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MCL coexpression mm9:303: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.14e-30!54;UBERON:0001049!1.08e-28!52;UBERON:0005068!1.08e-28!52;UBERON:0006241!1.08e-28!52;UBERON:0007135!1.08e-28!52;UBERON:0001017!2.28e-28!73;UBERON:0002346!5.39e-27!64;UBERON:0003075!5.39e-27!64;UBERON:0007284!5.39e-27!64;UBERON:0001016!5.71e-27!75;UBERON:0000955!3.59e-24!47;UBERON:0006238!3.59e-24!47;UBERON:0002616!1.79e-23!46;UBERON:0004121!3.17e-22!95;UBERON:0000924!3.17e-22!95;UBERON:0006601!3.17e-22!95;UBERON:0010314!2.77e-21!92;UBERON:0010371!5.33e-21!73;UBERON:0003056!3.14e-19!49;UBERON:0002020!1.71e-18!34;UBERON:0003080!1.95e-18!40;UBERON:0002780!1.22e-17!39;UBERON:0001890!1.22e-17!39;UBERON:0006240!1.22e-17!39;UBERON:0003528!1.43e-14!29;UBERON:0002791!1.43e-14!29;UBERON:0001893!1.43e-14!29;UBERON:0003076!4.08e-11!12;UBERON:0003057!4.08e-11!12;UBERON:0000956!1.08e-09!21;UBERON:0001869!1.08e-09!21;UBERON:0000203!1.08e-09!21;UBERON:0002619!2.63e-09!17;UBERON:0000025!3.37e-09!114;UBERON:0002021!1.43e-08!10;UBERON:0000411!1.43e-08!10;UBERON:0001950!1.43e-08!10;UBERON:0004111!6.68e-08!122
|ontology_enrichment_uberon=UBERON:0000073!1.14e-30!54;UBERON:0001049!1.08e-28!52;UBERON:0005068!1.08e-28!52;UBERON:0006241!1.08e-28!52;UBERON:0007135!1.08e-28!52;UBERON:0001017!2.28e-28!73;UBERON:0002346!5.39e-27!64;UBERON:0003075!5.39e-27!64;UBERON:0007284!5.39e-27!64;UBERON:0001016!5.71e-27!75;UBERON:0000955!3.59e-24!47;UBERON:0006238!3.59e-24!47;UBERON:0002616!1.79e-23!46;UBERON:0004121!3.17e-22!95;UBERON:0000924!3.17e-22!95;UBERON:0006601!3.17e-22!95;UBERON:0010314!2.77e-21!92;UBERON:0010371!5.33e-21!73;UBERON:0003056!3.14e-19!49;UBERON:0002020!1.71e-18!34;UBERON:0003080!1.95e-18!40;UBERON:0002780!1.22e-17!39;UBERON:0001890!1.22e-17!39;UBERON:0006240!1.22e-17!39;UBERON:0003528!1.43e-14!29;UBERON:0002791!1.43e-14!29;UBERON:0001893!1.43e-14!29;UBERON:0003076!4.08e-11!12;UBERON:0003057!4.08e-11!12;UBERON:0000956!1.08e-09!21;UBERON:0001869!1.08e-09!21;UBERON:0000203!1.08e-09!21;UBERON:0002619!2.63e-09!17;UBERON:0000025!3.37e-09!114;UBERON:0002021!1.43e-08!10;UBERON:0000411!1.43e-08!10;UBERON:0001950!1.43e-08!10;UBERON:0004111!6.68e-08!122
|tfbs_overrepresentation_for_novel_motifs=0.282271,0.242881,0.90749,0.10379,0.125245,0.359101,0.955578,0.140657,0.15395,0.413774,0.137777,0.475202,0.140984,0.172248,0.329595,0,0.309751,1.20909,0.969939,0.0862686,0.0558898,0.0929341,0.17167,0.123801,1.93176,0.19018,0.110597,0.389073,0.170987,0.66723,0.115155,0.390688,0.278799,1.81963,2.89275,0.598606,0.107578,0.154752,0.0893077,0.177786,0.535222,0.376228,0.144845,0.0360344,0.407249,1.10422,0.249844,0.131897,1.24786,0.174161,0.296304,0.59969,0.135351,0.511069,0.526356,0.176842,0.0489568,0.455754,1.17736,0.175527,0.37428,0.214788,0.0648948,0.287721,0.184085,0.318903,0.648538,0.976882,0.370478,0.836509,0.489831,0.512402,0.191772,0.555978,0.0311842,0.0804149,0.345431,0.678017,0.360359,0.0575393,0.150594,0.32329,0.612722,0.27149,0.455476,0.949552,0.000471751,0.931187,0.253413,2.55781,0.712592,1.16313,0.401262,0.892801,0.0193136,0.0728776,0.137297,0.403591,0.697528,0.0468111,0.0253676,0.390457,0.495886,0.29676,0.295953,0.117743,0.342607,0.406177,0.470494,0.0565866,0.273137,0.497436,0.211055,0.140823,0.719117,1.65508,0.125669,0.105758,0.31076,1.12635,0.560777,0.271955,0.19139,0.240971,0.769516,0.953191,0.169628,0.395657,0.647155,1.75533,0.481183,0.100024,0.620289,0.185736,0.739171,0.59964,0.611408,0.378248,1.65678,1.49553,1.10287,0.652839,0.199449,0.399329,0.291009,0.376878,0.252115,1.45635,0.296414,0.875254,0.94828,0.142541,0.512441,0.198234,0.544151,0.584782,0.208987,0.153464,0.0817634,0.0867803,0.702412,0.454746,0.363706,0.964644,0.785711,0.180287,0.782143,0.472773,0.0439875
}}
}}

