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MCL coexpression mm9:815: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=0.0325577858047273,0.00749397747881354,0.0292408108345024,-0.00695091500809223,-0.00695091500809223,0.0070188584044431,0.00318006397670095,0.0272862531501491,0.0187663314807034,0.0249338904088842,0.0347776871926336,0.0542223790937898,0.000674788812035629,0.0596092349427352,0.0264806769277423,0.0159525222453323,-0.00695091500809223,0.0062800140639412,0.0141490133994646,0.0101189527542263,0.0858376746955148,0.0545294666438498,0.0557631831397318,-0.00695091500809223,0.0229479141175312,0.0149456101380998,0.0103343512050279,0.00246516105670812,0.00144414147161851,0.00389517167825801,-0.00695091500809223,0.0563339181461283,0.0161813014964499,-0.00695091500809223,0.0052938540666457,0.00046974486662728,-0.00695091500809223,-0.00695091500809223,-0.00695091500809223,-0.00695091500809223,-0.00695091500809223,-0.00695091500809223,-0.00695091500809223,0.796122697159305,0.723676520071784,0.43845703629185,0.135014361335638,0.0909771711512233,0.134492062841202,0.160544609765495,0.143825807570719,0.0790377946206496,0.000533751904568661,0.0193691143800847,0.0266962589295676,0.105901728174731,0.0691611913809218,0.226386514753142,0.00194006199796236,0.0135385209000178,-0.00695091500809223,0.165707979556644,0.178264212537473,0.0109771943212973,0.0788814534904312,-0.00695091500809223,0.0943272244914818,0.116048734265435,0.045579246870752,0.0179404749659498,0.00226041722854906,0.0269805006983966,0.0203329707546211,0.0292984665007401,-0.00253432422028236,-0.00695091500809223,-0.00695091500809223,0.0144969025157867,0.0320234969865741,-0.000972826265956612,-0.00272660127941862,0.0132829158644323,0.0286933112518948,0.0361364209783509,0.0309865709529612,0.0430830422611484,0.0268906437175161,-0.00695091500809223,0.0339785415312604,0.0368676362019815,0.0371785482371391,0.0230059632897938,0.0759160743969851,-0.00695091500809223,-0.00695091500809223,-0.00695091500809223,0.0346441527952544,0.231370261736901,0.256780279110058,0.229446858364401,0.0164143688861704,0.797793000848136,0.176379093257915,-0.00695091500809223,0.130488944911293,0.110942627759573,0.105645967915965,0.0315627361104949,0.00416067415005965,0.0175018694421119,0.0353612681618101,0.0288235292272089,0.0130762805246806,0.0290528269866109,0.027574356246184,0.00447347984744439,0.0124339665448283,0.0745994351698153,-0.00695091500809223,0.0210460809896225,-0.00695091500809223,-0.00695091500809223,-0.00695091500809223,0.0400749630553391,0.0257526249752033,0.0150050542383393,-0.00695091500809223,0.0157261494066682,-0.00695091500809223,-0.000215496266262067,-0.00695091500809223,0.019303168763503,0.00744649360154363,0.012981118435199,0.0624178810370934,0.0352728801974234,0.026535168367433,0.037104230841297,0.0376316966654438,0.0100000334110977,0.0379573717689212,0.0113040418210249,0.0238700109452922,0.0057617536516404,0.00238156636886528,0.0261937267331959,-0.00695091500809223,0.0152542839286697,-0.00695091500809223,0.0014069294100119,0.0280520813782097,0.0121765147318001,0.0223194067852907,0.0218871131771611,-0.00695091500809223,0.0354961122880548,0.0187173017408159,-0.00695091500809223,0.00511800960576881,0.0112163121814407,0.00321578077160434,0.00902794014492519,0.0117543113188741,0.00171670729768014,0.0183259373387335,0.013226615848299,0.0252444936234359,0.0075411949763851,0.0197623347751911,0.0373031607247408,0.0043335308193936,0.0128025514443066,0.017466289837658,0.00520288515613305,0.116177836583343,0.0448200026115759,0.00682557028825677,-0.00695091500809223,0.02885164607749,0.0553165494686841,0.0323873961552472,0.0215928895558417,0.00273858950024042,-0.00695091500809223,-0.00695091500809223,0.00776323737135886,0.0309829346155242,0.0331464445421917,0.0347220759349488,-0.00695091500809223,0.0024916268430472,0.010575829708071,0.00981036139611563,0.0293730357372827,-0.00695091500809223,0.0160583222243733,0.0174209490893481,0.0265576570