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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.554785308251162,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.978748387393722,1.00433070349492,0.142671721075526,0.0997909775761048,0,0.0481920468563092,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0403878614760544,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0048863;stem cell differentiation;2.7667001875512e-06;18999,18119,71950!GO:0048864;stem cell development;0.000451023744568524;18999,18119!GO:0019827;stem cell maintenance;0.000451023744568524;18999,18119!GO:0042074;cell migration involved in gastrulation;0.000630972040384902;13590,18119!GO:0045596;negative regulation of cell differentiation;0.000948523766910004;18999,18119,71950!GO:0045120;pronucleus;0.00124038586237459;21432,73708!GO:0051093;negative regulation of developmental process;0.00124038586237459;18999,18119,71950!GO:0008083;growth factor activity;0.00304482699284934;320202,13590,18119!GO:0045595;regulation of cell differentiation;0.00304482699284934;18999,18119,71950!GO:0009790;embryonic development;0.00342597435615527;13590,73708,18119,71950!GO:0005125;cytokine activity;0.00670187390332782;320202,13590,18119!GO:0007389;pattern specification process;0.00788911411822714;13590,18119,71950!GO:0050793;regulation of developmental process;0.00788911411822714;18999,18119,71950!GO:0001714;endodermal cell fate specification;0.00788911411822714;71950!GO:0042664;negative regulation of endodermal cell fate specification;0.00788911411822714;71950!GO:0002085;repression of premature neural plate formation;0.00788911411822714;18119!GO:0030718;germ-line stem cell maintenance;0.00788911411822714;18999!GO:0042663;regulation of endodermal cell fate specification;0.00788911411822714;71950!GO:0004577;N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity;0.00788911411822714;67574!GO:0007369;gastrulation;0.00835616358503614;13590,18119!GO:0032502;developmental process;0.00842780921854488;378430,320202,13590,73708,18999,18119,71950!GO:0032501;multicellular organismal process;0.0105943426963285;18796,13590,320202,378430,73708,12877,71950,18119!GO:0007275;multicellular organismal development;0.010703428565192;378430,320202,13590,73708,18119,71950!GO:0001711;endodermal cell fate commitment;0.010703428565192;71950!GO:0042659;regulation of cell fate specification;0.010703428565192;71950!GO:0010453;regulation of cell fate commitment;0.010703428565192;71950!GO:0009996;negative regulation of cell fate specification;0.010703428565192;71950!GO:0010454;negative regulation of cell fate commitment;0.010703428565192;71950!GO:0048523;negative regulation of cellular process;0.0116737389182239;13590,18999,18119,71950!GO:0009952;anterior/posterior pattern formation;0.012727101419578;13590,18119!GO:0045165;cell fate commitment;0.0138066231261762;18119,71950!GO:0048519;negative regulation of biological process;0.0138066231261762;13590,18999,18119,71950!GO:0030259;lipid glycosylation;0.0176185544395488;67574!GO:0001940;male pronucleus;0.0176185544395488;73708!GO:0006417;regulation of translation;0.0196990255106665;378430,12877!GO:0048505;regulation of timing of cell differentiation;0.0196990255106665;18119!GO:0040034;regulation of development, heterochronic;0.0196990255106665;18119!GO:0001939;female pronucleus;0.0196990255106665;73708!GO:0031326;regulation of cellular biosynthetic process;0.0211316487213253;378430,12877!GO:0005160;transforming growth factor beta receptor binding;0.0218905462024405;320202!GO:0040016;embryonic cleavage;0.0218905462024405;73708!GO:0003002;regionalization;0.0218905462024405;13590,18119!GO:0009889;regulation of biosynthetic process;0.0237110789038901;378430,12877!GO:0007130;synaptonemal complex assembly;0.0238035645283384;12877!GO:0065007;biological regulation;0.0271473139901545;378430,320202,13590,12877,18999,18119,71950!GO:0017145;stem cell division;0.0288307489318434;71950!GO:0005102;receptor binding;0.0288307489318434;320202,13590,18119!GO:0009948;anterior/posterior axis specification;0.0342471769361994;13590!GO:0007129;synapsis;0.0365870750233847;12877!GO:0001947;heart looping;0.0406109439809507;18119!GO:0048168;regulation of neuronal synaptic plasticity;0.0406109439809507;12877!GO:0050794;regulation of cellular process;0.0406109439809507;378430,13590,12877,18999,18119,71950!GO:0051246;regulation of protein metabolic process;0.0413016207316092;378430,12877!GO:0051301;cell division;0.0419009446029893;73708,71950!GO:0009798;axis specification;0.0461078486046946;13590!