Revision as of 18:08, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:69413509..69413520,-p@chr11:69413509..69413520
-
Mm9::chr11:69413515..69413542,+p@chr11:69413515..69413542
+
Mm9::chr11:69413654..69413671,-p@chr11:69413654..69413671
-
Mm9::chr11:69413749..69413773,-p@chr11:69413749..69413773
-
Mm9::chr11:69414255..69414260,-p@chr11:69414255..69414260
-
Mm9::chr11:69414283..69414297,-p@chr11:69414283..69414297
-
Mm9::chr11:69414455..69414467,-p@chr11:69414455..69414467
-
Mm9::chr11:69414477..69414488,-p@chr11:69414477..69414488
-
Mm9::chr11:69414521..69414532,-p@chr11:69414521..69414532
-
Mm9::chr11:69414640..69414649,-p@chr11:69414640..69414649
-
Mm9::chr11:69414665..69414705,+p@chr11:69414665..69414705
+
Mm9::chr11:69414740..69414751,+p@chr11:69414740..69414751
+
Mm9::chr11:69415954..69415967,-p@chr11:69415954..69415967
-
Mm9::chr11:69416245..69416285,-p2@Atp1b2
Mm9::chr11:69416312..69416334,-p4@Atp1b2
Mm9::chr11:69416350..69416362,-p3@Atp1b2
Mm9::chr11:69417040..69417064,-p6@Atp1b2
Mm9::chr11:69419455..69419473,-p1@Atp1b2
Mm9::chr12:112908947..112908956,-p@chr12:112908947..112908956
-
Mm9::chr12:112909692..112909703,-p@chr12:112909692..112909703
-
Mm9::chr1:137271496..137271510,-p4@Shisa4
Mm9::chr2:25978289..25978358,-p1@Nacc2
Mm9::chr2:92229169..92229176,-p@chr2:92229169..92229176
-
Mm9::chr7:4084759..4084771,+p6@Ttyh1
Mm9::chr8:113251010..113251031,+p6@Mtss1l
Mm9::chr8:113264957..113264971,+p@chr8:113264957..113264971
+
Mm9::chr9:37193490..37193505,+p@chr9:37193490..37193505
+


