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MCL coexpression mm9:204: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0002453!2.68e-10!8;CL:0002319!2.25e-08!43;CL:0000221!4.61e-08!44;CL:0000133!4.61e-08!44;CL:0000333!6.74e-08!10;CL:0000095!6.74e-08!10;CL:0000243!6.74e-08!10;CL:0000123!6.74e-08!10;CL:0000125!6.74e-08!10;CL:0000030!6.74e-08!10;CL:0000339!6.74e-08!10;CL:0000128!2.54e-07!6;CL:0000126!2.54e-07!6;CL:0000127!2.54e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!3.41e-13!73;UBERON:0001016!1.37e-12!75;UBERON:0000073!2.91e-12!54;UBERON:0001049!9.05e-12!52;UBERON:0005068!9.05e-12!52;UBERON:0006241!9.05e-12!52;UBERON:0007135!9.05e-12!52;UBERON:0003076!3.26e-11!12;UBERON:0003057!3.26e-11!12;UBERON:0002346!3.11e-08!64;UBERON:0003075!3.11e-08!64;UBERON:0007284!3.11e-08!64;UBERON:0004121!4.88e-08!95;UBERON:0000924!4.88e-08!95;UBERON:0006601!4.88e-08!95;UBERON:0002616!7.16e-08!46;UBERON:0002420!7.26e-08!8;UBERON:0007245!7.26e-08!8;UBERON:0010009!7.26e-08!8;UBERON:0010011!7.26e-08!8;UBERON:0000454!7.26e-08!8;UBERON:0000955!1.37e-07!47;UBERON:0006238!1.37e-07!47;UBERON:0002020!1.46e-07!34;UBERON:0000025!5.52e-07!114;UBERON:0002950!7.54e-07!4;UBERON:0001891!7.54e-07!4;UBERON:0009616!7.54e-07!4;UBERON:0010286!7.54e-07!4;UBERON:0002240!9.20e-07!6;UBERON:0005174!9.20e-07!6;UBERON:0001137!9.20e-07!6
|tfbs_overrepresentation_for_novel_motifs=0.0979835,0.777901,0.395496,0.130832,1.02901,0.333277,0.502643,0.944493,1.29873,0.330797,0.187045,0.21991,0.507427,0.5274,0.827043,0,0.165877,0.707727,0.620117,1.15992,0.531841,1.09782,0.245485,0.311695,0.413127,0.278145,1.01498,0.661002,0.681,0.501888,0.622184,0.229773,0.290109,0.468013,0.0932995,0.187051,0.00327964,0.471655,1.06077,0.278976,0.305421,0.636334,1.15958,0.364805,0.250786,0.29051,0.386024,0.398692,0.717759,0.124785,0.472049,0.64189,0.628884,0.882144,0.344664,0.54202,0.475128,0.453861,0.716157,0.916326,0.216485,0.322212,0.611528,0.149292,0.26734,0.514367,0.453796,0.762091,0.213428,0.628327,0.179033,0.361846,0.0603462,0.370715,0.0282554,0.430974,3.94111,0.370963,0.205336,0.54512,0.366248,0.176256,0.320416,0.318025,0.283628,0.000431219,0.0121761,0.236027,0.124296,0.913913,0.512525,0.28723,0.238418,0.0831374,0.0451308,0.173985,0.926301,0.240329,0.121891,0.099889,0.654242,1.21293,0.318186,0.472898,0.918131,0.153558,0.191295,0.391308,0.167713,0.0592277,0.716341,0.855718,0.325502,0.427206,0.518556,0.717758,0.0101637,0.315124,0.166646,0.636901,0.374962,0.137672,0.280295,0.369772,0.565403,0.598312,0.51906,0.233828,0.452538,1.08315,0.824266,0.29679,0.428195,0.0786006,0.537141,0.41327,0.478484,0.155239,0.495055,1.26906,0.883804,0.457711,0.0874132,0.666858,0.462174,0.154369,0.780349,1.23035,0.105918,0.513333,0.516958,0.00780133,0.33253,0.0940299,0.568364,1.02561,0.311764,0.104386,0.022114,0.769554,0.503133,0.773234,0.208006,0.228374,0.457493,0.260631,2.76363,0.218219,0.647497
