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MCL coexpression mm9:328: Difference between revisions

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{{MCL_coexpression_mm9
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cortex radial glia guided migration;0.0156138716923246;13131!GO:0021799;cerebral cortex radially oriented cell migration;0.0156138716923246;13131!GO:0021589;cerebellum structural organization;0.0156138716923246;13131!GO:0021813;cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration;0.0156138716923246;13131!GO:0021577;hindbrain structural organization;0.0156138716923246;13131!GO:0048532;organization of an anatomical structure;0.0156138716923246;13131!GO:0021812;neuronal-glial interaction involved in cerebral cortex radial glia guided migration;0.0156138716923246;13131!GO:0021942;radial glia guided migration of Purkinje cell;0.0156138716923246;13131!GO:0021932;hindbrain radial glia guided cell migration;0.0249760353894974;13131!GO:0007168;receptor guanylyl cyclase signaling pathway;0.0249760353894974;14708!GO:0005516;calmodulin binding;0.0307942104658189;12323,17919!GO:0021535;cell migration in hindbrain;0.0312123473389508;13131!GO:0021795;cerebral cortex cell migration;0.0384057263879851;13131!GO:0042169;SH2 domain binding;0.0415856935171347;13131!GO:0005083;small GTPase regulator activity;0.0415856935171347;105445,14708!GO:0005954;calcium- and calmodulin-dependent protein kinase complex;0.0415856935171347;12323!GO:0021885;forebrain cell migration;0.0415856935171347;13131!GO:0022029;telencephalon cell migration;0.0415856935171347;13131!GO:0004274;dipeptidyl-peptidase IV activity;0.0459518053958278;13483!GO:0021987;cerebral cortex development;0.0498455976785651;13131!GO:0015629;actin 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|gostat_on_MCL_coexpression=GO:0021801;cerebral cortex radial glia guided migration;0.0156138716923246;13131!GO:0021799;cerebral cortex radially oriented cell migration;0.0156138716923246;13131!GO:0021589;cerebellum structural organization;0.0156138716923246;13131!GO:0021813;cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration;0.0156138716923246;13131!GO:0021577;hindbrain structural organization;0.0156138716923246;13131!GO:0048532;organization of an anatomical structure;0.0156138716923246;13131!GO:0021812;neuronal-glial interaction involved in cerebral cortex radial glia guided migration;0.0156138716923246;13131!GO:0021942;radial glia guided migration of Purkinje cell;0.0156138716923246;13131!GO:0021932;hindbrain radial glia guided cell migration;0.0249760353894974;13131!GO:0007168;receptor guanylyl cyclase signaling pathway;0.0249760353894974;14708!GO:0005516;calmodulin binding;0.0307942104658189;12323,17919!GO:0021535;cell migration in hindbrain;0.0312123473389508;13131!GO:0021795;cerebral cortex cell migration;0.0384057263879851;13131!GO:0042169;SH2 domain binding;0.0415856935171347;13131!GO:0005083;small GTPase regulator activity;0.0415856935171347;105445,14708!GO:0005954;calcium- and calmodulin-dependent protein kinase complex;0.0415856935171347;12323!GO:0021885;forebrain cell migration;0.0415856935171347;13131!GO:0022029;telencephalon cell migration;0.0415856935171347;13131!GO:0004274;dipeptidyl-peptidase IV activity;0.0459518053958278;13483!GO:0021987;cerebral cortex development;0.0498455976785651;13131!GO:0015629;actin cytoskeleton;0.0498455976785651;83767,17919!
