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MCL coexpression mm9:848: Difference between revisions

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{{MCL_coexpression_mm9
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1,0.711210370736315,0.647125944391591,0.709649495381685,0.708462977800011,0.619116386125096,0.757787438810128,0.76427855486364,0.570409181558021,0.752804369432746,0,0,0,0,0,0.135986724295729,0.0871588832444397,0.081359932135904,0,0.0978461107777356,0.178101321237085,0.0750453505157095,0.0745542549075041,0.0763037466917402,0.0242538736058389,0.169172763866184,0.0476191773904887,0.0766073954291401,0,0.0596387295197733,0,0.0709519923534245,0.092873634605593,0.0589368614163519,0.0748964051866952,0.0678996586311492,0,0.101427320830301,0.0553034373508932,0,0.0486884105045233,0.0408018333703219,0.148982201447044,0,0.0766064454112358,0.0968441960560167,0.166685587652774,0.0845301845292944,0.140689222355642,0.220572027003917,0.0905641158318875|gostat_on_MCL_coexpression=GO:0042670;retinal cone cell differentiation;0.00597162110338027;21838!GO:0046549;retinal cone cell development;0.00597162110338027;21838!GO:0060042;retina morphogenesis in camera-type eye;0.00716555271254392;21838!GO:0031362;anchored to external side of plasma membrane;0.00716555271254392;21838!GO:0031233;intrinsic to external side of plasma membrane;0.00716555271254392;21838!GO:0050858;negative regulation of antigen receptor-mediated signaling pathway;0.00852995250122804;21838!GO:0050860;negative regulation of T cell receptor signaling pathway;0.00852995250122804;21838!GO:0042393;histone binding;0.010103051914287;114642!GO:0060041;retina development in camera-type eye;0.010103051914287;21838!GO:0050856;regulation of T cell receptor signaling pathway;0.010103051914287;21838!GO:0031225;anchored to membrane;0.010103051914287;21838!GO:0046658;anchored to plasma membrane;0.010103051914287;21838!GO:0050854;regulation of antigen receptor-mediated signaling pathway;0.010103051914287;21838!GO:0042462;eye photoreceptor cell development;0.0119376802103351;21838!GO:0001754;eye photoreceptor cell differentiation;0.0119376802103351;21838!GO:0042461;photoreceptor cell development;0.0119376802103351;21838!GO:0048593;camera-type eye morphogenesis;0.0119376802103351;21838!GO:0050852;T cell receptor signaling pathway;0.0119376802103351;21838!GO:0046530;photoreceptor cell differentiation;0.0131931932796124;21838!GO:0050851;antigen receptor-mediated signaling pathway;0.0161118930923894;21838!GO:0002429;immune response-activating cell surface receptor signaling pathway;0.0181353277613955;21838!GO:0002768;immune response-regulating cell surface receptor signaling pathway;0.0181353277613955;21838!GO:0002757;immune response-activating signal transduction;0.0181353277613955;21838!GO:0006338;chromatin remodeling;0.0181353277613955;114642!GO:0002764;immune response-regulating signal transduction;0.0181353277613955;21838!GO:0048592;eye morphogenesis;0.0197295590217139;21838!GO:0043010;camera-type eye development;0.0327755362301843;21838!GO:0002253;activation of immune response;0.0327755362301843;21838!GO:0050778;positive regulation of immune response;0.0389109199577307;21838!GO:0002684;positive regulation of immune system process;0.0389109199577307;21838!GO:0001654;eye development;0.0399545960452431;21838!GO:0050776;regulation of immune response;0.0401367309985071;21838!GO:0002682;regulation of immune system process;0.0401367309985071;21838!GO:0051240;positive regulation of multicellular organismal process;0.0401367309985071;21838!GO:0048503;GPI anchor binding;0.0401367309985071;21838!GO:0001525;angiogenesis;0.0437371347021604;21838!GO:0009897;external side of plasma membrane;0.0437371347021604;21838!GO:0016043;cellular component organization and biogenesis;0.0460427918832516;114642,21838!GO:0035091;phosphoinositide