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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0.028634144538123,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0948150061477135,0.0486434570126431,0,0,0,0,0,0,0.141585146406929,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.222898696087275,0,0,0,0,0,0,0,0,0,0.109385271437853,0.0674541896311435,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0601047609904605,0.0735024167162535,0,0.195853163289917,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0274425697329547,0.0200772476130825,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.124359684677195,0.210511970731412,0.165938108170999,0,0,0,0.0409115770312979,0.0488578057762586,0,0,0,0,0,0,0.116477838004171,0.111921665553284,0,0.193144374620797,0.109220265464527,0.0462323500298593,0.0737599324415275,0.0389057955862181,0,0,0,0,0,1.17287126299839,0.765810059972191,1.13615381717177,0,0.0955099827348378,0,0.043091003966008,0,0,0.0368915873061208,0,0,0,0,0,0.218271929570873,0.260237021365284,0.258138737031236,0.309589338478661,0,0,0,0,0.0315769459313356,0.102652952998,0,0,0,0.0704711668661905,0,0,0,0,0,0.0268778959456436,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0491651531067128,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0470116456051225,0,0.0191274234626113,0,0,0,0.0255225165518001,0,0.00371961432030532,0,0.0150861578868698,0.187714149751285,0,0,0.168731663884515,0,0,0,0,0.13886178198573,0,0,0,0,0,0.552081338731016,0,0,0,0.108749900605002,0,0,0,0,0,0,0,0,0,0.081690510286996,0.0381727496096321,0.0260799816909174,0.124784362006013,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0494890391677645,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0199492791535359,0.118636512662129,0,0.524007057962459,0,0,0.137869874270884,0.0820941343801505,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.09676009440352,0.134651449134576,0,0,0,0,0,0,0.149878655281768,0.351891361498639,0,0,0.015102493169016,0.0728306106181875,0.0529736480204785,0.088604497554754,0,0,0,0.0186870206110147,0.066456656622747,0,0.072220723274582,0,0,0.443136730842731,0.422988937621355,0,0.12536649610766,0.0350041483061456,0.179252786239994,0.0445261220331668,0,0.0698055338742055,0,0,0,0.442712183231462,0.355184038695554,0,0.18099954196763,0.20169617591284,0,0.0224537236175799,0.075879647038307,0.0502830992415575,0.0234313003199337,0,0.139099640262965,0,0,0.0190312847642998,0,0,0,0,0,0,0,0,0,0,0,0.0287100059321783,0,0,0.206837282313239,0.26853917391645,0,0,0,0.542574711919846,0,0.528876430235764,0,0.0388046890849592,0.0471971940941162,0,0.172187014549508,0.0579836861320005,0.0596168721809695,0,0.0214231979817236,0,0,0,0,0,0,0,0.055963310743525,0.0181265992698805,0.0349684140344003,0,0.0384135155082754,0.0556912948411375,0.0330195635144494,0.099594193731599,0,0.473921283548165,0,0,0.152527675384129,0.0716796069902135,0,0.221047270975146,0.127544360324407,0.0988279329297035,0,0,0,0.0254319378601874,0.116127204725986,0,0.0412500915278073,0,0,0.772036773303397,0.890333914674653,0,0,0,0.053483212730439,0,0,0.0395325284566706,0,0.0437436691566279,0.0628897971277475,0,0.167724887724989,0.62211578637496,0.507992530966876,0.54507188148275,0.0203856949807491,0,0.413376786607389,0.316346884126087,0,0,0,0,0.116747424500323,0.0897514814751763,0.18476922128841,0.172793600408162,0.106021193294471,0,0.343874260504686,0.038122678605483,0.234186964128339,0.183135248021629,0,0,0,0,0,0,0,0,0.816178186829712,1.1790883744162,0.793707226733825,0.843780117875678,0.0342945499340054,0,0.21833928623098,0.105936176093491,0.212192199304138,0,0,0,0,0.0559136822081735,0.0485748203103998,0,0,0,0.359185988645896,0.263586001002477,0.527840418241696,0.643775958726934,0.67113865187077,0.306286152070362,0,0,0,0.054530184537229,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0421883161150136,0,0,0,0,0,0,0,0,0,0,0,0.064430608766392,0,0.478824226384254,0,0,0,0,0,0,0,0,0,0,0,0.0535640988402175,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.137325537934018,0.191635249296839,0.692922417161277,0.372323971685461,0,0.137367147633154,0.303075694256934,0.868657808051376,0,0.0242150211128343,0.005751508945759,0.045138081246376,0,0,0,0.069317366406359,0,0.118520820056196,0.0505136221569435,0,0.0562542693604755,0.143184082295681,0.653012569191112,0.59449747346862,0.156490202967336,0,0,0.149690703132035,0,0.138728620224051,0,0.062949339066792,0.103003290575171,0.0814799028177415,0.018454584201652,0,0,0.270912302615351,0.24393395016608,0.0460773347506069,0,0.113738814901745,0.335574406756852,0,0.140875500847939,0,0.0848007320360465,0.175695076475432,0,0,0,0,0.0247369286046295,0.0061032521575735,0.114105145323331,0,0,0,0,0.105299503402751,0,0,0.40203769485959,0.0719133411296425,0.119212194772075,0,0.164117496515407,0,0,0,0,0,0,0,0,0.265253456943828,0,0,0.0476105437811573,0,0.829207083863547,0.901959799284958,0.4244273788878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|full_id=C2327_Hepatocyte_spinal_liver_normal_optic_tubular_corpus