|ontology_enrichment_celltype=CL:0000117!4.05e-12!23;CL:0000337!4.05e-12!23;CL:0000540!2.36e-07!33;CL:0000047!2.36e-07!33;CL:0000031!2.36e-07!33;CL:0000404!2.36e-07!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.86e-32!54;UBERON:0002020!6.42e-32!34;UBERON:0001049!1.64e-31!52;UBERON:0005068!1.64e-31!52;UBERON:0006241!1.64e-31!52;UBERON:0007135!1.64e-31!52;UBERON:0002346!1.60e-28!64;UBERON:0003075!1.60e-28!64;UBERON:0007284!1.60e-28!64;UBERON:0001017!4.23e-26!73;UBERON:0000955!3.32e-25!47;UBERON:0006238!3.32e-25!47;UBERON:0003528!3.88e-25!29;UBERON:0002791!3.88e-25!29;UBERON:0001893!3.88e-25!29;UBERON:0001016!3.99e-25!75;UBERON:0002616!7.98e-24!46;UBERON:0010371!9.42e-24!73;UBERON:0003080!3.50e-22!40;UBERON:0000956!9.24e-22!21;UBERON:0001869!9.24e-22!21;UBERON:0000203!9.24e-22!21;UBERON:0003056!3.25e-21!49;UBERON:0004121!3.96e-21!95;UBERON:0000924!3.96e-21!95;UBERON:0006601!3.96e-21!95;UBERON:0002780!7.02e-21!39;UBERON:0001890!7.02e-21!39;UBERON:0006240!7.02e-21!39;UBERON:0002619!5.11e-19!17;UBERON:0002021!1.92e-18!10;UBERON:0000411!1.92e-18!10;UBERON:0001950!1.92e-18!10;UBERON:0010314!9.00e-17!92;UBERON:0003076!1.13e-09!12;UBERON:0003057!1.13e-09!12;UBERON:0002240!1.90e-09!6;UBERON:0005174!1.90e-09!6;UBERON:0001137!1.90e-09!6;UBERON:0000025!2.59e-09!114;UBERON:0004111!3.94e-08!122;UBERON:0001948!4.81e-08!5;UBERON:0002315!4.81e-08!5
|tfbs_overrepresentation_for_novel_motifs=0.687857,0.0165293,0.300372,0.397943,0.161423,0.13486,1.06974,0.612769,0.0800865,1.28306,0.492054,0.184641,0.916936,0.20111,0.713621,0,0.346366,0.633115,0.062096,0.402773,0.53664,0.251378,0.200489,0.365428,0.64228,0.628182,0.52165,0.147544,0.213668,0.839421,0.138971,0.430274,0.150515,1.33137,0.405129,0.663832,0.328599,0.53714,0.0287464,0.0932741,1.43101,0.142092,0.120149,0.720278,0.313394,0.119992,1.41424,0.157367,1.01556,0.217247,0.332337,0.239655,1.09308,0.553844,0.569458,0.206047,0.22823,0.176187,0.48745,0.590972,0.413329,0.246553,0.429195,0.323367,0.612775,0.355898,0.693798,1.02539,1.05417,0.883956,0.0802912,0.0773092,0.158212,0.599674,0.0467969,0.422205,0.448367,0.274952,0.398928,0.546495,1.32158,0.360462,0.245495,0.17831,0.496926,0.0669719,0.0861456,0.20538,0.287376,1.18318,0.758722,0.501285,0.44118,1.98632,0.115402,1.49875,0.602892,0.44358,0.775065,0.0715943,0.596413,0.430036,0.538321,0.332812,1.58789,0.141825,0.38053,0.154838,0.0761427,0.253898,1.11249,1.33434,0.074417,0.167109,0.765328,0.356538,0.197255,0.403561,0.917933,0.584419,0.604565,0.306855,0.631228,0.274265,0.816304,0.40202,0.575824,0.4354,0.692394,0.687924,1.29903,0.122184,0.665113,1.81142,0.785621,1.65482,0.708721,0.142948,0.739526,1.5459,1.15207,0.698162,0.230233,0.439187,0.326804,0.438656,4.93901,1.50665,0.108773,0.0423084,0.210657,0.00550839,0.555246,0.773127,0.214931,0.629009,0.240389,0.0522118,0.101676,0.107341,0.748413,1.24129,0.402392,0.0980788,0.324177,0.209743,0.592606,0.183582,0.140368