|tfbs_overrepresentation_jaspar=MA0003.1;0.212406,MA0004.1;0.131237,MA0006.1;0.00535505,MA0007.1;0.839532,MA0009.1;0.247754,MA0014.1;0.249607,MA0017.1;0.114651,MA0019.1;0.420019,MA0024.1;0.218258,MA0025.1;0.424514,MA0027.1;1.761,MA0028.1;0.0336367,MA0029.1;0.20414,MA0030.1;0.208367,MA0031.1;0.185868,MA0038.1;0.0813956,MA0040.1;0.256435,MA0041.1;0.194889,MA0042.1;0.177441,MA0043.1;0.317434,MA0046.1;0.272953,MA0048.1;0.388907,MA0050.1;0.165699,MA0051.1;0.288655,MA0052.1;0.262081,MA0055.1;0.746439,MA0056.1;0,MA0057.1;0.0807685,MA0058.1;0.0637459,MA0059.1;0.184648,MA0060.1;0.164242,MA0061.1;0.117458,MA0063.1;0,MA0066.1;0.0768108,MA0067.1;0.517464,MA0068.1;0.485903,MA0069.1;0.26232,MA0070.1;0.25553,MA0071.1;0.164915,MA0072.1;0.249646,MA0073.1;0.00132064,MA0074.1;0.2252,MA0076.1;0.277538,MA0077.1;0.662185,MA0078.1;0.329145,MA0081.1;0.415346,MA0083.1;0.31684,MA0084.1;0.812114,MA0087.1;0.285092,MA0088.1;0.328432,MA0089.1;0,MA0090.1;0.254892,MA0091.1;0.331811,MA0092.1;0.479228,MA0093.1;0.226059,MA0095.1;0,MA0098.1;0,MA0100.1;0.465778,MA0101.1;0.0764809,MA0103.1;0.261157,MA0105.1;0.19209,MA0106.1;0.691765,MA0107.1;0.119527,MA0108.2;0.147584,MA0109.1;0,MA0111.1;0.514081,MA0113.1;0.30385,MA0114.1;0.560203,MA0115.1;0.319533,MA0116.1;0.0886148,MA0117.1;0.2956,MA0119.1;0.197444,MA0122.1;0.834889,MA0124.1;0.472367,MA0125.1;0.411352,MA0130.1;0,MA0131.1;1.33062,MA0132.1;0,MA0133.1;0,MA0135.1;0.345083,MA0136.1;0.247061,MA0139.1;0.110836,MA0140.1;0.21277,MA0141.1;0.0548179,MA0142.1;0.17699,MA0143.1;0.324036,MA0144.1;0.810962,MA0145.1;0.51599,MA0146.1;1.76822,MA0147.1;0.135201,MA0148.1;0.145175,MA0149.1;0.0176552,MA0062.2;0.0265873,MA0035.2;0.0602517,MA0039.2;0.124552,MA0138.2;0.802283,MA0002.2;0.702125,MA0137.2;0.767123,MA0104.2;0.138802,MA0047.2;0.0810714,MA0112.2;0.117647,MA0065.2;0.519104,MA0150.1;0.526845,MA0151.1;0,MA0152.1;0.582863,MA0153.1;0.357941,MA0154.1;1.63571,MA0155.1;0.638688,MA0156.1;0.134443,MA0157.1;0.477763,MA0158.1;0,MA0159.1;0.453782,MA0160.1;0.147833,MA0161.1;0,MA0162.1;0.0303695,MA0163.1;0.432781,MA0164.1;1.35749,MA0080.2;0.251015,MA0018.2;0.074393,MA0099.2;0.394501,MA0079.2;0.00180017,MA0102.2;0.861175,MA0258.1;1.59623,MA0259.1;0.230375,MA0442.1;0
}}

Latest revision as of 14:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:25341361..25341374,-p@chr10:25341361..25341374
-
Mm9::chr10:59862497..59862520,+p2@Gm17455
Mm9::chr10:59862550..59862553,+p3@Gm17455
Mm9::chr10:59862597..59862624,+p1@Gm17455
