013beta-catenin binding0.0108076287272309
GO:0046928regulation of neurotransmitter secretion0.0120079460631646
GO:0042310vasoconstriction0.0135077461451033
GO:0009593detection of chemical stimulus0.0135077461451033
GO:0042391regulation of membrane potential0.015179589722366
GO:0015269calcium-activated potassium channel activity0.015179589722366
GO:0022839ion gated channel activity0.015179589722366
GO:0005227calcium activated cation channel activity0.015179589722366
GO:0001508regulation of action potential0.015179589722366
GO:0007269neurotransmitter secretion0.015179589722366
GO:0035150regulation of tube size0.015179589722366
GO:0050880regulation of blood vessel size0.015179589722366
GO:0003018vascular process in circulatory system0.015179589722366
GO:0008017microtubule binding0.0157910906900584
GO:0019897extrinsic to plasma membrane0.0157910906900584
GO:0045055regulated secretory pathway0.0159009256768253
GO:0051046regulation of secretion0.0168566343658797
GO:0015631tubulin binding0.0182573598082459
GO:0003001generation of a signal involved in cell-cell signaling0.0182573598082459
GO:0044459plasma membrane part0.0184552706464487
GO:0001505regulation of neurotransmitter levels0.0184552706464487
GO:0051606detection of stimulus0.0184552706464487
GO:0035239tube morphogenesis0.0186592293268234
GO:0019898extrinsic to membrane0.0229116677526957
GO:0035295tube development0.0237832898150614
GO:0043234protein complex0.0237832898150614
GO:0008076voltage-gated potassium channel complex0.0237832898150614
GO:0016055Wnt receptor signaling pathway0.027152237988412
GO:0016043cellular component organization and biogenesis0.0273869361726116
GO:0008015blood circulation0.0273869361726116
GO:0003013circulatory system process0.0273869361726116
GO:0005267potassium channel activity0.0347753819963962
GO:0005886plasma membrane0.0347753819963962
GO:0032991macromolecular complex0.0350272484805176
GO:0055082cellular chemical homeostasis0.0350272484805176
GO:0006873cellular ion homeostasis0.0350272484805176
GO:0045045secretory pathway0.0350272484805176
GO:0006813potassium ion transport0.0364641979791503
GO:0050801ion homeostasis0.0371405398920149
GO:0051239regulation of multicellular organismal process0.0376502896809556
GO:0007268synaptic transmission0.0384140263190828
GO:0032940secretion by cell0.0384140263190828
GO:0048878chemical homeostasis0.0384140263190828
GO:0019226transmission of nerve impulse0.0410840863746678
GO:0006461protein complex assembly0.0414590676224523
GO:0019725cellular homeostasis0.0447891739188977
GO:0046903secretion0.0449588284627961
GO:0005261cation channel activity0.0482023710215125



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
central nervous system2.46e-3182
neural tube4.97e-3057
neural rod4.97e-3057
future spinal cord4.97e-3057
neural keel4.97e-3057
regional part of nervous system1.23e-2994
nervous system1.23e-2994
adult organism8.10e-29115
neural plate7.00e-2686
presumptive neural plate7.00e-2686
regional part of brain1.13e-2559
neurectoderm2.22e-2590
brain2.13e-2469
future brain2.13e-2469
tube1.12e-22194
anterior neural tube1.49e-2242
regional part of forebrain1.88e-2241
forebrain1.88e-2241
future forebrain1.88e-2241
telencephalon8.11e-2034
gray matter1.09e-1934
brain grey matter1.09e-1934
regional part of telencephalon3.33e-1933
cerebral hemisphere1.90e-1832
pre-chordal neural plate8.03e-1761
anatomical conduit1.19e-15241
ectoderm1.36e-15173
presumptive ectoderm1.36e-15173
ectoderm-derived structure1.42e-15169
regional part of cerebral cortex1.67e-1522
neocortex2.47e-1420
cerebral cortex2.49e-1425
pallium2.49e-1425
anterior region of body3.70e-13129
craniocervical region3.70e-13129
anatomical cluster3.87e-13286
head7.28e-13123
epithelium8.04e-10309
cell layer1.47e-09312
posterior neural tube1.40e-0815
chordal neural plate1.40e-0815
organ part1.80e-08219
segmental subdivision of nervous system1.44e-0713
segmental subdivision of hindbrain6.70e-0712
hindbrain6.70e-0712
presumptive hindbrain6.70e-0712
basal ganglion6.84e-079
nuclear complex of neuraxis6.84e-079
aggregate regional part of brain6.84e-079
collection of basal ganglia6.84e-079
cerebral subcortex6.84e-079
nucleus of brain7.45e-079
neural nucleus7.45e-079
multi-tissue structure7.53e-07347


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
EGR1#195854.156815912341780.001617966818864440.0101312330832414
ZBTB7A#5134144.901272871917260.004079628118843750.0194847158322551
ZNF263#1012745.481227758007120.002675609380607230.0147429549488888



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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