315978,0.00984821722373676,0.0107396735943212,0.0257465637497411,0.0274682913915773,-0.00695091500809223,0.000494997093922832,0.0190271236322539,0.00283655179075041,0.0108746687452446,0.00347505999876266,0.0348035448525992,0.0271826521614119,0.0296476421274362,0.00475583679853887,-0.00695091500809223,-0.00695091500809223,0.00615423002602733,-0.00695091500809223,-0.00695091500809223,0.0310442308703176,0.180737732428837,0.0302753345250761,0.00761944850813681,0.0443716600577028,0.0406832983095579,0.0864134630043719,0.115704748054027,0.092159382449945,0.0948919172631006,0.0590506619792945,0.0651465812023665,0.100455074739433,0.106406001460216,0.164537663676187,0.0374171337525586,-0.00695091500809223,-0.00695091500809223,0.0165666727842655,0.0400976544921795,0.0169504133901125,0.202897472147126,0.014775230249694,0.0487955569837731,0.0861592147221431,0.0673100950754976,0.0671734384422085,0.106968465256535,0.0295879243294773,0.0600324287144584,0.1309466012047,0.0533068884899519,0.0573344643635551,0.101236103735923,0.0156569945507886,0.0450558651769901,0.133223454867756,0.0338135981092944,0.0140256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class receptor binding;0.0120528132361804;211323!GO:0046579;positive regulation of Ras protein signal transduction;0.0120528132361804;211323!GO:0045213;neurotransmitter receptor metabolic process;0.0120528132361804;211323!GO:0051057;positive regulation of small GTPase mediated signal transduction;0.0120528132361804;211323!GO:0043624;cellular protein complex disassembly;0.0120528132361804;211323!GO:0043241;protein complex disassembly;0.0120528132361804;211323!GO:0032984;macromolecular complex disassembly;0.0120528132361804;211323!GO:0007416;synaptogenesis;0.0125550137876879;211323!GO:0048663;neuron fate commitment;0.0125550137876879;211323!GO:0022411;cellular component disassembly;0.0125550137876879;211323!GO:0007422;peripheral nervous system development;0.0125550137876879;211323!GO:0043112;receptor metabolic process;0.0125550137876879;211323!GO:0010001;glial cell differentiation;0.0176156501144174;211323!GO:0042063;gliogenesis;0.0176487622386927;211323!GO:0050808;synapse organization and biogenesis;0.0176774594130645;211323!GO:0045860;positive regulation of protein kinase activity;0.028697174371858;211323!GO:0033674;positive regulation of kinase activity;0.028697174371858;211323!GO:0051347;positive regulation of transferase activity;0.028697174371858;211323!GO:0043062;extracellular structure organization and biogenesis;0.028697174371858;211323!GO:0046578;regulation of Ras protein signal transduction;0.028697174371858;211323!GO:0045165;cell fate commitment;0.028697174371858;211323!GO:0000165;MAPKKK cascade;0.0292711178592952;211323!GO:0051056;regulation of small GTPase mediated signal transduction;0.0292711178592952;211323!GO:0045859;regulation of protein kinase activity;0.0292711178592952;211323!GO:0043549;regulation of kinase activity;0.0292711178592952;211323!GO:0043085;positive regulation of catalytic activity;0.0292711178592952;211323!GO:0051338;regulation of transferase activity;0.0292711178592952;211323!GO:0003712;transcription cofactor activity;0.0292711178592952;211323!GO:0007265;Ras protein signal transduction;0.0307346737522599;211323!GO:0045595;regulation of cell differentiation;0.0307346737522599;211323!GO:0007517;muscle development;0.0320152851586041;211323!GO:0007507;heart development;0.0320152851586041;211323!GO:0008134;transcription factor binding;0.0336769781599157;211323!GO:0007268;synaptic transmission;0.0336769781599157;211323!GO:0007626;locomotory behavior;0.0347809753386919;211323!GO:0005125;cytokine activity;0.0356698121449121;211323!GO:0007243;protein kinase cascade;0.0356698121449121;211323!GO:0019226;transmission of nerve impulse;0.0356826707650076;211323!GO:0016481;negative regulation of transcription;0.0367765326950119;211323!GO:0045934;negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0370350079438996;211323!GO:0050793;regulation