binding;0.04904453936278;21838!GO:0016568;chromatin modification;0.04904453936278;114642!GO:0048514;blood vessel morphogenesis;0.0491152203408847;21838!GO:0009986;cell surface;0.0491152203408847;21838!GO:0000904;cellular morphogenesis during differentiation;0.0491152203408847;21838!GO:0048646;anatomical structure formation;0.0491152203408847;21838!GO:0007423;sensory organ 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|gostat_on_MCL_coexpression=GO:0042670;retinal cone cell differentiation;0.00597162110338027;21838!GO:0046549;retinal cone cell development;0.00597162110338027;21838!GO:0060042;retina morphogenesis in camera-type eye;0.00716555271254392;21838!GO:0031362;anchored to external side of plasma membrane;0.00716555271254392;21838!GO:0031233;intrinsic to external side of plasma membrane;0.00716555271254392;21838!GO:0050858;negative regulation of antigen receptor-mediated signaling pathway;0.00852995250122804;21838!GO:0050860;negative regulation of T cell receptor signaling pathway;0.00852995250122804;21838!GO:0042393;histone binding;0.010103051914287;114642!GO:0060041;retina development in camera-type eye;0.010103051914287;21838!GO:0050856;regulation of T cell receptor signaling pathway;0.010103051914287;21838!GO:0031225;anchored to membrane;0.010103051914287;21838!GO:0046658;anchored to plasma membrane;0.010103051914287;21838!GO:0050854;regulation of antigen receptor-mediated signaling pathway;0.010103051914287;21838!GO:0042462;eye photoreceptor cell development;0.0119376802103351;21838!GO:0001754;eye photoreceptor cell differentiation;0.0119376802103351;21838!GO:0042461;photoreceptor cell development;0.0119376802103351;21838!GO:0048593;camera-type eye morphogenesis;0.0119376802103351;21838!GO:0050852;T cell receptor signaling pathway;0.0119376802103351;21838!GO:0046530;photoreceptor cell differentiation;0.0131931932796124;21838!GO:0050851;antigen receptor-mediated signaling pathway;0.0161118930923894;21838!GO:0002429;immune response-activating cell surface receptor signaling pathway;0.0181353277613955;21838!GO:0002768;immune response-regulating cell surface receptor signaling pathway;0.0181353277613955;21838!GO:0002757;immune response-activating signal transduction;0.0181353277613955;21838!GO:0006338;chromatin remodeling;0.0181353277613955;114642!GO:0002764;immune response-regulating signal transduction;0.0181353277613955;21838!GO:0048592;eye morphogenesis;0.0197295590217139;21838!GO:0043010;camera-type eye development;0.0327755362301843;21838!GO:0002253;activation of immune response;0.0327755362301843;21838!GO:0050778;positive regulation of immune response;0.0389109199577307;21838!GO:0002684;positive regulation of immune system process;0.0389109199577307;21838!GO:0001654;eye development;0.0399545960452431;21838!GO:0050776;regulation of immune response;0.0401367309985071;21838!GO:0002682;regulation of immune system process;0.0401367309985071;21838!GO:0051240;positive regulation of multicellular organismal process;0.0401367309985071;21838!GO:0048503;GPI anchor binding;0.0401367309985071;21838!GO:0001525;angiogenesis;0.0437371347021604;21838!GO:0009897;external side of plasma membrane;0.0437371347021604;21838!GO:0016043;cellular component organization and biogenesis;0.0460427918832516;114642,21838!GO:0035091;phosphoinositide binding;0.04904453936278;21838!GO:0016568;chromatin modification;0.04904453936278;114642!GO:0048514;blood vessel morphogenesis;0.0491152203408847;21838!GO:0009986;cell surface;0.0491152203408847;21838!GO:0000904;cellular morphogenesis during differentiation;0.0491152203408847;21838!GO:0048646;anatomical structure formation;0.0491152203408847;21838!GO:0007423;sensory organ development;0.0491152203408847;21838!