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MCL coexpression mm9:1610: Difference between revisions

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{{MCL_coexpression_mm9
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of localization;0.0013477236618638;50884!GO:0045175;basal protein localization;0.0013477236618638;50884!GO:0030952;establishment and/or maintenance of cytoskeleton polarity;0.0013477236618638;50884!GO:0030950;establishment and/or maintenance of actin cytoskeleton polarity;0.0013477236618638;50884!GO:0032880;regulation of protein localization;0.0013477236618638;50884!GO:0007354;zygotic determination of anterior/posterior axis, embryo;0.00168465457732975;50884!GO:0007509;mesoderm migration;0.00168465457732975;50884!GO:0008078;mesodermal cell migration;0.00168465457732975;50884!GO:0048617;embryonic foregut morphogenesis;0.00210581822166219;50884!GO:0048570;notochord morphogenesis;0.00210581822166219;50884!GO:0010172;embryonic body morphogenesis;0.00210581822166219;50884!GO:0008595;determination of anterior/posterior axis, embryo;0.00210581822166219;50884!GO:0000578;embryonic axis specification;0.00210581822166219;50884!GO:0007351;tripartite regional subdivision;0.00210581822166219;50884!GO:0007440;foregut morphogenesis;0.00210581822166219;50884!GO:0010171;body morphogenesis;0.00210581822166219;50884!GO:0048613;embryonic ectodermal gut morphogenesis;0.00212798472925864;50884!GO:0048611;embryonic ectodermal gut development;0.00212798472925864;50884!GO:0007350;blastoderm segmentation;0.00212798472925864;50884!GO:0045176;apical protein localization;0.00216598445656683;50884!GO:0030903;notochord development;0.00216598445656683;50884!GO:0042074;cell migration involved in gastrulation;0.00216598445656683;50884!GO:0050821;protein stabilization;0.00216598445656683;50884!GO:0048558;embryonic gut morphogenesis;0.00216598445656683;50884!GO:0031647;regulation of protein stability;0.00216598445656683;50884!GO:0048557;embryonic digestive tract morphogenesis;0.00216598445656683;50884!GO:0008105;asymmetric protein localization;0.00216598445656683;50884!GO:0048340;paraxial mesoderm morphogenesis;0.00216598445656683;50884!GO:0007439;ectodermal gut 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epithelium;0.00819865227633814;50884!GO:0048729;tissue morphogenesis;0.00826024179852008;50884!GO:0031252;leading edge;0.00826024179852008;50884!GO:0009952;anterior/posterior pattern formation;0.0100544463662855;50884!GO:0001701;in utero embryonic development;0.0125296184188901;50884!GO:0002009;morphogenesis of an epithelium;0.0127515392622498;50884!GO:0003002;regionalization;0.0148853061161077;50884!GO:0035239;tube morphogenesis;0.0148853061161077;50884!GO:0030036;actin cytoskeleton organization and biogenesis;0.015260988524046;50884!GO:0030029;actin filament-based process;0.016114087261415;50884!GO:0007507;heart development;0.0163652158940605;50884!GO:0048646;anatomical structure formation;0.0176532817680752;50884!GO:0048598;embryonic morphogenesis;0.0185542778105907;50884!GO:0035295;tube development;0.0185542778105907;50884!GO:0016337;cell-cell adhesion;0.0189409811937616;50884!GO:0043009;chordate embryonic development;0.01985646195146;50884!GO:0009792;embryonic development ending in birth or egg hatching;0.0198611908064139;50884!GO:0007389;pattern specification process;0.02047839849845;50884!GO:0032990;cell part morphogenesis;0.0224901386073522;50884!GO:0030030;cell projection organization and biogenesis;0.0224901386073522;50884!GO:0048858;cell projection morphogenesis;0.0224901386073522;50884!GO:0016477;cell migration;0.0227116394869641;50884!GO:0009888;tissue development;0.0230920944502274;50884!GO:0051674;localization of cell;0.0259918134788019;50884!GO:0006928;cell motility;0.0259918134788019;50884!GO:0042995;cell projection;0.0288571419363779;50884!GO:0009790;embryonic development;0.0346225561409839;50884!GO:0007010;cytoskeleton organization and biogenesis;0.0346225561409839;50884!GO:0000902;cell morphogenesis;0.034828813733559;50884!GO:0032989;cellular structure morphogenesis;0.034828813733559;50884!GO:0009887;organ morphogenesis;0.0372870213115652;50884!GO:0022610;biological adhesion;0.0430685604986911;50884!GO:0007155;cell 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specification;0.00210581822166219;50884!GO:0007351;tripartite regional subdivision;0.00210581822166219;50884!GO:0007440;foregut morphogenesis;0.00210581822166219;50884!GO:0010171;body morphogenesis;0.00210581822166219;50884!GO:0048613;embryonic ectodermal gut morphogenesis;0.00212798472925864;50884!GO:0048611;embryonic ectodermal gut development;0.00212798472925864;50884!GO:0007350;blastoderm segmentation;0.00212798472925864;50884!GO:0045176;apical