of developmental process;0.0370350079438996;211323!GO:0050790;regulation of catalytic activity;0.0370350079438996;211323!GO:0016477;cell migration;0.0370350079438996;211323!GO:0030182;neuron differentiation;0.0370350079438996;211323!GO:0031324;negative regulation of cellular metabolic process;0.0370350079438996;211323!GO:0065009;regulation of a molecular function;0.0370350079438996;211323!GO:0007610;behavior;0.0370350079438996;211323!GO:0048699;generation of neurons;0.0370350079438996;211323!GO:0051674;localization of cell;0.0370350079438996;211323!GO:0006928;cell motility;0.0370350079438996;211323!GO:0007267;cell-cell signaling;0.0370350079438996;211323!GO:0009892;negative regulation of metabolic process;0.0370350079438996;211323!GO:0009966;regulation of signal transduction;0.0370350079438996;211323!GO:0007264;small GTPase mediated signal transduction;0.0370350079438996;211323!GO:0022008;neurogenesis;0.0370350079438996;211323!GO:0009790;embryonic development;0.047795638695198;211323!GO:0000902;cell morphogenesis;0.047795638695198;211323!GO:0032989;cellular structure 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|gostat_on_MCL_coexpression=GO:0005176;ErbB-2 class receptor binding;0.0120528132361804;211323!GO:0046579;positive regulation of Ras protein signal transduction;0.0120528132361804;211323!GO:0045213;neurotransmitter receptor metabolic process;0.0120528132361804;211323!GO:0051057;positive regulation of small GTPase mediated signal transduction;0.0120528132361804;211323!GO:0043624;cellular protein complex disassembly;0.0120528132361804;211323!GO:0043241;protein complex disassembly;0.0120528132361804;211323!GO:0032984;macromolecular complex disassembly;0.0120528132361804;211323!GO:0007416;synaptogenesis;0.0125550137876879;211323!GO:0048663;neuron fate commitment;0.0125550137876879;211323!GO:0022411;cellular component disassembly;0.0125550137876879;211323!GO:0007422;peripheral nervous system development;0.0125550137876879;211323!GO:0043112;receptor metabolic process;0.0125550137876879;211323!GO:0010001;glial cell differentiation;0.0176156501144174;211323!GO:0042063;gliogenesis;0.0176487622386927;211323!GO:0050808;synapse organization and biogenesis;0.0176774594130645;211323!GO:0045860;positive regulation of protein kinase activity;0.028697174371858;211323!GO:0033674;positive regulation of kinase activity;0.028697174371858;211323!GO:0051347;positive regulation of transferase activity;0.028697174371858;211323!GO:0043062;extracellular structure organization and biogenesis;0.028697174371858;211323!GO:0046578;regulation of Ras protein signal transduction;0.028697174371858;211323!GO:0045165;cell fate commitment;0.028697174371858;211323!GO:0000165;MAPKKK cascade;0.0292711178592952;211323!GO:0051056;regulation of small GTPase mediated signal transduction;0.0292711178592952;211323!GO:0045859;regulation of protein kinase activity;0.0292711178592952;211323!GO:0043549;regulation of kinase activity;0.0292711178592952;211323!GO:0043085;positive regulation of catalytic activity;0.0292711178592952;211323!GO:0051338;regulation of transferase activity;0.0292711178592952;211323!GO:0003712;transcription cofactor activity;0.0292711178592952;211323!GO:0007265;Ras protein signal transduction;0.0307346737522599;211323!GO:0045595;regulation of cell differentiation;0.0307346737522599;211323!GO:0007517;muscle development;0.0320152851586041;211323!GO:0007507;heart development;0.0320152851586041;211323!GO:0008134;transcription factor binding;0.0336769781599157;211323!GO:0007268;synaptic transmission;0.0336769781599157;211323!GO:0007626;locomotory behavior;0.0347809753386919;211323!GO:0005125;cytokine activity;0.0356698121449121;211323!GO:0007243;protein kinase cascade;0.0356698121449121;211323!GO:0019226;transmission of nerve impulse;0.0356826707650076;211323!GO:0016481;negative regulation of transcription;0.0367765326950119;211323!GO:0045934;negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0370350079438996;211323!GO:0050793;regulation