|tfbs_overrepresentation_jaspar=MA0003.1;0.0493132,MA0004.1;0.794862,MA0006.1;0.0460466,MA0007.1;0.118104,MA0009.1;0.452863,MA0014.1;0.043395,MA0017.1;0.0561984,MA0019.1;0.818593,MA0024.1;0.415603,MA0025.1;0.660968,MA0027.1;2.04174,MA0028.1;0.186822,MA0029.1;0.397373,MA0030.1;0.402861,MA0031.1;0.373333,MA0038.1;0.220281,MA0040.1;0.463641,MA0041.1;0.0860551,MA0042.1;0.0797095,MA0043.1;0.53743,MA0046.1;0.483941,MA0048.1;0.023533,MA0050.1;0.149886,MA0051.1;0.226644,MA0052.1;0.47061,MA0055.1;0.349671,MA0056.1;0,MA0057.1;0.430886,MA0058.1;1.95905,MA0059.1;2.64889,MA0060.1;0.0217699,MA0061.1;0.0296722,MA0063.1;0,MA0066.1;0.212546,MA0067.1;0.764133,MA0068.1;0.449127,MA0069.1;0.470904,MA0070.1;0.462521,MA0071.1;0.149369,MA0072.1;0.455219,MA0073.1;3.23975,MA0074.1;0.187944,MA0076.1;0.229034,MA0077.1;0.436665,MA0078.1;0.250627,MA0081.1;0.644573,MA0083.1;0.536725,MA0084.1;1.07765,MA0087.1;0.4987,MA0088.1;1.39052,MA0089.1;0,MA0090.1;0.348685,MA0091.1;0.134352,MA0092.1;0.107655,MA0093.1;1.63531,MA0095.1;0,MA0098.1;0,MA0100.1;0.180237,MA0101.1;0.08669,MA0103.1;0.218786,MA0105.1;2.09451,MA0106.1;0.256379,MA0107.1;0.211319,MA0108.2;0.320962,MA0109.1;0,MA0111.1;0.744051,MA0113.1;0.664215,MA0114.1;0.0290062,MA0115.1;0.539917,MA0116.1;0.0459718,MA0117.1;0.511373,MA0119.1;0.0869793,MA0122.1;0.528896,MA0124.1;0.714453,MA0125.1;0.646095,MA0130.1;0,MA0131.1;0.299487,MA0132.1;0,MA0133.1;0,MA0135.1;0.569948,MA0136.1;0.583392,MA0139.1;0.0699025,MA0140.1;0.532112,MA0141.1;0.0690765,MA0142.1;0.361451,MA0143.1;0.247626,MA0144.1;0.0298861,MA0145.1;0.034487,MA0146.1;0.000260983,MA0147.1;0.578585,MA0148.1;0.136186,MA0149.1;0.0894222,MA0062.2;0.00879313,MA0035.2;0.539678,MA0039.2;0.145091,MA0138.2;0.796689,MA0002.2;0.91042,MA0137.2;0.0677978,MA0104.2;0.667344,MA0047.2;0.219739,MA0112.2;0.0857672,MA0065.2;0.66648,MA0150.1;0.756591,MA0151.1;0,MA0152.1;0.219814,MA0153.1;0.584906,MA0154.1;0.973726,MA0155.1;0.354426,MA0156.1;0.227959,MA0157.1;0.335532,MA0158.1;0,MA0159.1;0.956625,MA0160.1;0.137981,MA0161.1;0,MA0162.1;0.0935743,MA0163.1;0.0779391,MA0164.1;0.201705,MA0080.2;0.806441,MA0018.2;0.208409,MA0099.2;0.288477,MA0079.2;2.8347,MA0102.2;1.12863,MA0258.1;0.0253198,MA0259.1;0.296386,MA0442.1;0
}}

Latest revision as of 15:06, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:40603275..40603289,+p5@Wasf1
Mm9::chr10:40603299..40603314,+p3@Wasf1
Mm9::chr10:40603426..40603440,+p4@Wasf1
Mm9::chr10:80464083..80464115,-p3@Gng7
Mm9::chr11:5966357..5966368,-p14@Camk2b
Mm9::chr11:5966374..5966387,-p8@Camk2b
Mm9::chr13:55050724..55050747,+p2@Unc5a
Mm9::chr14:122137717..122137728,-p15@Dock9
Mm9::chr14:122137765..122137775,-p16@Dock9
Mm9::chr14:56130053..56130057,-p@chr14:56130053..56130057
-
Mm9::chr15:37447238..37447243,+p@chr15:37447238..37447243
+
