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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003056!1.99e-17!49;UBERON:0002346!8.06e-16!64;UBERON:0003075!8.06e-16!64;UBERON:0007284!8.06e-16!64;UBERON:0004121!4.78e-15!95;UBERON:0000924!4.78e-15!95;UBERON:0006601!4.78e-15!95;UBERON:0000970!8.43e-15!9;UBERON:0000019!8.43e-15!9;UBERON:0000047!8.43e-15!9;UBERON:0010312!8.43e-15!9;UBERON:0004088!8.43e-15!9;UBERON:0002104!8.43e-15!9;UBERON:0001456!8.43e-15!9;UBERON:0003072!8.43e-15!9;UBERON:0004128!8.43e-15!9;UBERON:0003071!8.43e-15!9;UBERON:0010371!3.07e-14!73;UBERON:0000020!3.42e-13!12;UBERON:0001032!3.42e-13!12;UBERON:0004456!3.42e-13!12;UBERON:0000033!5.03e-12!13;UBERON:0005085!5.03e-12!13;UBERON:0001444!8.33e-12!11;UBERON:0000073!1.68e-10!54;UBERON:0001017!3.01e-10!73;UBERON:0010314!6.86e-10!92;UBERON:0001016!8.12e-10!75;UBERON:0002950!2.27e-09!4;UBERON:0001891!2.27e-09!4;UBERON:0009616!2.27e-09!4;UBERON:0010286!2.27e-09!4;UBERON:0002420!8.06e-09!8;UBERON:0007245!8.06e-09!8;UBERON:0010009!8.06e-09!8;UBERON:0010011!8.06e-09!8;UBERON:0000454!8.06e-09!8;UBERON:0001049!2.44e-08!52;UBERON:0005068!2.44e-08!52;UBERON:0006241!2.44e-08!52;UBERON:0007135!2.44e-08!52;UBERON:0003080!3.48e-08!40;UBERON:0002616!9.75e-08!46;UBERON:0002038!1.44e-07!3;UBERON:0009663!1.44e-07!3;UBERON:0009661!1.44e-07!3;UBERON:0000125!1.44e-07!3;UBERON:0002308!1.44e-07!3;UBERON:0000955!1.71e-07!47;UBERON:0006238!1.71e-07!47;UBERON:0004684!2.02e-07!3;UBERON:0002275!2.02e-07!3;UBERON:0002780!3.21e-07!39;UBERON:0001890!3.21e-07!39;UBERON:0006240!3.21e-07!39;UBERON:0001894!4.91e-07!10;UBERON:0006222!4.91e-07!10
|ontology_enrichment_uberon=UBERON:0003056!1.99e-17!49;UBERON:0002346!8.06e-16!64;UBERON:0003075!8.06e-16!64;UBERON:0007284!8.06e-16!64;UBERON:0004121!4.78e-15!95;UBERON:0000924!4.78e-15!95;UBERON:0006601!4.78e-15!95;UBERON:0000970!8.43e-15!9;UBERON:0000019!8.43e-15!9;UBERON:0000047!8.43e-15!9;UBERON:0010312!8.43e-15!9;UBERON:0004088!8.43e-15!9;UBERON:0002104!8.43e-15!9;UBERON:0001456!8.43e-15!9;UBERON:0003072!8.43e-15!9;UBERON:0004128!8.43e-15!9;UBERON:0003071!8.43e-15!9;UBERON:0010371!3.07e-14!73;UBERON:0000020!3.42e-13!12;UBERON:0001032!3.42e-13!12;UBERON:0004456!3.42e-13!12;UBERON:0000033!5.03e-12!13;UBERON:0005085!5.03e-12!13;UBERON:0001444!8.33e-12!11;UBERON:0000073!1.68e-10!54;UBERON:0001017!3.01e-10!73;UBERON:0010314!6.86e-10!92;UBERON:0001016!8.12e-10!75;UBERON:0002950!2.27e-09!4;UBERON:0001891!2.27e-09!4;UBERON:0009616!2.27e-09!4;UBERON:0010286!2.27e-09!4;UBERON:0002420!8.06e-09!8;UBERON:0007245!8.06e-09!8;UBERON:0010009!8.06e-09!8;UBERON:0010011!8.06e-09!8;UBERON:0000454!8.06e-09!8;UBERON:0001049!2.44e-08!52;UBERON:0005068!2.44e-08!52;UBERON:0006241!2.44e-08!52;UBERON:0007135!2.44e-08!52;UBERON:0003080!3.48e-08!40;UBERON:0002616!9.75e-08!46;UBERON:0002038!1.44e-07!3;UBERON:0009663!1.44e-07!3;UBERON:0009661!1.44e-07!3;UBERON:0000125!1.44e-07!3;UBERON:0002308!1.44e-07!3;UBERON:0000955!1.71e-07!47;UBERON:0006238!1.71e-07!47;UBERON:0004684!2.02e-07!3;UBERON:0002275!2.02e-07!3;UBERON:0002780!3.21e-07!39;UBERON:0001890!3.21e-07!39;UBERON:0006240!3.21e-07!39;UBERON:0001894!4.91e-07!10;UBERON:0006222!4.91e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.087078,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.746305,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,1.41491,0.545768,0.489529,0.44579,0.727684,0.404661,0.537749,0.757752,1.38127,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.253145,0.425309,0.20704,0.384813,0.699032,0.360612,0.328675,1.03785,0.631725,0.419293,0.426986,0.4934,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.257421,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.796301,1.1148,0.0793594,0.0882907,1.20595,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,1.46478,1.05152,0.848095,0.590368,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.0998646,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,1.77493,1.43666,2.70447,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,1.98178,2.18247,0.569503,0.408309,0.230371,0.133815,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,1.14345
}}
}}