protein localization;0.00216598445656683;50884!GO:0030903;notochord development;0.00216598445656683;50884!GO:0042074;cell migration involved in gastrulation;0.00216598445656683;50884!GO:0050821;protein stabilization;0.00216598445656683;50884!GO:0048558;embryonic gut morphogenesis;0.00216598445656683;50884!GO:0031647;regulation of protein stability;0.00216598445656683;50884!GO:0048557;embryonic digestive tract morphogenesis;0.00216598445656683;50884!GO:0008105;asymmetric protein localization;0.00216598445656683;50884!GO:0048340;paraxial mesoderm morphogenesis;0.00216598445656683;50884!GO:0007439;ectodermal gut development;0.00224620610310634;50884!GO:0048567;ectodermal gut morphogenesis;0.00224620610310634;50884!GO:0048547;gut morphogenesis;0.00231640004382841;50884!GO:0009948;anterior/posterior axis specification;0.00231640004382841;50884!GO:0048339;paraxial mesoderm development;0.00243338994503187;50884!GO:0035050;embryonic heart tube development;0.00243338994503187;50884!GO:0048566;embryonic gut development;0.00243338994503187;50884!GO:0048546;digestive tract morphogenesis;0.00243338994503187;50884!GO:0030032;lamellipodium biogenesis;0.00273187228756176;50884!GO:0009798;axis specification;0.00293734644252367;50884!GO:0007492;endoderm development;0.00293734644252367;50884!GO:0048565;gut development;0.00303237823919356;50884!GO:0048562;embryonic organ morphogenesis;0.00345148742672437;50884!GO:0001707;mesoderm formation;0.00401108232697561;50884!GO:0048332;mesoderm morphogenesis;0.00407451339633243;50884!GO:0001704;formation of primary germ layer;0.00413506123526394;50884!GO:0001756;somitogenesis;0.00494165342683394;50884!GO:0048568;embryonic organ development;0.00542019298793051;50884!GO:0009880;embryonic pattern specification;0.00573499430580342;50884!GO:0035282;segmentation;0.00589629102065414;50884!GO:0001843;neural tube closure;0.00591348137348403;50884!GO:0014020;primary neural tube formation;0.00606475647838711;50884!GO:0030031;cell projection biogenesis;0.00623004334257796;50884!GO:0030027;lamellipodium;0.00623004334257796;50884!GO:0007498;mesoderm development;0.00623004334257796;50884!GO:0001841;neural tube formation;0.00673861830931902;50884!GO:0001839;neural plate morphogenesis;0.00673861830931902;50884!GO:0001840;neural plate development;0.00673861830931902;50884!GO:0001838;embryonic epithelial tube formation;0.00673861830931902;50884!GO:0007369;gastrulation;0.00720335060651343;50884!GO:0021915;neural tube development;0.00742390152721586;50884!GO:0016331;morphogenesis of embryonic epithelium;0.00819865227633814;50884!GO:0048729;tissue morphogenesis;0.00826024179852008;50884!GO:0031252;leading edge;0.00826024179852008;50884!GO:0009952;anterior/posterior pattern formation;0.0100544463662855;50884!GO:0001701;in utero embryonic development;0.0125296184188901;50884!GO:0002009;morphogenesis of an epithelium;0.0127515392622498;50884!GO:0003002;regionalization;0.0148853061161077;50884!GO:0035239;tube morphogenesis;0.0148853061161077;50884!GO:0030036;actin cytoskeleton organization and biogenesis;0.015260988524046;50884!GO:0030029;actin filament-based process;0.016114087261415;50884!GO:0007507;heart development;0.0163652158940605;50884!GO:0048646;anatomical structure formation;0.0176532817680752;50884!GO:0048598;embryonic morphogenesis;0.0185542778105907;50884!GO:0035295;tube development;0.0185542778105907;50884!GO:0016337;cell-cell adhesion;0.0189409811937616;50884!GO:0043009;chordate embryonic development;0.01985646195146;50884!GO:0009792;embryonic development ending in birth or egg hatching;0.0198611908064139;50884!GO:0007389;pattern specification process;0.02047839849845;50884!GO:0032990;cell part morphogenesis;0.0224901386073522;50884!GO:0030030;cell projection organization and biogenesis;0.0224901386073522;50884!GO:0048858;cell projection morphogenesis;0.0224901386073522;50884!GO:0016477;cell migration;0.0227116394869641;50884!GO:0009888;tissue development;0.0230920944502274;50884!GO:0051674;localization of cell;0.0259918134788019;50884!GO:0006928;cell motility;0.0259918134788019;50884!GO:0042995;cell projection;0.0288571419363779;50884!GO:0009790;embryonic development;0.0346225561409839;50884!GO:0007010;cytoskeleton organization and biogenesis;0.0346225561409839;50884!GO:0000902;cell morphogenesis;0.034828813733559;50884!GO:0032989;cellular structure morphogenesis;0.034828813733559;50884!GO:0009887;organ morphogenesis;0.0372870213115652;50884!GO:0022610;biological adhesion;0.0430685604986911;50884!GO:0007155;cell adhesion;0.0430685604986911;50884!GO:0065008;regulation of biological quality;0.0441995394482215;50884!GO:0007399;nervous system development;0.0443028310123314;50884!