Mm9::chr16:75447352..75447361,-p@chr16:75447352..75447361
-
Mm9::chr17:13044761..13044782,-p1@Mas1
Mm9::chr17:70871052..70871078,+p13@Dlgap1
Mm9::chr18:74874391..74874406,+p13@Myo5b
Mm9::chr18:74874419..74874428,+p18@Myo5b
Mm9::chr18:74874437..74874450,+p12@Myo5b
Mm9::chr19:28084383..28084396,-p@chr19:28084383..28084396
-
Mm9::chr4:103292185..103292197,+p9@Dab1
Mm9::chr5:27588740..27588750,+p19@Dpp6
Mm9::chr5:27588762..27588776,+p10@Dpp6
Mm9::chr7:3390657..3390678,+p@chr7:3390657..3390678
+
Mm9::chr7:3391221..3391241,+p@chr7:3391221..3391241
+
Mm9::chr7:3391251..3391262,+p@chr7:3391251..3391262
+


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:0021801cerebral cortex radial glia guided migration0.0156138716923246
GO:0021799cerebral cortex radially oriented cell migration0.0156138716923246
GO:0021589cerebellum structural organization0.0156138716923246
GO:0021813cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration0.0156138716923246
GO:0021577hindbrain structural organization0.0156138716923246
GO:0048532organization of an anatomical structure0.0156138716923246
GO:0021812neuronal-glial interaction involved in cerebral cortex radial glia guided migration0.0156138716923246
GO:0021942radial glia guided migration of Purkinje cell0.0156138716923246
GO:0021932hindbrain radial glia guided cell migration0.0249760353894974
GO:0007168receptor guanylyl cyclase signaling pathway0.0249760353894974
GO:0005516calmodulin binding0.0307942104658189
GO:0021535cell migration in hindbrain0.0312123473389508
GO:0021795cerebral cortex cell migration0.0384057263879851
GO:0042169SH2 domain binding0.0415856935171347
GO:0005083small GTPase regulator activity0.0415856935171347
GO:0005954calcium- and calmodulin-dependent protein kinase complex0.0415856935171347
GO:0021885forebrain cell migration0.0415856935171347
GO:0022029telencephalon cell migration0.0415856935171347
GO:0004274dipeptidyl-peptidase IV activity0.0459518053958278
GO:0021987cerebral cortex development0.0498455976785651
GO:0015629actin cytoskeleton0.0498455976785651



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
CNS neuron (sensu Vertebrata)4.05e-1223
neuroblast (sensu Vertebrata)4.05e-1223
neuron2.36e-0733
neuronal stem cell2.36e-0733
neuroblast2.36e-0733
electrically signaling cell2.36e-0733

Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.86e-3254
gray matter6.42e-3234
neural tube1.64e-3152
neural rod1.64e-3152
future spinal cord1.64e-3152
neural keel1.64e-3152
neurectoderm1.60e-2864
neural plate1.60e-2864
presumptive neural plate1.60e-2864
central nervous system4.23e-2673
brain3.32e-2547
future brain3.32e-2547
brain grey matter3.88e-2529
regional part of telencephalon3.88e-2529
telencephalon3.88e-2529
nervous system3.99e-2575
regional part of brain7.98e-2446
ecto-epithelium9.42e-2473
anterior neural tube3.50e-2240
cerebral cortex9.24e-2221
