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MCL coexpression mm9:3505: Difference between revisions

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{{MCL_coexpression_mm9
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foregut morphogenesis;0.011145798098101;11481!GO:0007440;foregut morphogenesis;0.011145798098101;11481!GO:0060021;palate development;0.011145798098101;11481!GO:0048613;embryonic ectodermal gut morphogenesis;0.011145798098101;11481!GO:0005881;cytoplasmic microtubule;0.011145798098101;269713!GO:0048611;embryonic ectodermal gut development;0.011145798098101;11481!GO:0048185;activin binding;0.011145798098101;11481!GO:0004712;protein serine/threonine/tyrosine kinase activity;0.011145798098101;11481!GO:0048558;embryonic gut morphogenesis;0.011145798098101;11481!GO:0048557;embryonic digestive tract morphogenesis;0.011145798098101;11481!GO:0007439;ectodermal gut development;0.011145798098101;11481!GO:0048567;ectodermal gut morphogenesis;0.011145798098101;11481!GO:0006367;transcription initiation from RNA polymerase II promoter;0.011145798098101;269713!GO:0048547;gut morphogenesis;0.011145798098101;11481!GO:0004675;transmembrane receptor protein serine/threonine kinase activity;0.011145798098101;11481!GO:0005024;transforming growth factor beta receptor activity;0.011145798098101;11481!GO:0048546;digestive tract morphogenesis;0.0117080755149383;11481!GO:0048566;embryonic gut development;0.0117080755149383;11481!GO:0048565;gut development;0.0153558571126666;11481!GO:0048562;embryonic organ morphogenesis;0.0170180089459955;11481!GO:0048705;skeletal morphogenesis;0.0177502380498165;11481!GO:0006352;transcription initiation;0.0184157393298989;269713!GO:0001702;gastrulation with mouth forming second;0.0212276851367173;11481!GO:0007368;determination of left/right symmetry;0.0212276851367173;11481!GO:0009799;determination of symmetry;0.0212276851367173;11481!GO:0009855;determination of bilateral symmetry;0.0212276851367173;11481!GO:0042475;odontogenesis of dentine-containing teeth;0.0212276851367173;11481!GO:0048568;embryonic organ development;0.0212276851367173;11481!GO:0042476;odontogenesis;0.0212276851367173;11481!GO:0004702;receptor signaling protein 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|gostat_on_MCL_coexpression=GO:0048617;embryonic foregut morphogenesis;0.011145798098101;11481!GO:0007440;foregut morphogenesis;0.011145798098101;11481!GO:0060021;palate development;0.011145798098101;11481!GO:0048613;embryonic ectodermal gut morphogenesis;0.011145798098101;11481!GO:0005881;cytoplasmic microtubule;0.011145798098101;269713!GO:0048611;embryonic ectodermal gut development;0.011145798098101;11481!GO:0048185;activin binding;0.011145798098101;11481!GO:0004712;protein serine/threonine/tyrosine kinase activity;0.011145798098101;11481!GO:0048558;embryonic gut morphogenesis;0.011145798098101;11481!GO:0048557;embryonic digestive tract morphogenesis;0.011145798098101;11481!GO:0007439;ectodermal gut development;0.011145798098101;11481!GO:0048567;ectodermal gut morphogenesis;0.011145798098101;11481!GO:0006367;transcription initiation from RNA polymerase II promoter;0.011145798098101;269713!GO:0048547;gut morphogenesis;0.011145798098101;11481!GO:0004675;transmembrane receptor protein serine/threonine kinase activity;0.011145798098101;11481!GO:0005024;transforming growth factor beta receptor activity;0.011145798098101;11481!GO:0048546;digestive tract morphogenesis;0.0117080755149383;11481!GO:0048566;embryonic gut development;0.0117080755149383;11481!GO:0048565;gut development;0.0153558571126666;11481!GO:0048562;embryonic organ morphogenesis;0.0170180089459955;11481!GO:0048705;skeletal morphogenesis;0.0177502380498165;11481!GO:0006352;transcription initiation;0.0184157393298989;269713!GO:0001702;gastrulation with mouth forming second;0.0212276851367173;11481!GO:0007368;determination of left/right symmetry;0.0212276851367173;11481!GO:0009799;determination of symmetry;0.0212276851367173;11481!GO:0009855;determination of bilateral symmetry;0.0212276851367173;11481!GO:0042475;odontogenesis of dentine-containing teeth;0.0212276851367173;11481!GO:0048568;embryonic organ development;0.0212276851367173;11481!GO:0042476;odontogenesis;0.0212276851367173;11481!GO:0004702;receptor signaling protein serine/threonine kinase activity;0.0247988829518103;11481!GO:0019838;growth factor binding;0.0247988829518103;11481!GO:0007498;mesoderm development;0.0247988829518103;11481!GO:0007369;gastrulation;0.0304164743280477;11481!GO:0001822;kidney development;0.0336412387697396;11481!GO:0019199;transmembrane receptor protein kinase activity;0.0336412387697396;11481!GO:0003702;RNA polymerase II transcription factor activity;0.0336412387697396;269713!GO:0001655;urogenital system development;0.0336412387697396;11481!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0336412387697396;11481!GO:0005057;receptor signaling protein activity;0.0356762223841759;11481!GO:0009952;anterior/posterior pattern formation;0.0380117155275296;11481!GO:0065004;protein-DNA complex assembly;0.0473082376810146;269713!GO:0030145;manganese ion binding;0.0496332098555546;11481!
}}