Revision as of 20:29, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr6:124789985..124790034,-p1@Gnb3
Mm9::chr7:130174860..130174906,+p1@uc009jpa.1
Mm9::chr8:28479265..28479279,+p1@Chrnb3
Mm9::chr8:28524351..28524364,-p1@Chrna6
Mm9::chr8:28524409..28524418,-p2@Chrna6


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

GO IDGO nameFDR corrected p-value
GO:0007271synaptic transmission, cholinergic8.6003638539287e-05
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity8.6003638539287e-05
GO:0005231excitatory extracellular ligand-gated ion channel activity0.000541929406359434
GO:0005230extracellular ligand-gated ion channel activity0.000902009987176167
GO:0015276ligand-gated ion channel activity0.000902009987176167
GO:0022834ligand-gated channel activity0.000902009987176167
GO:0030594neurotransmitter receptor activity0.000902009987176167
GO:0042165neurotransmitter binding0.000902009987176167
GO:0045211postsynaptic membrane0.00123189256685554
GO:0044456synapse part0.0013669119896086
GO:0007268synaptic transmission0.00306546162485347
GO:0019226transmission of nerve impulse0.00390432643555917
GO:0044459plasma membrane part0.00390432643555917
GO:0005261cation channel activity0.00390432643555917
GO:0022836gated channel activity0.00417251402309012
GO:0046873metal ion transmembrane transporter activity0.00466767539808082
GO:0014059regulation of dopamine secretion0.0047926820287058
GO:0014046dopamine secretion0.0047926820287058
GO:0007267cell-cell signaling0.00497758359007022
GO:0050433regulation of catecholamine secretion0.00497758359007022
GO:0005216ion channel activity0.00497758359007022
GO:0005886plasma membrane0.00497758359007022
GO:0022838substrate specific channel activity0.00497758359007022
GO:0050432catecholamine secretion0.00497758359007022
GO:0022803passive transmembrane transporter activity0.00497758359007022
GO:0015267channel activity0.00497758359007022
GO:0030054cell junction0.0050521666090356
GO:0005892nicotinic acetylcholine-gated receptor-channel complex0.00594790648019933
GO:0003993acid phosphatase activity0.00594790648019933
GO:0008324cation transmembrane transporter activity0.00643070053725156
GO:0051899membrane depolarization0.00945546203797659
GO:0046928regulation of neurotransmitter secretion0.00969826959635346
GO:0015075ion transmembrane transporter activity0.0107477629438982
GO:0004890GABA-A receptor activity0.0123374528278361
GO:0006811ion transport0.0123374528278361
GO:0060089molecular transducer activity0.0123374528278361
GO:0004871signal transducer activity0.0123374528278361
GO:0022891substrate-specific transmembrane transporter activity0.0123374528278361
GO:0016917GABA receptor activity0.0123716352329554
GO:0005834heterotrimeric G-protein complex0.0142124383203555
GO:0022857transmembrane transporter activity0.0152784281800477
GO:0046879hormone secretion0.0168096521810302
GO:0042391regulation of membrane potential0.0168182646960398
GO:0022892substrate-specific transporter activity0.017037543320729
GO:0019897extrinsic to plasma membrane0.0187752593651088
GO:0007269neurotransmitter secretion0.0187752593651088
GO:0051046regulation of secretion0.0187752593651088
GO:0007154cell communication0.0187752593651088
GO:0045055regulated secretory pathway0.0224626122373204
GO:0019898extrinsic to membrane0.0237266452172607
GO:0043235receptor complex0.0242687884136653
GO:0003001generation of a signal involved in cell-cell signaling0.0285174909041151
GO:0001505regulation of neurotransmitter levels0.0285174909041151
GO:0043234protein complex0.0400603620266142
GO:0003924GTPase activity0.041739751496872
GO:0055082cellular chemical homeostasis0.0437631748158408
GO:0006873cellular ion homeostasis0.0437631748158408
GO:0050877neurological system process0.0437631748158408
GO:0005083small GTPase regulator activity0.0438053474380967
GO:0050801ion homeostasis0.0473152438728316
GO:0003008system process0.0482476081683852
GO:0045045secretory pathway0.0482476081683852