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!9.92e-13!54;UBERON:0001049!2.39e-11!52;UBERON:0005068!2.39e-11!52;UBERON:0006241!2.39e-11!52;UBERON:0007135!2.39e-11!52;UBERON:0002370!1.04e-10!23;UBERON:0000974!1.04e-10!23;UBERON:0004807!1.04e-10!23;UBERON:0005058!1.04e-10!23;UBERON:0003351!1.04e-10!23;UBERON:0009113!1.04e-10!23;UBERON:0003295!1.04e-10!23;UBERON:0009722!1.04e-10!23;UBERON:0005562!1.04e-10!23;UBERON:0007690!1.04e-10!23;UBERON:0006562!6.58e-10!24;UBERON:0003408!6.58e-10!24;UBERON:0001557!6.58e-10!24;UBERON:0001042!6.58e-10!24;UBERON:0008814!6.58e-10!24;UBERON:0009145!6.58e-10!24;UBERON:0000955!1.04e-09!47;UBERON:0006238!1.04e-09!47;UBERON:0001017!1.48e-09!73;UBERON:0010371!2.42e-09!73;UBERON:0002616!2.92e-09!46;UBERON:0002346!6.12e-09!64;UBERON:0003075!6.12e-09!64;UBERON:0007284!6.12e-09!64;UBERON:0001016!7.06e-09!75;UBERON:0002021!7.64e-09!10;UBERON:0000411!7.64e-09!10;UBERON:0001950!7.64e-09!10;UBERON:0000063!8.33e-09!35;UBERON:0002020!1.07e-08!34;UBERON:0000064!1.53e-08!99;UBERON:0004121!3.17e-08!95;UBERON:0000924!3.17e-08!95;UBERON:0006601!3.17e-08!95;UBERON:0000072!6.61e-08!27;UBERON:0002619!1.19e-07!17;UBERON:0003080!2.50e-07!40;UBERON:0003528!3.30e-07!29;UBERON:0002791!3.30e-07!29;UBERON:0001893!3.30e-07!29;UBERON:0004177!7.78e-07!29;UBERON:0005057!7.78e-07!29;UBERON:0002780!8.02e-07!39;UBERON:0001890!8.02e-07!39;UBERON:0006240!8.02e-07!39
}}

Latest revision as of 15:59, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr5:107788562..107788605,+p2@Brdt
Mm9::chr9:43851294..43851336,+p2@Thy1
Mm9::chr9:43851473..43851517,+p1@Thy1
Mm9::chr9:43854810..43854849,-p@chr9:43854810..43854849
-
Mm9::chr9:43854871..43854901,+p@chr9:43854871..43854901
+
Mm9::chr9:43854935..43854978,-p@chr9:43854935..43854978
-
Mm9::chr9:43854987..43854999,+p@chr9:43854987..43854999
+
Mm9::chr9:43855655..43855666,+p@chr9:43855655..43855666
+
Mm9::chr9:43856002..43856018,+p@chr9:43856002..43856018
+


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:0042670retinal cone cell differentiation0.00597162110338027
GO:0046549retinal cone cell development0.00597162110338027
GO:0060042retina morphogenesis in camera-type eye0.00716555271254392
GO:0031362anchored to external side of plasma membrane0.00716555271254392
GO:0031233intrinsic to external side of plasma membrane0.00716555271254392
GO:0050858negative regulation of antigen receptor-mediated signaling pathway0.00852995250122804
GO:0050860negative regulation of T cell receptor signaling pathway0.00852995250122804
GO:0042393histone binding0.010103051914287
GO:0060041retina development in camera-type eye0.010103051914287
GO:0050856regulation of T cell receptor signaling pathway0.010103051914287
GO:0031225anchored to membrane0.010103051914287
GO:0046658anchored to plasma membrane0.010103051914287
GO:0050854regulation of antigen receptor-mediated signaling pathway0.010103051914287
GO:0042462eye photoreceptor cell development0.0119376802103351
GO:0001754eye photoreceptor cell differentiation0.0119376802103351
GO:0042461photoreceptor cell development0.0119376802103351
GO:0048593camera-type eye morphogenesis0.0119376802103351
GO:0050852T cell receptor signaling pathway0.0119376802103351
GO:0046530photoreceptor cell differentiation0.0131931932796124
GO:0050851antigen receptor-mediated signaling pathway0.0161118930923894
GO:0002429immune response-activating cell surface receptor signaling pathway0.0181353277613955
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0181353277613955
GO:0002757immune response-activating signal transduction0.0181353277613955
GO:0006338chromatin remodeling0.0181353277613955
GO:0002764immune response-regulating signal transduction0.0181353277613955
GO:0048592eye morphogenesis0.0197295590217139
GO:0043010camera-type eye development0.0327755362301843
GO:0002253activation of immune response0.0327755362301843
GO:0050778positive regulation of immune response0.0389109199577307
GO:0002684positive regulation of immune system process0.0389109199577307
GO:0001654eye development0.0399545960452431
