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MCL coexpression mm9:950: Difference between revisions

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{{MCL_coexpression_mm9
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development;0.0182440954919215;18992,13865!GO:0007399;nervous system development;0.0182440954919215;18992,13865,76829!GO:0021985;neurohypophysis development;0.0182440954919215;18992!GO:0021979;hypothalamus cell differentiation;0.0182440954919215;18992!GO:0021854;hypothalamus development;0.0182440954919215;18992!GO:0014002;astrocyte development;0.0182440954919215;18992!GO:0007275;multicellular organismal development;0.0182440954919215;18992,13865,210801,76829!GO:0007420;brain development;0.0188232323511003;18992,13865!GO:0007417;central nervous system development;0.0262641336253937;18992,13865!GO:0048708;astrocyte differentiation;0.0272494907522483;18992!GO:0048468;cell development;0.0272494907522483;18992,13865,210801!GO:0005066;transmembrane receptor protein tyrosine kinase signaling protein activity;0.0272494907522483;76829!GO:0032502;developmental process;0.0272494907522483;18992,13865,210801,76829!GO:0021761;limbic system development;0.0272494907522483;18992!GO:0021782;glial cell development;0.0272494907522483;18992!GO:0048699;generation of neurons;0.0272494907522483;18992,13865!GO:0022008;neurogenesis;0.0284510300394729;18992,13865!GO:0051726;regulation of cell cycle;0.0284510300394729;67874,13865!GO:0005158;insulin receptor binding;0.0284510300394729;76829!GO:0021983;pituitary gland development;0.0346253249444564;18992!GO:0005667;transcription factor complex;0.0346253249444564;18992,13865!GO:0043565;sequence-specific DNA binding;0.0346253249444564;18992,13865!GO:0021536;diencephalon development;0.0346253249444564;18992!GO:0007346;regulation of progression through mitotic cell cycle;0.0346253249444564;67874!GO:0040018;positive regulation of multicellular organism growth;0.0363934379296313;18992!GO:0048731;system development;0.0363934379296313;18992,13865,76829!GO:0048869;cellular developmental process;0.0364605932289762;18992,13865,210801!GO:0030154;cell differentiation;0.0364605932289762;18992,13865,210801!GO:0045927;positive regulation of growth;0.037227588631002;18992!GO:0044451;nucleoplasm part;0.038908235570802;18992,13865!GO:0050770;regulation of axonogenesis;0.03957321597384;18992!GO:0005654;nucleoplasm;0.03957321597384;18992,13865!GO:0022402;cell cycle process;0.03957321597384;67874,13865!GO:0032501;multicellular organismal process;0.0406879389792971;18992,13865,210801,76829!GO:0048856;anatomical structure development;0.0418516328902436;18992,13865,76829!GO:0010001;glial cell differentiation;0.043772319167139;18992!GO:0042063;gliogenesis;0.0455443637192678;18992!GO:0031981;nuclear lumen;0.0455443637192678;18992,13865!GO:0007050;cell cycle arrest;0.0455443637192678;67874!GO:0050767;regulation of neurogenesis;0.0455443637192678;18992!GO:0003707;steroid hormone receptor activity;0.0455443637192678;13865!GO:0004879;ligand-dependent nuclear receptor activity;0.0455443637192678;13865!GO:0035270;endocrine system development;0.0455443637192678;18992!GO:0032403;protein complex binding;0.0455443637192678;76829!GO:0007049;cell cycle;0.0455443637192678;67874,13865!GO:0040014;regulation of multicellular organism growth;0.0464596593620089;18992!GO:0031974;membrane-enclosed lumen;0.0464596593620089;18992,13865!GO:0043233;organelle