of developmental process;0.0370350079438996;211323!GO:0050790;regulation of catalytic activity;0.0370350079438996;211323!GO:0016477;cell migration;0.0370350079438996;211323!GO:0030182;neuron differentiation;0.0370350079438996;211323!GO:0031324;negative regulation of cellular metabolic process;0.0370350079438996;211323!GO:0065009;regulation of a molecular function;0.0370350079438996;211323!GO:0007610;behavior;0.0370350079438996;211323!GO:0048699;generation of neurons;0.0370350079438996;211323!GO:0051674;localization of cell;0.0370350079438996;211323!GO:0006928;cell motility;0.0370350079438996;211323!GO:0007267;cell-cell signaling;0.0370350079438996;211323!GO:0009892;negative regulation of metabolic process;0.0370350079438996;211323!GO:0009966;regulation of signal transduction;0.0370350079438996;211323!GO:0007264;small GTPase mediated signal transduction;0.0370350079438996;211323!GO:0022008;neurogenesis;0.0370350079438996;211323!GO:0009790;embryonic development;0.047795638695198;211323!GO:0000902;cell morphogenesis;0.047795638695198;211323!GO:0032989;cellular structure morphogenesis;0.047795638695198;211323!
}}

Latest revision as of 15:56, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:115246787..115246797,-p@chr13:115246787..115246797
-
Mm9::chr15:62082108..62082111,+p@chr15:62082108..62082111
+
Mm9::chr1:166561874..166561885,+p@chr1:166561874..166561885
+
Mm9::chr2:178190105..178190122,+p@chr2:178190105..178190122
+
Mm9::chr4:124799704..124799713,-p4@Zc3h12a
Mm9::chr4:145000183..145000220,+p1@ENSMUST00000150529
Mm9::chr8:33120000..33120013,-p5@Nrg1
Mm9::chr9:50913937..50913956,-p@chr9:50913937..50913956
-
Mm9::chr9:50913979..50913993,-p@chr9:50913979..50913993
-


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:0005176ErbB-2 class receptor binding0.0120528132361804
GO:0046579positive regulation of Ras protein signal transduction0.0120528132361804
GO:0045213neurotransmitter receptor metabolic process0.0120528132361804
GO:0051057positive regulation of small GTPase mediated signal transduction0.0120528132361804
GO:0043624cellular protein complex disassembly0.0120528132361804
GO:0043241protein complex disassembly0.0120528132361804
GO:0032984macromolecular complex disassembly0.0120528132361804
GO:0007416synaptogenesis0.0125550137876879
GO:0048663neuron fate commitment0.0125550137876879
GO:0022411cellular component disassembly0.0125550137876879
GO:0007422peripheral nervous system development0.0125550137876879
GO:0043112receptor metabolic process0.0125550137876879
GO:0010001glial cell differentiation0.0176156501144174
GO:0042063gliogenesis0.0176487622386927
GO:0050808synapse organization and biogenesis0.0176774594130645
GO:0045860positive regulation of protein kinase activity0.028697174371858
GO:0033674positive regulation of kinase activity0.028697174371858
GO:0051347positive regulation of transferase activity0.028697174371858
GO:0043062extracellular structure organization and biogenesis0.028697174371858
GO:0046578regulation of Ras protein signal transduction0.028697174371858
GO:0045165cell fate commitment0.028697174371858
GO:0000165MAPKKK cascade0.0292711178592952
GO:0051056regulation of small GTPase mediated signal transduction0.0292711178592952
GO:0045859regulation of protein kinase activity0.0292711178592952
GO:0043549regulation of kinase activity0.0292711178592952
GO:0043085positive regulation of catalytic activity0.0292711178592952
GO:0051338regulation of transferase activity0.0292711178592952
GO:0003712transcription cofactor activity0.0292711178592952
GO:0007265Ras protein signal transduction0.0307346737522599
GO:0045595regulation of cell differentiation0.0307346737522599
GO:0007517muscle development0.0320152851586041
GO:0007507heart development0.0320152851586041
GO:0008134transcription factor binding0.0336769781599157
GO:0007268synaptic transmission0.0336769781599157
GO:0007626locomotory behavior0.0347809753386919