cerebral hemisphere9.24e-2221
pallium9.24e-2221
pre-chordal neural plate3.25e-2149
ectoderm-derived structure3.96e-2195
ectoderm3.96e-2195
presumptive ectoderm3.96e-2195
regional part of forebrain7.02e-2139
forebrain7.02e-2139
future forebrain7.02e-2139
regional part of cerebral cortex5.11e-1917
occipital lobe1.92e-1810
visual cortex1.92e-1810
neocortex1.92e-1810
structure with developmental contribution from neural crest9.00e-1792
posterior neural tube1.13e-0912
chordal neural plate1.13e-0912
spinal cord1.90e-096
dorsal region element1.90e-096
dorsum1.90e-096
tube2.59e-09114
anatomical conduit3.94e-08122
regional part of spinal cord4.81e-085
gray matter of spinal cord4.81e-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)
MA0003.10.0493132
MA0004.10.794862
MA0006.10.0460466
MA0007.10.118104
MA0009.10.452863
MA0014.10.043395
MA0017.10.0561984
MA0019.10.818593
MA0024.10.415603
MA0025.10.660968
MA0027.12.04174
MA0028.10.186822
MA0029.10.397373
MA0030.10.402861
MA0031.10.373333
MA0038.10.220281
MA0040.10.463641
MA0041.10.0860551
MA0042.10.0797095
MA0043.10.53743
MA0046.10.483941
MA0048.10.023533
MA0050.10.149886
MA0051.10.226644
MA0052.10.47061
MA0055.10.349671
MA0056.10
MA0057.10.430886
MA0058.11.95905
MA0059.12.64889
MA0060.10.0217699
MA0061.10.0296722
MA0063.10
MA0066.10.212546
MA0067.10.764133
MA0068.10.449127
MA0069.10.470904
MA0070.10.462521
MA0071.10.149369
MA0072.10.455219
MA0073.13.23975
MA0074.10.187944
MA0076.10.229034
MA0077.10.436665
MA0078.10.250627
MA0081.10.644573
MA0083.10.536725
MA0084.11.07765
MA0087.10.4987
MA0088.11.39052
MA0089.10
MA0090.10.348685
MA0091.10.134352
MA0092.10.107655
MA0093.11.63531
MA0095.10
MA0098.10
MA0100.10.180237
MA0101.10.08669
MA0103.10.218786
MA0105.12.09451
MA0106.10.256379
MA0107.10.211319
MA0108.20.320962
MA0109.10
MA0111.10.744051
MA0113.10.664215
MA0114.10.0290062
MA0115.10.539917
MA0116.10.0459718
MA0117.10.511373
MA0119.10.0869793
MA0122.10.528896
MA0124.10.714453
MA0125.10.646095
MA0130.10
MA0131.10.299487
MA0132.10
MA0133.10
MA0135.10.569948
MA0136.10.583392
MA0139.10.0699025
MA0140.10.532112
MA0141.10.0690765
MA0142.10.361451
MA0143.10.247626
MA0144.10.0298861
MA0145.10.034487
MA0146.10.000260983
MA0147.10.578585
MA0148.10.136186
MA0149.10.0894222
MA0062.20.00879313
MA0035.20.539678
MA0039.20.145091
MA0138.20.796689
MA0002.20.91042
MA0137.20.0677978
MA0104.20.667344
MA0047.20.219739
MA0112.20.0857672
MA0065.20.66648
MA0150.10.756591
MA0151.10
MA0152.10.219814
MA0153.10.584906
MA0154.10.973726
MA0155.10.354426
MA0156.10.227959
MA0157.10.335532
MA0158.10
MA0159.10.956625
MA0160.10.137981
MA0161.10
MA0162.10.0935743
MA0163.10.0779391
MA0164.10.201705
MA0080.20.806441
MA0018.20.208409
MA0099.20.288477
MA0079.22.8347
MA0102.21.12863
MA0258.10.0253198
MA0259.10.296386
MA0442.10
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