lumen;0.0464596593620089;18992,13865!GO:0001764;neuron 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|gostat_on_MCL_coexpression=GO:0030900;forebrain development;0.0182440954919215;18992,13865!GO:0007399;nervous system development;0.0182440954919215;18992,13865,76829!GO:0021985;neurohypophysis development;0.0182440954919215;18992!GO:0021979;hypothalamus cell differentiation;0.0182440954919215;18992!GO:0021854;hypothalamus development;0.0182440954919215;18992!GO:0014002;astrocyte development;0.0182440954919215;18992!GO:0007275;multicellular organismal development;0.0182440954919215;18992,13865,210801,76829!GO:0007420;brain development;0.0188232323511003;18992,13865!GO:0007417;central nervous system development;0.0262641336253937;18992,13865!GO:0048708;astrocyte differentiation;0.0272494907522483;18992!GO:0048468;cell development;0.0272494907522483;18992,13865,210801!GO:0005066;transmembrane receptor protein tyrosine kinase signaling protein activity;0.0272494907522483;76829!GO:0032502;developmental process;0.0272494907522483;18992,13865,210801,76829!GO:0021761;limbic system development;0.0272494907522483;18992!GO:0021782;glial cell development;0.0272494907522483;18992!GO:0048699;generation of neurons;0.0272494907522483;18992,13865!GO:0022008;neurogenesis;0.0284510300394729;18992,13865!GO:0051726;regulation of cell cycle;0.0284510300394729;67874,13865!GO:0005158;insulin receptor binding;0.0284510300394729;76829!GO:0021983;pituitary gland development;0.0346253249444564;18992!GO:0005667;transcription factor complex;0.0346253249444564;18992,13865!GO:0043565;sequence-specific DNA binding;0.0346253249444564;18992,13865!GO:0021536;diencephalon development;0.0346253249444564;18992!GO:0007346;regulation of progression through mitotic cell cycle;0.0346253249444564;67874!GO:0040018;positive regulation of multicellular organism growth;0.0363934379296313;18992!GO:0048731;system development;0.0363934379296313;18992,13865,76829!GO:0048869;cellular developmental process;0.0364605932289762;18992,13865,210801!GO:0030154;cell differentiation;0.0364605932289762;18992,13865,210801!GO:0045927;positive regulation of growth;0.037227588631002;18992!GO:0044451;nucleoplasm part;0.038908235570802;18992,13865!GO:0050770;regulation of axonogenesis;0.03957321597384;18992!GO:0005654;nucleoplasm;0.03957321597384;18992,13865!GO:0022402;cell cycle process;0.03957321597384;67874,13865!GO:0032501;multicellular organismal process;0.0406879389792971;18992,13865,210801,76829!GO:0048856;anatomical structure development;0.0418516328902436;18992,13865,76829!GO:0010001;glial cell differentiation;0.043772319167139;18992!GO:0042063;gliogenesis;0.0455443637192678;18992!GO:0031981;nuclear lumen;0.0455443637192678;18992,13865!GO:0007050;cell cycle arrest;0.0455443637192678;67874!GO:0050767;regulation of neurogenesis;0.0455443637192678;18992!GO:0003707;steroid hormone receptor activity;0.0455443637192678;13865!GO:0004879;ligand-dependent nuclear receptor activity;0.0455443637192678;13865!GO:0035270;endocrine system development;0.0455443637192678;18992!GO:0032403;protein complex binding;0.0455443637192678;76829!GO:0007049;cell cycle;0.0455443637192678;67874,13865!GO:0040014;regulation of multicellular organism growth;0.0464596593620089;18992!GO:0031974;membrane-enclosed lumen;0.0464596593620089;18992,13865!GO:0043233;organelle lumen;0.0464596593620089;18992,13865!GO:0001764;neuron migration;0.0464596593620089;13865!
}}