GO:0005125cytokine activity0.0356698121449121
GO:0007243protein kinase cascade0.0356698121449121
GO:0019226transmission of nerve impulse0.0356826707650076
GO:0016481negative regulation of transcription0.0367765326950119
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0370350079438996
GO:0050793regulation of developmental process0.0370350079438996
GO:0050790regulation of catalytic activity0.0370350079438996
GO:0016477cell migration0.0370350079438996
GO:0030182neuron differentiation0.0370350079438996
GO:0031324negative regulation of cellular metabolic process0.0370350079438996
GO:0065009regulation of a molecular function0.0370350079438996
GO:0007610behavior0.0370350079438996
GO:0048699generation of neurons0.0370350079438996
GO:0051674localization of cell0.0370350079438996
GO:0006928cell motility0.0370350079438996
GO:0007267cell-cell signaling0.0370350079438996
GO:0009892negative regulation of metabolic process0.0370350079438996
GO:0009966regulation of signal transduction0.0370350079438996
GO:0007264small GTPase mediated signal transduction0.0370350079438996
GO:0022008neurogenesis0.0370350079438996
GO:0009790embryonic development0.047795638695198
GO:0000902cell morphogenesis0.047795638695198
GO:0032989cellular structure morphogenesis0.047795638695198



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
smooth muscle tissue5.18e-143
blood vessel smooth muscle5.18e-143
arterial system smooth muscle5.18e-143
artery smooth muscle tissue5.18e-143
aorta smooth muscle tissue5.18e-143
skeletal muscle tissue6.45e-129
striated muscle tissue6.45e-129
muscle tissue6.45e-129
multilaminar epithelium6.45e-129
epithelial vesicle6.45e-129
musculature6.45e-129
somite6.45e-129
myotome6.45e-129
presomitic mesoderm6.45e-129
presumptive segmental plate6.45e-129
dermomyotome6.45e-129
trunk paraxial mesoderm6.45e-129
musculature of body1.06e-1010
aorta1.26e-104
artery1.26e-104
systemic artery1.26e-104
arterial blood vessel1.26e-104
systemic arterial system1.26e-104
aortic system1.26e-104
arterial system1.26e-104
dense mesenchyme tissue1.05e-0911
paraxial mesoderm1.05e-0911
presumptive paraxial mesoderm1.05e-0911
vessel1.39e-085
epithelial tube open at both ends1.39e-085
blood vessel1.39e-085
vasculature1.39e-085
vascular system1.39e-085
blood vasculature1.39e-085
vascular cord1.39e-085


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)
MA0003.10.0343274
MA0004.10.394951
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.248772
MA0017.10.726051
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.11.28203
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.837668
MA0043.10.918718
MA0046.10.858391
MA0048.10.589612
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.11.4071
MA0056.10
MA0057.10.258928
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.12.40227
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.0771206
MA0074.10.488775
MA0076.10.765781
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.413524
MA0089.10
MA0090.10.951436
MA0091.10.407455
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.867731
MA0103.10.272167
MA0105.10.720048
MA0106.13.55967
MA0107.12.08048
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.10.670446
MA0117.10.88947
MA0119.11.56471
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.441109
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.11.07908
MA0145.10.442138
MA0146.10.0548413
MA0147.10.593505
MA0148.10.410398
MA0149.16.45016
MA0062.20.738221
MA0035.20.482026
MA0039.20.175249
MA0138.20.630612
MA0002.20.447007
MA0137.20.287486
MA0104.20.476119
MA0047.20.533516
MA0112.20.0543294
MA0065.20.0545595
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.0809407
MA0155.10.226288
MA0156.10.763978
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.0143037
MA0163.10.0600297
MA0164.10.508398
MA0080.20.737531
MA0018.20.51781
MA0099.20.624421
MA0079.22.46822
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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