Mm9::chr10:61656947..61656959,-p@chr10:61656947..61656959
-
Mm9::chr10:75403311..75403323,-p3@ENSMUST00000059658
p3@uc007fts.1
Mm9::chr10:75403348..75403368,-p2@ENSMUST00000059658
p2@uc007fts.1
Mm9::chr11:102749101..102749112,-p@chr11:102749101..102749112
-
Mm9::chr11:116196664..116196679,-p1@Foxj1
Mm9::chr11:32036107..32036145,-p@chr11:32036107..32036145
-
Mm9::chr11:45567111..45567116,-p@chr11:45567111..45567116
-
Mm9::chr11:68884359..68884382,+p2@Tmem107
Mm9::chr12:112646729..112646768,+p@chr12:112646729..112646768
+
Mm9::chr12:17018318..17018367,-p1@2410004P03Rik
Mm9::chr13:34129535..34129551,+p@chr13:34129535..34129551
+
Mm9::chr14:56362683..56362711,-p@chr14:56362683..56362711
-
Mm9::chr15:25682615..25682652,+p6@Myo10
Mm9::chr15:57540476..57540491,-p1@ENSMUST00000160938
Mm9::chr15:78235786..78235811,-p@chr15:78235786..78235811
-
Mm9::chr15:78236613..78236617,+p@chr15:78236613..78236617
+
Mm9::chr15:88808274..88808289,-p@chr15:88808274..88808289
-
Mm9::chr15:89209677..89209693,-p4@Odf3b
Mm9::chr15:89209695..89209731,-p1@Odf3b
Mm9::chr16:17646606..17646623,+p2@Ccdc74a
Mm9::chr16:17646685..17646713,+p@chr16:17646685..17646713
+
Mm9::chr17:35822365..35822376,-p@chr17:35822365..35822376
-
Mm9::chr17:72022595..72022611,+p1@Fam179a
Mm9::chr17:81296183..81296194,+p2@uc008drl.1
p2@uc008drm.1
Mm9::chr1:122016630..122016662,-p6@Dbi
Mm9::chr1:87791024..87791029,+p3@Itm2c
Mm9::chr4:116799381..116799402,+p2@Tctex1d4
Mm9::chr4:116799405..116799423,+p1@Tctex1d4
Mm9::chr4:135525988..135526004,-p@chr4:135525988..135526004
-
Mm9::chr4:43441943..43441960,-p@chr4:43441943..43441960
-
Mm9::chr4:43442000..43442011,-p1@Fam166b
Mm9::chr5:23889365..23889379,+p@chr5:23889365..23889379
+
Mm9::chr5:5314611..5314624,-p@chr5:5314611..5314624
-
Mm9::chr5:66842890..66842903,-p11@Apbb2
Mm9::chr6:113277237..113277258,+p2@Ogg1
Mm9::chr6:47998855..47998863,-p5@Zfp777
Mm9::chr7:148211055..148211073,+p@chr7:148211055..148211073
+
Mm9::chr8:113227136..113227143,+p@chr8:113227136..113227143
+
Mm9::chr8:96676922..96676933,+p@chr8:96676922..96676933
+
Mm9::chr8:96677795..96677811,+p@chr8:96677795..96677811
+
Mm9::chr9:103595089..103595100,-p4@Tmem108
Mm9::chr9:103595115..103595142,-p3@Tmem108


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

no results for this coexpression

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
central nervous system3.41e-1373
nervous system1.37e-1275
regional part of nervous system2.91e-1254
neural tube9.05e-1252
neural rod9.05e-1252
future spinal cord9.05e-1252
neural keel9.05e-1252
posterior neural tube3.26e-1112
chordal neural plate3.26e-1112
neurectoderm3.11e-0864
neural plate3.11e-0864
presumptive neural plate3.11e-0864
ectoderm-derived structure4.88e-0895
