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MCL coexpression mm9:399: Difference between revisions

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{{MCL_coexpression_mm9
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ion binding;0.0109632657125492;21408,232966,22718,237758,22775,22696!GO:0044424;intracellular part;0.0109632657125492;21408,20822,22718,237758,12419,22775,22696,232966,16579,68519!GO:0046914;transition metal ion binding;0.0109632657125492;21408,232966,22718,237758,22775,22696!GO:0046587;positive regulation of calcium-dependent cell-cell adhesion;0.0109632657125492;16579!GO:0016939;kinesin II complex;0.0109632657125492;16579!GO:0046586;regulation of calcium-dependent cell-cell adhesion;0.0109632657125492;16579!GO:0005622;intracellular;0.0109632657125492;21408,20822,22718,237758,12419,22775,22696,232966,16579,68519!GO:0043229;intracellular organelle;0.0170505484654286;21408,22718,237758,12419,22775,22696,232966,16579,68519!GO:0043226;organelle;0.0170505484654286;21408,22718,237758,12419,22775,22696,232966,16579,68519!GO:0005634;nucleus;0.0174100124011624;21408,232966,22718,237758,12419,22775,22696!GO:0043169;cation binding;0.0339239644478828;21408,232966,22718,237758,22775,22696!GO:0010369;chromocenter;0.0344723512049932;12419!GO:0019894;kinesin binding;0.04006297551357;16579!GO:0046872;metal ion binding;0.04006297551357;21408,232966,22718,237758,22775,22696!GO:0022407;regulation of cell-cell adhesion;0.04006297551357;16579!GO:0043167;ion binding;0.04006297551357;21408,232966,22718,237758,22775,22696!GO:0016339;calcium-dependent cell-cell adhesion;0.040515738197994;16579!GO:0045785;positive regulation of cell 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|gostat_on_MCL_coexpression=GO:0008270;zinc ion binding;0.0109632657125492;21408,232966,22718,237758,22775,22696!GO:0044424;intracellular part;0.0109632657125492;21408,20822,22718,237758,12419,22775,22696,232966,16579,68519!GO:0046914;transition metal ion binding;0.0109632657125492;21408,232966,22718,237758,22775,22696!GO:0046587;positive regulation of calcium-dependent cell-cell adhesion;0.0109632657125492;16579!GO:0016939;kinesin II complex;0.0109632657125492;16579!GO:0046586;regulation of calcium-dependent cell-cell adhesion;0.0109632657125492;16579!GO:0005622;intracellular;0.0109632657125492;21408,20822,22718,237758,12419,22775,22696,232966,16579,68519!GO:0043229;intracellular organelle;0.0170505484654286;21408,22718,237758,12419,22775,22696,232966,16579,68519!GO:0043226;organelle;0.0170505484654286;21408,22718,237758,12419,22775,22696,232966,16579,68519!GO:0005634;nucleus;0.0174100124011624;21408,232966,22718,237758,12419,22775,22696!GO:0043169;cation binding;0.0339239644478828;21408,232966,22718,237758,22775,22696!GO:0010369;chromocenter;0.0344723512049932;12419!GO:0019894;kinesin binding;0.04006297551357;16579!GO:0046872;metal ion binding;0.04006297551357;21408,232966,22718,237758,22775,22696!GO:0022407;regulation of cell-cell adhesion;0.04006297551357;16579!GO:0043167;ion binding;0.04006297551357;21408,232966,22718,237758,22775,22696!GO:0016339;calcium-dependent cell-cell adhesion;0.040515738197994;16579!GO:0045785;positive regulation of cell adhesion;0.0458952073181271;16579!
|ontology_enrichment_celltype=CL:0000540!2.90e-10!33;CL:0000047!2.90e-10!33;CL:0000031!2.90e-10!33;CL:0000404!2.90e-10!33;CL:0000393!1.57e-08!39;CL:0000211!1.57e-08!39;CL:0000117!1.06e-07!23;CL:0000337!1.06e-07!23
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!2.53e-23!64;UBERON:0003075!2.53e-23!64;UBERON:0007284!2.53e-23!64;UBERON:0010371!6.36e-21!73;UBERON:0004121!9.11e-21!95;UBERON:0000924!9.11e-21!95;UBERON:0006601!9.11e-21!95;UBERON:0001017!2.07e-20!73;UBERON:0003056!4.16e-20!49;UBERON:0001016!4.81e-20!75;UBERON:0010314!1.17e-18!92;UBERON:0000073!1.84e-18!54;UBERON:0001049!4.20e-18!52;UBERON:0005068!4.20e-18!52;UBERON:0006241!4.20e-18!52;UBERON:0007135!4.20e-18!52;UBERON:0000955!2.75e-17!47;UBERON:0006238!2.75e-17!47;UBERON:0002616!1.06e-16!46;UBERON:0003080!4.65e-16!40;UBERON:0002780!1.98e-15!39;UBERON:0001890!1.98e-15!39;UBERON:0006240!1.98e-15!39;UBERON:0002020!6.26e-13!34;UBERON:0003528!3.95e-12!29;UBERON:0002791!3.95e-12!29;UBERON:0001893!3.95e-12!29;UBERON:0000468!5.38e-11!333;UBERON:0000922!4.83e-09!320;UBERON:0000956!8.31e-09!21;UBERON:0001869!8.31e-09!21;UBERON:0000203!8.31e-09!21;UBERON:0002619!4.09e-07!17;UBERON:0000025!6.74e-07!114;UBERON:0002021!9.55e-07!10;UBERON:0000411!9.55e-07!10;UBERON:0001950!9.55e-07!10
}}