Latest revision as of 20:12, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr5:135028251..135028283,-p4@Clip2
Mm9::chr5:135028284..135028314,-p2@Clip2
Mm9::chr9:119311199..119311271,+p1@Acvr2b


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:0048617embryonic foregut morphogenesis0.011145798098101
GO:0007440foregut morphogenesis0.011145798098101
GO:0060021palate development0.011145798098101
GO:0048613embryonic ectodermal gut morphogenesis0.011145798098101
GO:0005881cytoplasmic microtubule0.011145798098101
GO:0048611embryonic ectodermal gut development0.011145798098101
GO:0048185activin binding0.011145798098101
GO:0004712protein serine/threonine/tyrosine kinase activity0.011145798098101
GO:0048558embryonic gut morphogenesis0.011145798098101
GO:0048557embryonic digestive tract morphogenesis0.011145798098101
GO:0007439ectodermal gut development0.011145798098101
GO:0048567ectodermal gut morphogenesis0.011145798098101
GO:0006367transcription initiation from RNA polymerase II promoter0.011145798098101
GO:0048547gut morphogenesis0.011145798098101
GO:0004675transmembrane receptor protein serine/threonine kinase activity0.011145798098101
GO:0005024transforming growth factor beta receptor activity0.011145798098101
GO:0048546digestive tract morphogenesis0.0117080755149383
GO:0048566embryonic gut development0.0117080755149383
GO:0048565gut development0.0153558571126666
GO:0048562embryonic organ morphogenesis0.0170180089459955
GO:0048705skeletal morphogenesis0.0177502380498165
GO:0006352transcription initiation0.0184157393298989
GO:0001702gastrulation with mouth forming second0.0212276851367173
GO:0007368determination of left/right symmetry0.0212276851367173
GO:0009799determination of symmetry0.0212276851367173
GO:0009855determination of bilateral symmetry0.0212276851367173
GO:0042475odontogenesis of dentine-containing teeth0.0212276851367173
GO:0048568embryonic organ development0.0212276851367173
GO:0042476odontogenesis0.0212276851367173
GO:0004702receptor signaling protein serine/threonine kinase activity0.0247988829518103
GO:0019838growth factor binding0.0247988829518103
GO:0007498mesoderm development0.0247988829518103
GO:0007369gastrulation0.0304164743280477
GO:0001822kidney development0.0336412387697396
GO:0019199transmembrane receptor protein kinase activity0.0336412387697396
GO:0003702RNA polymerase II transcription factor activity0.0336412387697396
GO:0001655urogenital system development0.0336412387697396
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0336412387697396
GO:0005057receptor signaling protein activity0.0356762223841759
GO:0009952anterior/posterior pattern formation0.0380117155275296
GO:0065004protein-DNA complex assembly0.0473082376810146
GO:0030145manganese ion binding0.0496332098555546



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 system5.01e-2175
central nervous system2.97e-2073
neurectoderm7.53e-1864
neural plate7.53e-1864
presumptive neural plate7.53e-1864
ectoderm-derived structure1.30e-1695
ectoderm1.30e-1695
presumptive ectoderm1.30e-1695
regional part of nervous system3.77e-1554
neural tube3.37e-1452
neural rod3.37e-1452
future spinal cord3.37e-1452
neural keel3.37e-1452
pre-chordal neural plate6.25e-1449
gray matter3.29e-1234
ecto-epithelium4.29e-1273
brain6.18e-1247
future brain6.18e-1247
anterior neural tube6.54e-1240
regional part of forebrain2.09e-1139
forebrain2.09e-1139
future forebrain2.09e-1139
regional part of brain2.29e-1146
brain grey matter9.91e-1029
regional part of telencephalon9.91e-1029
telencephalon9.91e-1029
structure with developmental contribution from neural crest5.69e-0992


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)
MA0003.10.899234
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.14.96439
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.11.60767
MA0058.10.690848
MA0059.11.68104
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.13.3888
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.117.0441
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.11.7994
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.11.46662
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.46063
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.23.91141
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.499274
MA0163.10.477233
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.29.2373
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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