|gostat_on_MCL_coexpression=GO:0048863;stem cell differentiation;2.7667001875512e-06;18999,18119,71950!GO:0048864;stem cell development;0.000451023744568524;18999,18119!GO:0019827;stem cell maintenance;0.000451023744568524;18999,18119!GO:0042074;cell migration involved in gastrulation;0.000630972040384902;13590,18119!GO:0045596;negative regulation of cell differentiation;0.000948523766910004;18999,18119,71950!GO:0045120;pronucleus;0.00124038586237459;21432,73708!GO:0051093;negative regulation of developmental process;0.00124038586237459;18999,18119,71950!GO:0008083;growth factor activity;0.00304482699284934;320202,13590,18119!GO:0045595;regulation of cell differentiation;0.00304482699284934;18999,18119,71950!GO:0009790;embryonic development;0.00342597435615527;13590,73708,18119,71950!GO:0005125;cytokine activity;0.00670187390332782;320202,13590,18119!GO:0007389;pattern specification process;0.00788911411822714;13590,18119,71950!GO:0050793;regulation of developmental process;0.00788911411822714;18999,18119,71950!GO:0001714;endodermal cell fate specification;0.00788911411822714;71950!GO:0042664;negative regulation of endodermal cell fate specification;0.00788911411822714;71950!GO:0002085;repression of premature neural plate formation;0.00788911411822714;18119!GO:0030718;germ-line stem cell maintenance;0.00788911411822714;18999!GO:0042663;regulation of endodermal cell fate specification;0.00788911411822714;71950!GO:0004577;N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity;0.00788911411822714;67574!GO:0007369;gastrulation;0.00835616358503614;13590,18119!GO:0032502;developmental process;0.00842780921854488;378430,320202,13590,73708,18999,18119,71950!GO:0032501;multicellular organismal process;0.0105943426963285;18796,13590,320202,378430,73708,12877,71950,18119!GO:0007275;multicellular organismal development;0.010703428565192;378430,320202,13590,73708,18119,71950!GO:0001711;endodermal cell fate commitment;0.010703428565192;71950!GO:0042659;regulation of cell fate specification;0.010703428565192;71950!GO:0010453;regulation of cell fate commitment;0.010703428565192;71950!GO:0009996;negative regulation of cell fate specification;0.010703428565192;71950!GO:0010454;negative regulation of cell fate commitment;0.010703428565192;71950!GO:0048523;negative regulation of cellular process;0.0116737389182239;13590,18999,18119,71950!GO:0009952;anterior/posterior pattern formation;0.012727101419578;13590,18119!GO:0045165;cell fate commitment;0.0138066231261762;18119,71950!GO:0048519;negative regulation of biological process;0.0138066231261762;13590,18999,18119,71950!GO:0030259;lipid glycosylation;0.0176185544395488;67574!GO:0001940;male pronucleus;0.0176185544395488;73708!GO:0006417;regulation of translation;0.0196990255106665;378430,12877!GO:0048505;regulation of timing of cell differentiation;0.0196990255106665;18119!GO:0040034;regulation of development, heterochronic;0.0196990255106665;18119!GO:0001939;female pronucleus;0.0196990255106665;73708!GO:0031326;regulation of cellular biosynthetic process;0.0211316487213253;378430,12877!GO:0005160;transforming growth factor beta receptor binding;0.0218905462024405;320202!GO:0040016;embryonic cleavage;0.0218905462024405;73708!GO:0003002;regionalization;0.0218905462024405;13590,18119!GO:0009889;regulation of biosynthetic process;0.0237110789038901;378430,12877!GO:0007130;synaptonemal complex assembly;0.0238035645283384;12877!GO:0065007;biological regulation;0.0271473139901545;378430,320202,13590,12877,18999,18119,71950!GO:0017145;stem cell division;0.0288307489318434;71950!GO:0005102;receptor binding;0.0288307489318434;320202,13590,18119!GO:0009948;anterior/posterior axis specification;0.0342471769361994;13590!GO:0007129;synapsis;0.0365870750233847;12877!GO:0001947;heart looping;0.0406109439809507;18119!GO:0048168;regulation of neuronal synaptic plasticity;0.0406109439809507;12877!GO:0050794;regulation of cellular process;0.0406109439809507;378430,13590,12877,18999,18119,71950!GO:0051246;regulation of protein metabolic process;0.0413016207316092;378430,12877!GO:0051301;cell division;0.0419009446029893;73708,71950!GO:0009798;axis specification;0.0461078486046946;13590!