ectoderm4.88e-0895
presumptive ectoderm4.88e-0895
regional part of brain7.16e-0846
basal ganglion7.26e-088
nuclear complex of neuraxis7.26e-088
aggregate regional part of brain7.26e-088
collection of basal ganglia7.26e-088
cerebral subcortex7.26e-088
brain1.37e-0747
future brain1.37e-0747
gray matter1.46e-0734
tube5.52e-07114
regional part of midbrain7.54e-074
midbrain7.54e-074
presumptive midbrain7.54e-074
midbrain neural tube7.54e-074
spinal cord9.20e-076
dorsal region element9.20e-076
dorsum9.20e-076


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)
MA0003.10.212406
MA0004.10.131237
MA0006.10.00535505
MA0007.10.839532
MA0009.10.247754
MA0014.10.249607
MA0017.10.114651
MA0019.10.420019
MA0024.10.218258
MA0025.10.424514
MA0027.11.761
MA0028.10.0336367
MA0029.10.20414
MA0030.10.208367
MA0031.10.185868
MA0038.10.0813956
MA0040.10.256435
MA0041.10.194889
MA0042.10.177441
MA0043.10.317434
MA0046.10.272953
MA0048.10.388907
MA0050.10.165699
MA0051.10.288655
MA0052.10.262081
MA0055.10.746439
MA0056.10
MA0057.10.0807685
MA0058.10.0637459
MA0059.10.184648
MA0060.10.164242
MA0061.10.117458
MA0063.10
MA0066.10.0768108
MA0067.10.517464
MA0068.10.485903
MA0069.10.26232
MA0070.10.25553
MA0071.10.164915
MA0072.10.249646
MA0073.10.00132064
MA0074.10.2252
MA0076.10.277538
MA0077.10.662185
MA0078.10.329145
MA0081.10.415346
MA0083.10.31684
MA0084.10.812114
MA0087.10.285092
MA0088.10.328432
MA0089.10
MA0090.10.254892
MA0091.10.331811
MA0092.10.479228
MA0093.10.226059
MA0095.10
MA0098.10
MA0100.10.465778
MA0101.10.0764809
MA0103.10.261157
MA0105.10.19209
MA0106.10.691765
MA0107.10.119527
MA0108.20.147584
MA0109.10
MA0111.10.514081
MA0113.10.30385
MA0114.10.560203
MA0115.10.319533
MA0116.10.0886148
MA0117.10.2956
MA0119.10.197444
MA0122.10.834889
MA0124.10.472367
MA0125.10.411352
MA0130.10
MA0131.11.33062
MA0132.10
MA0133.10
MA0135.10.345083
MA0136.10.247061
MA0139.10.110836
MA0140.10.21277
MA0141.10.0548179
MA0142.10.17699
MA0143.10.324036
MA0144.10.810962
MA0145.10.51599
MA0146.11.76822
MA0147.10.135201
MA0148.10.145175
MA0149.10.0176552
MA0062.20.0265873
MA0035.20.0602517
MA0039.20.124552
MA0138.20.802283
MA0002.20.702125
MA0137.20.767123
MA0104.20.138802
MA0047.20.0810714
MA0112.20.117647
MA0065.20.519104
MA0150.10.526845
MA0151.10
MA0152.10.582863
MA0153.10.357941
MA0154.11.63571
MA0155.10.638688
MA0156.10.134443
MA0157.10.477763
MA0158.10
MA0159.10.453782
MA0160.10.147833
MA0161.10
MA0162.10.0303695
MA0163.10.432781
MA0164.11.35749
MA0080.20.251015
MA0018.20.074393
MA0099.20.394501
MA0079.20.00180017
MA0102.20.861175
MA0258.11.59623
MA0259.10.230375
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:204&oldid=3072203"