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:0031527filopodium membrane0.00438284117679286
GO:0032433filopodium tip0.00438284117679286
GO:0046847filopodium formation0.0101871281319128
GO:0022610biological adhesion0.0101871281319128
GO:0007155cell adhesion0.0101871281319128
GO:0030035microspike biogenesis0.0101871281319128
GO:0031253cell projection membrane0.0101871281319128
GO:0005391sodium:potassium-exchanging ATPase activity0.0101871281319128
GO:0015075ion transmembrane transporter activity0.0101871281319128
GO:0030175filopodium0.0101871281319128
GO:0006811ion transport0.0101871281319128
GO:0022891substrate-specific transmembrane transporter activity0.0101871281319128
GO:0022857transmembrane transporter activity0.0126179115188622
GO:0022892substrate-specific transporter activity0.0140635193250359
GO:0030031cell projection biogenesis0.0258363874601177
GO:0043168anion binding0.0258363874601177
GO:0031404chloride ion binding0.0258363874601177
GO:0005254chloride channel activity0.0258363874601177
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0258363874601177
GO:0005253anion channel activity0.0258363874601177
GO:0030424axon0.0258363874601177
GO:0031589cell-substrate adhesion0.0258683639415299
GO:0044463cell projection part0.0258683639415299
GO:0031402sodium ion binding0.0283385692941129
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.0283385692941129
GO:0030955potassium ion binding0.0316754946025582
GO:0008509anion transmembrane transporter activity0.0316754946025582
GO:0006814sodium ion transport0.0316754946025582
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.0316754946025582
GO:0043492ATPase activity, coupled to movement of substances0.0316754946025582
GO:0043005neuron projection0.0316754946025582
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.0316754946025582
GO:0015399primary active transmembrane transporter activity0.0328854058322195
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0328854058322195
GO:0006810transport0.0349959185640569
GO:0051234establishment of localization0.0358865332238167
GO:0006813potassium ion transport0.0360963500426349
GO:0031420alkali metal ion binding0.0406327701735411
GO:0051179localization0.0422168481824396
GO:0016337cell-cell adhesion0.0453230729897579
GO:0042623ATPase activity, coupled0.0478091709644383



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)1.11e-0923
neuroblast (sensu Vertebrata)1.11e-0923
neural cell1.19e-0843
oligodendrocyte precursor cell2.96e-088
ectodermal cell3.09e-0844
neurectodermal cell3.09e-0844

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.14e-3054
neural tube1.08e-2852
neural rod1.08e-2852
future spinal cord1.08e-2852
neural keel1.08e-2852
central nervous system2.28e-2873
neurectoderm5.39e-2764
neural plate5.39e-2764
presumptive neural plate5.39e-2764
nervous system5.71e-2775
brain3.59e-2447
future brain3.59e-2447
regional part of brain1.79e-2346
ectoderm-derived structure3.17e-2295
ectoderm3.17e-2295
presumptive ectoderm3.17e-2295
structure with developmental contribution from neural crest2.77e-2192
ecto-epithelium5.33e-2173
pre-chordal neural plate3.14e-1949
gray matter1.71e-1834
anterior neural tube1.95e-1840
regional part of forebrain1.22e-1739
forebrain1.22e-1739
future forebrain1.22e-1739
brain grey matter1.43e-1429
regional part of telencephalon1.43e-1429
telencephalon1.43e-1429
posterior neural tube4.08e-1112
chordal neural plate4.08e-1112
cerebral cortex1.08e-0921
cerebral hemisphere1.08e-0921
pallium1.08e-0921
regional part of cerebral cortex2.63e-0917
tube3.37e-09114
occipital lobe1.43e-0810
visual cortex1.43e-0810
neocortex1.43e-0810
anatomical conduit6.68e-08122


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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