Relative expression of the co-expression cluster over median <br>Analyst:




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
CNS neuron (sensu Vertebrata)2.22e-1023
neuroblast (sensu Vertebrata)2.22e-1023
neuron of the substantia nigra1.44e-073
neuron1.47e-0733
neuronal stem cell1.47e-0733
neuroblast1.47e-0733
electrically signaling cell1.47e-0733
raphe nuclei neuron2.02e-073

Uber Anatomy
Ontology termp-valuen
pre-chordal neural plate1.99e-1749
neurectoderm8.06e-1664
neural plate8.06e-1664
presumptive neural plate8.06e-1664
ectoderm-derived structure4.78e-1595
ectoderm4.78e-1595
presumptive ectoderm4.78e-1595
eye8.43e-159
camera-type eye8.43e-159
simple eye8.43e-159
immature eye8.43e-159
ocular region8.43e-159
visual system8.43e-159
face8.43e-159
optic cup8.43e-159
optic vesicle8.43e-159
eye primordium8.43e-159
ecto-epithelium3.07e-1473
sense organ3.42e-1312
sensory system3.42e-1312
entire sense organ system3.42e-1312
head5.03e-1213
ectodermal placode5.03e-1213
subdivision of head8.33e-1211
regional part of nervous system1.68e-1054
central nervous system3.01e-1073
structure with developmental contribution from neural crest6.86e-1092
nervous system8.12e-1075
regional part of midbrain2.27e-094
midbrain2.27e-094
presumptive midbrain2.27e-094
midbrain neural tube2.27e-094
basal ganglion8.06e-098
nuclear complex of neuraxis8.06e-098
aggregate regional part of brain8.06e-098
collection of basal ganglia8.06e-098
cerebral subcortex8.06e-098
neural tube2.44e-0852
neural rod2.44e-0852
future spinal cord2.44e-0852
neural keel2.44e-0852
anterior neural tube3.48e-0840
regional part of brain9.75e-0846
substantia nigra1.44e-073
telencephalic nucleus1.44e-073
midbrain nucleus1.44e-073
neural nucleus1.44e-073
nucleus of brain1.44e-073
brain1.71e-0747
future brain1.71e-0747
raphe nuclei2.02e-073
reticular formation2.02e-073
regional part of forebrain3.21e-0739
forebrain3.21e-0739
future forebrain3.21e-0739
diencephalon4.91e-0710
future diencephalon4.91e-0710


TFBS overrepresentation<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}}}

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