|full_id=C2327_Hepatocyte_spinal_liver_normal_optic_tubular_corpus
|gostat_on_coexpression_clusters=GO:0007267!cell-cell signaling!0.000805307766608751!5046;1942;7018$GO:0015682!ferric iron transport!0.00267131755563405!7018$GO:0015091!ferric iron transmembrane transporter activity!0.00267131755563405!7018$GO:0031643!positive regulation of myelination!0.00267131755563405!7018$GO:0031641!regulation of myelination!0.00854746129459153!7018$GO:0005381!iron ion transmembrane transporter activity!0.00915745506820525!7018$GO:0046875!ephrin receptor binding!0.00915745506820525!1942$GO:0031646!positive regulation of neurological process!0.0106830685655978!7018$GO:0014070!response to organic cyclic substance!0.0130559306666949!7018$GO:0030139!endocytic vesicle!0.021351044647696!7018$GO:0031644!regulation of neurological process!0.021351044647696!7018$GO:0042552!myelination!0.021351044647696!7018$GO:0046915!transition metal ion transmembrane transporter activity!0.021351044647696!7018$GO:0007272!ensheathment of neurons!0.021351044647696!7018$GO:0006953!acute-phase response!0.021351044647696!7018$GO:0008366!axon ensheathment!0.021351044647696!7018$GO:0004289!subtilase activity!0.0219408985330224!5046$GO:0008199!ferric iron binding!0.0219408985330224!7018$GO:0001508!regulation of action potential!0.0224694898948729!7018$GO:0001666!response to hypoxia!0.024322277194695!7018$GO:0007154!cell communication!0.024322277194695!5046;1942;7018$GO:0015082!di-, tri-valent inorganic cation transmembrane transporter activity!0.024322277194695!7018$GO:0055072!iron ion homeostasis!0.024322277194695!7018$GO:0006879!cellular iron ion homeostasis!0.024322277194695!7018$GO:0006826!iron ion transport!0.024322277194695!7018$GO:0010033!response to organic substance!0.0254345330902621!7018$GO:0002526!acute inflammatory response!0.0311925781763437!7018$GO:0000041!transition metal ion transport!0.0388092979149681!7018$GO:0048503!GPI anchor binding!0.0462550364175995!1942
|gostat_on_coexpression_clusters=GO:0007267!cell-cell signaling!0.000805307766608751!5046;1942;7018$GO:0015682!ferric iron transport!0.00267131755563405!7018$GO:0015091!ferric iron transmembrane transporter activity!0.00267131755563405!7018$GO:0031643!positive regulation of myelination!0.00267131755563405!7018$GO:0031641!regulation of myelination!0.00854746129459153!7018$GO:0005381!iron ion transmembrane transporter activity!0.00915745506820525!7018$GO:0046875!ephrin receptor binding!0.00915745506820525!1942$GO:0031646!positive regulation of neurological process!0.0106830685655978!7018$GO:0014070!response to organic cyclic substance!0.0130559306666949!7018$GO:0030139!endocytic vesicle!0.021351044647696!7018$GO:0031644!regulation of neurological process!0.021351044647696!7018$GO:0042552!myelination!0.021351044647696!7018$GO:0046915!transition metal ion transmembrane transporter activity!0.021351044647696!7018$GO:0007272!ensheathment of neurons!0.021351044647696!7018$GO:0006953!acute-phase response!0.021351044647696!7018$GO:0008366!axon ensheathment!0.021351044647696!7018$GO:0004289!subtilase activity!0.0219408985330224!5046$GO:0008199!ferric iron binding!0.0219408985330224!7018$GO:0001508!regulation of action potential!0.0224694898948729!7018$GO:0001666!response to hypoxia!0.024322277194695!7018$GO:0007154!cell communication!0.024322277194695!5046;1942;7018$GO:0015082!di-, tri-valent inorganic cation transmembrane transporter activity!0.024322277194695!7018$GO:0055072!iron ion homeostasis!0.024322277194695!7018$GO:0006879!cellular iron ion homeostasis!0.024322277194695!7018$GO:0006826!iron ion transport!0.024322277194695!7018$GO:0010033!response to organic substance!0.0254345330902621!7018$GO:0002526!acute inflammatory response!0.0311925781763437!7018$GO:0000041!transition metal ion transport!0.0388092979149681!7018$GO:0048503!GPI anchor binding!0.0462550364175995!1942