Latest revision as of 15:14, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:50700965..50701027,-p1@Zfp454
Mm9::chr11:50872733..50872809,+p1@Zfp354a
Mm9::chr12:109661279..109661346,+p1@Eml1
Mm9::chr15:103045716..103045792,-p2@Cbx5
Mm9::chr15:12754596..12754638,+p1@Drosha
Mm9::chr16:38550224..38550250,-p2@Poglut1
Mm9::chr17:32967140..32967197,-p1@Zfp799
Mm9::chr1:145624103..145624169,-p1@Trove2
Mm9::chr1:165709942..165709996,+p4@Kifap3
Mm9::chr2:73730355..73730425,-p@chr2:73730355..73730425
-
Mm9::chr4:61869460..61869521,-p1@Zfp37
Mm9::chr7:11080671..11080750,-p1@Zik1
Mm9::chr7:24960051..24960080,+p1@Zfp114
Mm9::chr7:28516417..28516460,+p1@Zfp60
Mm9::chr7:69354369..69354380,-p2@uc009hfe.1
p2@uc012fml.1
Mm9::chr7:69354385..69354432,-p1@uc009hfe.1
p1@uc012fml.1
Mm9::chrX:92853718..92853729,-p3@Zc4h2
Mm9::chrX:92853731..92853751,-p2@Zc4h2
Mm9::chrX:92853755..92853786,-p1@Zc4h2


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:0008270zinc ion binding0.0109632657125492
GO:0044424intracellular part0.0109632657125492
GO:0046914transition metal ion binding0.0109632657125492
GO:0046587positive regulation of calcium-dependent cell-cell adhesion0.0109632657125492
GO:0016939kinesin II complex0.0109632657125492
GO:0046586regulation of calcium-dependent cell-cell adhesion0.0109632657125492
GO:0005622intracellular0.0109632657125492
GO:0043229intracellular organelle0.0170505484654286
GO:0043226organelle0.0170505484654286
GO:0005634nucleus0.0174100124011624
GO:0043169cation binding0.0339239644478828
GO:0010369chromocenter0.0344723512049932
GO:0019894kinesin binding0.04006297551357
GO:0046872metal ion binding0.04006297551357
GO:0022407regulation of cell-cell adhesion0.04006297551357
GO:0043167ion binding0.04006297551357
GO:0016339calcium-dependent cell-cell adhesion0.040515738197994
GO:0045785positive regulation of cell adhesion0.0458952073181271



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>

Cell Type
Ontology termp-valuen
neuron2.90e-1033
neuronal stem cell2.90e-1033
neuroblast2.90e-1033
electrically signaling cell2.90e-1033
electrically responsive cell1.57e-0839
electrically active cell1.57e-0839
CNS neuron (sensu Vertebrata)1.06e-0723
neuroblast (sensu Vertebrata)1.06e-0723