}}
}}

Revision as of 12:40, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:60881031..60881037,+p1@Nodal
Mm9::chr12:106460922..106460932,-p1@Tcl1
Mm9::chr12:106460944..106460955,-p2@Tcl1
Mm9::chr16:48281766..48281778,+p@chr16:48281766..48281778
+
Mm9::chr17:35642973..35642994,+p2@Pou5f1
Mm9::chr17:35642997..35643014,+p1@Pou5f1
Mm9::chr1:182823238..182823239,+p1@Lefty2
Mm9::chr1:182865168..182865172,+p2@Lefty1
Mm9::chr2:118541186..118541194,-p@chr2:118541186..118541194
-
Mm9::chr2:165635739..165635747,+p@chr2:165635739..165635747
+
Mm9::chr2:25621051..25621055,+p1@Lcn3
Mm9::chr6:122576436..122576438,+p1@Dppa3
Mm9::chr6:122657610..122657626,+p1@Nanog
p1@Nanogpd
Mm9::chr7:19572867..19572873,+p1@Nanos2
Mm9::chr7:88599637..88599650,-p4@Cpeb1
Mm9::chr9:78215959..78215971,-p1@Dppa5a
Mm9::chr9:78215974..78215984,-p2@Dppa5a
Mm9::chr9:78215998..78216003,-p3@Dppa5a
Mm9::chrX:140770330..140770374,+p5@Alg13


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:0048863stem cell differentiation2.7667001875512e-06
GO:0048864stem cell development0.000451023744568524
GO:0019827stem cell maintenance0.000451023744568524
GO:0042074cell migration involved in gastrulation0.000630972040384902
GO:0045596negative regulation of cell differentiation0.000948523766910004
GO:0045120pronucleus0.00124038586237459
GO:0051093negative regulation of developmental process0.00124038586237459
GO:0008083growth factor activity0.00304482699284934
GO:0045595regulation of cell differentiation0.00304482699284934
GO:0009790embryonic development0.00342597435615527
GO:0005125cytokine activity0.00670187390332782
GO:0007389pattern specification process0.00788911411822714
GO:0050793regulation of developmental process0.00788911411822714
GO:0001714endodermal cell fate specification0.00788911411822714
GO:0042664negative regulation of endodermal cell fate specification0.00788911411822714
GO:0002085repression of premature neural plate formation0.00788911411822714
GO:0030718germ-line stem cell maintenance0.00788911411822714
GO:0042663regulation of endodermal cell fate specification0.00788911411822714
GO:0004577N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity0.00788911411822714
GO:0007369gastrulation0.00835616358503614
GO:0032502developmental process0.00842780921854488
GO:0032501multicellular organismal process0.0105943426963285
GO:0007275multicellular organismal development0.010703428565192
GO:0001711endodermal cell fate commitment0.010703428565192
GO:0042659regulation of cell fate specification0.010703428565192
GO:0010453regulation of cell fate commitment0.010703428565192
GO:0009996negative regulation of cell fate specification0.010703428565192
GO:0010454negative regulation of cell fate commitment0.010703428565192
GO:0048523negative regulation of cellular process0.0116737389182239
GO:0009952anterior/posterior pattern formation0.012727101419578
GO:0045165cell fate commitment0.0138066231261762
GO:0048519negative regulation of biological process0.0138066231261762
GO:0030259lipid glycosylation0.0176185544395488
GO:0001940male pronucleus0.0176185544395488
GO:0006417regulation of translation0.0196990255106665
GO:0048505regulation of timing of cell differentiation0.0196990255106665
GO:0040034regulation of development, heterochronic0.0196990255106665
GO:0001939female pronucleus0.0196990255106665
GO:0031326regulation of cellular biosynthetic process0.0211316487213253
GO:0005160transforming growth factor beta receptor binding0.0218905462024405
GO:0040016embryonic cleavage0.0218905462024405
GO:0003002regionalization0.0218905462024405
GO:0009889regulation of biosynthetic process0.0237110789038901
GO:0007130synaptonemal complex assembly0.0238035645283384
GO:0065007biological regulation0.0271473139901545
GO:0017145stem cell division0.0288307489318434
GO:0005102receptor binding0.0288307489318434
GO:0009948anterior/posterior axis specification0.0342471769361994
GO:0007129synapsis0.0365870750233847
GO:0001947heart looping0.0406109439809507
GO:0048168regulation of neuronal synaptic plasticity0.0406109439809507
GO:0050794regulation of cellular process0.0406109439809507
GO:0051246regulation of protein metabolic process0.0413016207316092
GO:0051301cell division0.0419009446029893
GO:0009798axis specification0.0461078486046946



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>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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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