Revision as of 15:02, 12 September 2012


Full id: C2327_Hepatocyte_spinal_liver_normal_optic_tubular_corpus



Phase1 CAGE Peaks

Hg19::chr15:102029900..102029917,-p1@PCSK6
Hg19::chr1:155099927..155099964,+p4@EFNA1
Hg19::chr3:133493719..133493723,+p11@TF
Hg19::chr3:133497553..133497587,+p@chr3:133497553..133497587
+


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:0007267cell-cell signaling0.000805307766608751
GO:0015682ferric iron transport0.00267131755563405
GO:0015091ferric iron transmembrane transporter activity0.00267131755563405
GO:0031643positive regulation of myelination0.00267131755563405
GO:0031641regulation of myelination0.00854746129459153
GO:0005381iron ion transmembrane transporter activity0.00915745506820525
GO:0046875ephrin receptor binding0.00915745506820525
GO:0031646positive regulation of neurological process0.0106830685655978
GO:0014070response to organic cyclic substance0.0130559306666949
GO:0030139endocytic vesicle0.021351044647696
GO:0031644regulation of neurological process0.021351044647696
GO:0042552myelination0.021351044647696
GO:0046915transition metal ion transmembrane transporter activity0.021351044647696
GO:0007272ensheathment of neurons0.021351044647696
GO:0006953acute-phase response0.021351044647696
GO:0008366axon ensheathment0.021351044647696
GO:0004289subtilase activity0.0219408985330224
GO:0008199ferric iron binding0.0219408985330224
GO:0001508regulation of action potential0.0224694898948729
GO:0001666response to hypoxia0.024322277194695
GO:0007154cell communication0.024322277194695
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.024322277194695
GO:0055072iron ion homeostasis0.024322277194695
GO:0006879cellular iron ion homeostasis0.024322277194695
GO:0006826iron ion transport0.024322277194695
GO:0010033response to organic substance0.0254345330902621
GO:0002526acute inflammatory response0.0311925781763437
GO:0000041transition metal ion transport0.0388092979149681
GO:0048503GPI anchor binding0.0462550364175995



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
adult organism1.98e-42115
neural tube3.05e-2657
neural rod3.05e-2657
future spinal cord3.05e-2657
neural keel3.05e-2657
central nervous system5.63e-2182
regional part of brain6.22e-2159
anterior neural tube1.11e-2042
regional part of forebrain1.91e-2041
forebrain1.91e-2041
future forebrain1.91e-2041
brain4.17e-2069
future brain4.17e-2069
organ1.81e-19511
neural plate6.86e-1986
presumptive neural plate6.86e-1986
neurectoderm7.15e-1990
regional part of nervous system8.94e-1994
nervous system8.94e-1994
gray matter2.63e-1834
brain grey matter2.63e-1834
telencephalon3.74e-1834
regional part of telencephalon1.27e-1733
cerebral hemisphere7.68e-1732
multi-cellular organism8.22e-17659
anatomical system3.62e-16625
anatomical group7.58e-16626
embryo3.01e-15612
organ part4.61e-15219
embryonic structure2.82e-14605
developing anatomical structure2.82e-14605
germ layer5.01e-14604
embryonic tissue5.01e-14604
presumptive structure5.01e-14604
epiblast (generic)5.01e-14604
tube1.23e-13194
anatomical conduit2.30e-13241
pre-chordal neural plate4.43e-1361
regional part of cerebral cortex5.84e-1322
cerebral cortex8.07e-1325
pallium8.07e-1325
neocortex8.38e-1220
anatomical cluster1.59e-11286
anterior region of body2.26e-11129
craniocervical region2.26e-11129
ectoderm2.45e-11173
presumptive ectoderm2.45e-11173
subdivision of digestive tract3.95e-11129
endodermal part of digestive tract3.95e-11129
ectoderm-derived structure3.97e-11169
head5.24e-11123
multi-tissue structure4.09e-10347
immaterial anatomical entity3.72e-09126
epithelium3.84e-09309
foregut4.17e-0998
cell layer8.77e-09312
endoderm-derived structure1.59e-08169
endoderm1.59e-08169
presumptive endoderm1.59e-08169
digestive system5.42e-08155
digestive tract5.42e-08155
primitive gut5.42e-08155
primordium8.46e-08168
trunk region element8.82e-08107
mixed endoderm/mesoderm-derived structure1.66e-07130
epithelium of foregut-midgut junction3.50e-0725
anatomical boundary3.50e-0725
hepatobiliary system3.50e-0725
foregut-midgut junction3.50e-0725
septum transversum3.50e-0725
organism subdivision3.82e-07365
nucleus of brain4.59e-079
neural nucleus4.59e-079
posterior neural tube8.60e-0715
chordal neural plate8.60e-0715


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

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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