GO:0050776regulation of immune response0.0401367309985071
GO:0002682regulation of immune system process0.0401367309985071
GO:0051240positive regulation of multicellular organismal process0.0401367309985071
GO:0048503GPI anchor binding0.0401367309985071
GO:0001525angiogenesis0.0437371347021604
GO:0009897external side of plasma membrane0.0437371347021604
GO:0016043cellular component organization and biogenesis0.0460427918832516
GO:0035091phosphoinositide binding0.04904453936278
GO:0016568chromatin modification0.04904453936278
GO:0048514blood vessel morphogenesis0.0491152203408847
GO:0009986cell surface0.0491152203408847
GO:0000904cellular morphogenesis during differentiation0.0491152203408847
GO:0048646anatomical structure formation0.0491152203408847
GO:0007423sensory organ development0.0491152203408847



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system9.92e-1354
neural tube2.39e-1152
neural rod2.39e-1152
future spinal cord2.39e-1152
neural keel2.39e-1152
thymus1.04e-1023
neck1.04e-1023
respiratory system epithelium1.04e-1023
hemolymphoid system gland1.04e-1023
pharyngeal epithelium1.04e-1023
thymic region1.04e-1023
pharyngeal gland1.04e-1023
entire pharyngeal arch endoderm1.04e-1023
thymus primordium1.04e-1023
early pharyngeal endoderm1.04e-1023
pharynx6.58e-1024
gland of gut6.58e-1024
upper respiratory tract6.58e-1024
chordate pharynx6.58e-1024
pharyngeal arch system6.58e-1024
pharyngeal region of foregut6.58e-1024
brain1.04e-0947
future brain1.04e-0947
central nervous system1.48e-0973
ecto-epithelium2.42e-0973
regional part of brain2.92e-0946
neurectoderm6.12e-0964
neural plate6.12e-0964
presumptive neural plate6.12e-0964
nervous system7.06e-0975
occipital lobe7.64e-0910
visual cortex7.64e-0910
neocortex7.64e-0910
organ segment8.33e-0935
gray matter1.07e-0834
organ part1.53e-0899
ectoderm-derived structure3.17e-0895
ectoderm3.17e-0895
presumptive ectoderm3.17e-0895
segment of respiratory tract6.61e-0827
regional part of cerebral cortex1.19e-0717
anterior neural tube2.50e-0740
brain grey matter3.30e-0729
regional part of telencephalon3.30e-0729
telencephalon3.30e-0729
hemopoietic organ7.78e-0729
immune organ7.78e-0729
regional part of forebrain8.02e-0739
forebrain8.02e-0739
future forebrain8.02e-0739


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)
MA0003.10.0854318
MA0004.11.80728
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.0421798
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.11.32237
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.0824771
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.692644
MA0056.10
MA0057.10.549903
MA0058.12.27565
MA0059.13.22258
MA0060.10.505012
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.11.4268
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.14.32293
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.897217
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.413524
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.11.30984
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.748482
MA0105.10.109964
MA0106.11.42499
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.19245
MA0115.10.921497
MA0116.13.56309
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.0543321
MA0146.10.30073
MA0147.10.593505
MA0148.10.410398
MA0149.10.330018
MA0062.20.113962
MA0035.20.482026
MA0039.21.08337
MA0138.20.630612
MA0002.20.145685
MA0137.20.287486
MA0104.20.476119
MA0047.20.533516
MA0112.21.6539
MA0065.20.0545595
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.12.01498
MA0155.10.0631765
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.614411
MA0160.10.413266
MA0161.10
MA0162.10.582797
MA0163.10.542069
MA0164.11.26737
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.21.32649
MA0102.21.5442
MA0258.11.61881
MA0259.11.08444
MA0442.10
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