}}

Latest revision as of 17:12, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:98698076..98698085,+p3@Rapgefl1
Mm9::chr11:98698089..98698145,+p1@Rapgefl1
Mm9::chr11:98698150..98698173,+p2@Rapgefl1
Mm9::chr11:98698181..98698192,+p4@Rapgefl1
Mm9::chr2:80421152..80421177,-p4@Nckap1


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:0032879regulation of localization0.0013477236618638
GO:0045175basal protein localization0.0013477236618638
GO:0030952establishment and/or maintenance of cytoskeleton polarity0.0013477236618638
GO:0030950establishment and/or maintenance of actin cytoskeleton polarity0.0013477236618638
GO:0032880regulation of protein localization0.0013477236618638
GO:0007354zygotic determination of anterior/posterior axis, embryo0.00168465457732975
GO:0007509mesoderm migration0.00168465457732975
GO:0008078mesodermal cell migration0.00168465457732975
GO:0048617embryonic foregut morphogenesis0.00210581822166219
GO:0048570notochord morphogenesis0.00210581822166219
GO:0010172embryonic body morphogenesis0.00210581822166219
GO:0008595determination of anterior/posterior axis, embryo0.00210581822166219
GO:0000578embryonic axis specification0.00210581822166219
GO:0007351tripartite regional subdivision0.00210581822166219
GO:0007440foregut morphogenesis0.00210581822166219
GO:0010171body morphogenesis0.00210581822166219
GO:0048613embryonic ectodermal gut morphogenesis0.00212798472925864
GO:0048611embryonic ectodermal gut development0.00212798472925864
GO:0007350blastoderm segmentation0.00212798472925864
GO:0045176apical protein localization0.00216598445656683
GO:0030903notochord development0.00216598445656683
GO:0042074cell migration involved in gastrulation0.00216598445656683
GO:0050821protein stabilization0.00216598445656683
GO:0048558embryonic gut morphogenesis0.00216598445656683
GO:0031647regulation of protein stability0.00216598445656683
GO:0048557embryonic digestive tract morphogenesis0.00216598445656683
GO:0008105asymmetric protein localization0.00216598445656683
GO:0048340paraxial mesoderm morphogenesis0.00216598445656683
GO:0007439ectodermal gut development0.00224620610310634
GO:0048567ectodermal gut morphogenesis0.00224620610310634
GO:0048547gut morphogenesis0.00231640004382841
GO:0009948anterior/posterior axis specification0.00231640004382841
GO:0048339paraxial mesoderm development0.00243338994503187
GO:0035050embryonic heart tube development0.00243338994503187
GO:0048566embryonic gut development0.00243338994503187
GO:0048546digestive tract morphogenesis0.00243338994503187
GO:0030032lamellipodium biogenesis0.00273187228756176
GO:0009798axis specification0.00293734644252367
GO:0007492endoderm development0.00293734644252367
GO:0048565gut development0.00303237823919356
GO:0048562embryonic organ morphogenesis0.00345148742672437
GO:0001707mesoderm formation0.00401108232697561
GO:0048332mesoderm morphogenesis0.00407451339633243
GO:0001704formation of primary germ layer0.00413506123526394
GO:0001756somitogenesis0.00494165342683394
GO:0048568embryonic organ development0.00542019298793051
GO:0009880embryonic pattern specification0.00573499430580342
GO:0035282segmentation0.00589629102065414
GO:0001843neural tube closure0.00591348137348403
GO:0014020primary neural tube formation0.00606475647838711
GO:0030031cell projection biogenesis0.00623004334257796
GO:0030027lamellipodium0.00623004334257796
GO:0007498mesoderm development0.00623004334257796
GO:0001841neural tube formation0.00673861830931902
GO:0001839neural plate morphogenesis0.00673861830931902
GO:0001840neural plate development0.00673861830931902
GO:0001838embryonic epithelial tube formation0.00673861830931902
GO:0007369gastrulation0.00720335060651343
GO:0021915neural tube development0.00742390152721586
GO:0016331morphogenesis of embryonic epithelium0.00819865227633814
GO:0048729tissue morphogenesis0.00826024179852008