Uber Anatomy
Ontology termp-valuen
neurectoderm2.53e-2364
neural plate2.53e-2364
presumptive neural plate2.53e-2364
ecto-epithelium6.36e-2173
ectoderm-derived structure9.11e-2195
ectoderm9.11e-2195
presumptive ectoderm9.11e-2195
central nervous system2.07e-2073
pre-chordal neural plate4.16e-2049
nervous system4.81e-2075
structure with developmental contribution from neural crest1.17e-1892
regional part of nervous system1.84e-1854
neural tube4.20e-1852
neural rod4.20e-1852
future spinal cord4.20e-1852
neural keel4.20e-1852
brain2.75e-1747
future brain2.75e-1747
regional part of brain1.06e-1646
anterior neural tube4.65e-1640
regional part of forebrain1.98e-1539
forebrain1.98e-1539
future forebrain1.98e-1539
gray matter6.26e-1334
brain grey matter3.95e-1229
regional part of telencephalon3.95e-1229
telencephalon3.95e-1229
multi-cellular organism5.38e-11333
embryo4.83e-09320
cerebral cortex8.31e-0921
cerebral hemisphere8.31e-0921
pallium8.31e-0921
regional part of cerebral cortex4.09e-0717
tube6.74e-07114
occipital lobe9.55e-0710
visual cortex9.55e-0710
neocortex9.55e-0710


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)
MA0003.10.365217
MA0004.10.178381
MA0006.10.0769247
MA0007.10.168178
MA0009.11.32592
MA0014.10.0736541
MA0017.10.30345
MA0019.10.376509
MA0024.12.1501
MA0025.10.751694
MA0027.12.14278
MA0028.10.588161
MA0029.10.477444
MA0030.10.483253
MA0031.10.451927
MA0038.10.779388
MA0040.10.547233
MA0041.10.129017
MA0042.10.121046
MA0043.10.624178
MA0046.10.568473
MA0048.10.768218
MA0050.10.205672
MA0051.10.2928
MA0052.10.554531
MA0055.10.018284
MA0056.10
MA0057.10.0454221
MA0058.10.117003
MA0059.10.392739
MA0060.10.659439
MA0061.10.438647
MA0063.10
MA0066.10.759694
MA0067.10.857286
MA0068.10.00953628
MA0069.10.554839
MA0070.10.54606
MA0071.10.20507
MA0072.11.33116
MA0073.10.0866236
MA0074.10.249359
MA0076.11.12482
MA0077.10.518913
MA0078.10.855296
MA0081.10.138626
MA0083.10.623446
MA0084.11.1752
MA0087.10.583879
MA0088.11.64676
MA0089.10
MA0090.10.917865
MA0091.10.187483
MA0092.10.471747
MA0093.10.292081
MA0095.10
MA0098.10
MA0100.10.2406
MA0101.10.40675
MA0103.10.319254
MA0105.10.213264
MA0106.10.325663
MA0107.10.310214
MA0108.20.395878
MA0109.10
MA0111.10.164756
MA0113.10.302851
MA0114.10.75813
MA0115.10.626759
MA0116.10.265278
MA0117.10.597086
MA0119.10.130171
MA0122.10.615314
MA0124.10.80652
MA0125.10.736412
MA0130.10
MA0131.10.973775
MA0132.10
MA0133.10
MA0135.10.657882
MA0136.10.264624
MA0139.12.1984
MA0140.10.240513
MA0141.10.348672
MA0142.10.439269
MA0143.10.31603
MA0144.10.769281
MA0145.11.05479
MA0146.10.595933
MA0147.10.215066
MA0148.10.189643
MA0149.10.133214
MA0062.21.41404
MA0035.20.244063
MA0039.20.714216
MA0138.20.959075
MA0002.20.560759
MA0137.21.15722
MA0104.20.145321
MA0047.20.285109
MA0112.20.17987
MA0065.20.0821754
MA0150.10.502665
MA0151.10
MA0152.10.285194
MA0153.10.67335
MA0154.10.0518625
MA0155.10.382638
MA0156.10.676622
MA0157.10.411541
MA0158.10
MA0159.10.228388
MA0160.10.560136
MA0161.10
MA0162.10.933846
MA0163.10.466163
MA0164.10.264905
MA0080.20.0935932
MA0018.20.272436
MA0099.20.360735
MA0079.20.0195458
MA0102.21.22663
MA0258.10.178572
MA0259.10.201267
MA0442.10
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