Latest revision as of 16:09, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:78339134..78339185,-p5@Nr2f1
Mm9::chr2:170557427..170557451,+p3@Dok5
Mm9::chr2:53937900..53937952,-p1@Rprm
Mm9::chr2:53937953..53937970,-p2@Rprm
Mm9::chr4:22413866..22413881,-p@chr4:22413866..22413881
-
Mm9::chr4:22415290..22415307,-p2@Pou3f2
Mm9::chr4:22415443..22415506,-p1@Pou3f2
Mm9::chr8:30330049..30330095,-p1@Unc5d


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:0030900forebrain development0.0182440954919215
GO:0007399nervous system development0.0182440954919215
GO:0021985neurohypophysis development0.0182440954919215
GO:0021979hypothalamus cell differentiation0.0182440954919215
GO:0021854hypothalamus development0.0182440954919215
GO:0014002astrocyte development0.0182440954919215
GO:0007275multicellular organismal development0.0182440954919215
GO:0007420brain development0.0188232323511003
GO:0007417central nervous system development0.0262641336253937
GO:0048708astrocyte differentiation0.0272494907522483
GO:0048468cell development0.0272494907522483
GO:0005066transmembrane receptor protein tyrosine kinase signaling protein activity0.0272494907522483
GO:0032502developmental process0.0272494907522483
GO:0021761limbic system development0.0272494907522483
GO:0021782glial cell development0.0272494907522483
GO:0048699generation of neurons0.0272494907522483
GO:0022008neurogenesis0.0284510300394729
GO:0051726regulation of cell cycle0.0284510300394729
GO:0005158insulin receptor binding0.0284510300394729
GO:0021983pituitary gland development0.0346253249444564
GO:0005667transcription factor complex0.0346253249444564
GO:0043565sequence-specific DNA binding0.0346253249444564
GO:0021536diencephalon development0.0346253249444564
GO:0007346regulation of progression through mitotic cell cycle0.0346253249444564
GO:0040018positive regulation of multicellular organism growth0.0363934379296313
GO:0048731system development0.0363934379296313
GO:0048869cellular developmental process0.0364605932289762
GO:0030154cell differentiation0.0364605932289762
GO:0045927positive regulation of growth0.037227588631002
GO:0044451nucleoplasm part0.038908235570802
GO:0050770regulation of axonogenesis0.03957321597384
GO:0005654nucleoplasm0.03957321597384
GO:0022402cell cycle process0.03957321597384
GO:0032501multicellular organismal process0.0406879389792971
GO:0048856anatomical structure development0.0418516328902436
GO:0010001glial cell differentiation0.043772319167139
GO:0042063gliogenesis0.0455443637192678
GO:0031981nuclear lumen0.0455443637192678
GO:0007050cell cycle arrest0.0455443637192678
GO:0050767regulation of neurogenesis0.0455443637192678
GO:0003707steroid hormone receptor activity0.0455443637192678
GO:0004879ligand-dependent nuclear receptor activity0.0455443637192678
GO:0035270endocrine system development0.0455443637192678
GO:0032403protein complex binding0.0455443637192678
GO:0007049cell cycle0.0455443637192678
GO:0040014regulation of multicellular organism growth0.0464596593620089
GO:0031974membrane-enclosed lumen0.0464596593620089
GO:0043233organelle lumen0.0464596593620089
GO:0001764neuron migration0.0464596593620089



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>

Uber Anatomy
Ontology termp-valuen
nervous system1.52e-3275
central nervous system2.25e-3273
ectoderm-derived structure1.98e-2995
ectoderm1.98e-2995
presumptive ectoderm1.98e-2995
neurectoderm1.12e-2564
neural plate1.12e-2564
presumptive neural plate1.12e-2564
regional part of nervous system8.09e-2554
neural tube1.39e-2352
neural rod1.39e-2352
future spinal cord1.39e-2352
neural keel1.39e-2352
ecto-epithelium4.17e-2373
brain8.33e-2147
future brain8.33e-2147
gray matter1.28e-2034
pre-chordal neural plate1.90e-2049
regional part of brain2.91e-2046
anterior neural tube2.97e-1940
structure with developmental contribution from neural crest8.02e-1992
regional part of forebrain8.95e-1939
forebrain8.95e-1939
future forebrain8.95e-1939
brain grey matter9.16e-1829
regional part of telencephalon9.16e-1829
telencephalon9.16e-1829
cerebral cortex1.50e-1321
cerebral hemisphere1.50e-1321
pallium1.50e-1321
regional part of cerebral cortex8.15e-1117
multi-cellular organism3.44e-08333
occipital lobe5.24e-0810
visual cortex5.24e-0810
neocortex5.24e-0810


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)
MA0003.11.81836
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.548455
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.947733
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.335404
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.523649
MA0056.10
MA0057.10.643187
MA0058.10.341628
MA0059.10.353484
MA0060.11.08928
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.0216016
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.980744
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.064239
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.11.33477
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.951747
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.11.55504
MA0140.10.519484
MA0141.10.325895
MA0142.11.79662
MA0143.10.615203
MA0144.10.225588
MA0145.10.0701568
MA0146.10.385068
MA0147.10.666991
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.254826
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.20.54394
MA0047.20.576767
MA0112.20.0701537
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.330759
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.11.05113
MA0163.10.991519
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.21.19114
MA0102.21.59466
MA0258.10.210437
MA0259.10.643936
MA0442.10
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