GO:0031252leading edge0.00826024179852008
GO:0009952anterior/posterior pattern formation0.0100544463662855
GO:0001701in utero embryonic development0.0125296184188901
GO:0002009morphogenesis of an epithelium0.0127515392622498
GO:0003002regionalization0.0148853061161077
GO:0035239tube morphogenesis0.0148853061161077
GO:0030036actin cytoskeleton organization and biogenesis0.015260988524046
GO:0030029actin filament-based process0.016114087261415
GO:0007507heart development0.0163652158940605
GO:0048646anatomical structure formation0.0176532817680752
GO:0048598embryonic morphogenesis0.0185542778105907
GO:0035295tube development0.0185542778105907
GO:0016337cell-cell adhesion0.0189409811937616
GO:0043009chordate embryonic development0.01985646195146
GO:0009792embryonic development ending in birth or egg hatching0.0198611908064139
GO:0007389pattern specification process0.02047839849845
GO:0032990cell part morphogenesis0.0224901386073522
GO:0030030cell projection organization and biogenesis0.0224901386073522
GO:0048858cell projection morphogenesis0.0224901386073522
GO:0016477cell migration0.0227116394869641
GO:0009888tissue development0.0230920944502274
GO:0051674localization of cell0.0259918134788019
GO:0006928cell motility0.0259918134788019
GO:0042995cell projection0.0288571419363779
GO:0009790embryonic development0.0346225561409839
GO:0007010cytoskeleton organization and biogenesis0.0346225561409839
GO:0000902cell morphogenesis0.034828813733559
GO:0032989cellular structure morphogenesis0.034828813733559
GO:0009887organ morphogenesis0.0372870213115652
GO:0022610biological adhesion0.0430685604986911
GO:0007155cell adhesion0.0430685604986911
GO:0065008regulation of biological quality0.0441995394482215
GO:0007399nervous system development0.0443028310123314



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
ecto-epithelium1.39e-1673
regional part of nervous system8.77e-1654
ectoderm-derived structure5.66e-1595
ectoderm5.66e-1595
presumptive ectoderm5.66e-1595
neural tube1.24e-1452
neural rod1.24e-1452
future spinal cord1.24e-1452
neural keel1.24e-1452
neurectoderm5.75e-1464
neural plate5.75e-1464
presumptive neural plate5.75e-1464
gray matter1.71e-1234
central nervous system2.25e-1273
brain2.36e-1247
future brain2.36e-1247
regional part of brain8.53e-1246
pre-chordal neural plate1.89e-1149
nervous system1.94e-1175
anterior neural tube5.87e-1140
regional part of forebrain2.19e-1039
forebrain2.19e-1039
future forebrain2.19e-1039
brain grey matter4.79e-1029
regional part of telencephalon4.79e-1029
telencephalon4.79e-1029
occipital lobe6.91e-0810
visual cortex6.91e-0810
neocortex6.91e-0810
structure with developmental contribution from neural crest3.10e-0792
cerebral cortex3.93e-0721
cerebral hemisphere3.93e-0721
pallium3.93e-0721


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)
MA0003.12.26461
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.736185
MA0017.12.9605
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.11.12075
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.602741
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.000589538
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.11.4237
MA0113.10.780358
MA0114.12.55088
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.12.22941
MA0140.10.695713
MA0141.11.21195
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.157686
MA0146.10.475727
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.706751
MA0035.20.700704
MA0039.22.26967
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.22.84751
MA0150.11.43499
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.11.11105
MA0155.10.515751
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.13.77769
MA0163.10.0644585
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.23.38617
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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