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MCL coexpression mm9:2219: Difference between revisions

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{{MCL_coexpression_mm9
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methylation;0.0162712978688435;20230!GO:0005720;nuclear heterochromatin;0.0162712978688435;20230!GO:0008213;protein amino acid alkylation;0.0162712978688435;20230!GO:0006479;protein amino acid methylation;0.0162712978688435;20230!GO:0000790;nuclear chromatin;0.0162712978688435;20230!GO:0016570;histone modification;0.0162712978688435;20230!GO:0000792;heterochromatin;0.0162712978688435;20230!GO:0016569;covalent chromatin modification;0.0162712978688435;20230!GO:0043414;biopolymer methylation;0.0162712978688435;20230!GO:0032259;methylation;0.0162712978688435;20230!GO:0044454;nuclear chromosome part;0.0216950638251246;20230!GO:0006730;one-carbon compound metabolic process;0.0216950638251246;20230!GO:0000228;nuclear chromosome;0.0216950638251246;20230!GO:0016568;chromatin 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|gostat_on_MCL_coexpression=GO:0016571;histone methylation;0.0162712978688435;20230!GO:0005720;nuclear heterochromatin;0.0162712978688435;20230!GO:0008213;protein amino acid alkylation;0.0162712978688435;20230!GO:0006479;protein amino acid methylation;0.0162712978688435;20230!GO:0000790;nuclear chromatin;0.0162712978688435;20230!GO:0016570;histone modification;0.0162712978688435;20230!GO:0000792;heterochromatin;0.0162712978688435;20230!GO:0016569;covalent chromatin modification;0.0162712978688435;20230!GO:0043414;biopolymer methylation;0.0162712978688435;20230!GO:0032259;methylation;0.0162712978688435;20230!GO:0044454;nuclear chromosome part;0.0216950638251246;20230!GO:0006730;one-carbon compound metabolic process;0.0216950638251246;20230!GO:0000228;nuclear chromosome;0.0216950638251246;20230!GO:0016568;chromatin modification;0.0426153039422091;20230!GO:0000785;chromatin;0.0465238590916562;20230!
|ontology_enrichment_celltype=CL:0000838!4.24e-09!12;CL:0000084!1.71e-08!11;CL:0000827!1.71e-08!11;CL:0000542!5.01e-08!13;CL:0000051!5.01e-08!13;CL:0000791!1.24e-07!9;CL:0000789!1.24e-07!9;CL:0002420!1.24e-07!9;CL:0002419!1.24e-07!9;CL:0000790!1.24e-07!9;CL:0000624!5.51e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!8.37e-14!29;UBERON:0005057!8.37e-14!29;UBERON:0002370!1.51e-12!23;UBERON:0000974!1.51e-12!23;UBERON:0004807!1.51e-12!23;UBERON:0005058!1.51e-12!23;UBERON:0003351!1.51e-12!23;UBERON:0009113!1.51e-12!23;UBERON:0003295!1.51e-12!23;UBERON:0009722!1.51e-12!23;UBERON:0005562!1.51e-12!23;UBERON:0007690!1.51e-12!23;UBERON:0000064!6.27e-12!99;UBERON:0006562!1.20e-11!24;UBERON:0003408!1.20e-11!24;UBERON:0001557!1.20e-11!24;UBERON:0001042!1.20e-11!24;UBERON:0008814!1.20e-11!24;UBERON:0009145!1.20e-11!24;UBERON:0000077!8.49e-11!35;UBERON:0000153!1.14e-10!43;UBERON:0007811!1.80e-09!36;UBERON:0000072!2.18e-09!27;UBERON:0002390!2.78e-09!45;UBERON:0003061!2.78e-09!45;UBERON:0003528!2.86e-09!29;UBERON:0002791!2.86e-09!29;UBERON:0001893!2.86e-09!29;UBERON:0002021!3.19e-09!10;UBERON:0000411!3.19e-09!10;UBERON:0001950!3.19e-09!10;UBERON:0002193!5.39e-09!48;UBERON:0002405!5.39e-09!48;UBERON:0002020!5.67e-09!34;UBERON:0003080!9.48e-09!40;UBERON:0002780!2.31e-08!39;UBERON:0001890!2.31e-08!39;UBERON:0006240!2.31e-08!39;UBERON:0001049!4.58e-08!52;UBERON:0005068!4.58e-08!52;UBERON:0006241!4.58e-08!52;UBERON:0007135!4.58e-08!52;UBERON:0000955!4.95e-08!47;UBERON:0006238!4.95e-08!47;UBERON:0000956!5.04e-08!21;UBERON:0001869!5.04e-08!21;UBERON:0000203!5.04e-08!21;UBERON:0003056!8.61e-08!49;UBERON:0000073!9.51e-08!54;UBERON:0002616!1.33e-07!46;UBERON:0002619!1.88e-07!17;UBERON:0010371!6.15e-07!73;UBERON:0000063!8.55e-07!35
|tfbs_overrepresentation_for_novel_motifs=0.641384,1.30284,0.612053,0.688265,1.21364,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,1.72258,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.683591,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,1.32554,0.290745,0.711848,1.12823,0.471365,0.854272,0.503207,0.30022,1.16474,0.786577,0.434783,1.03515,0.478558,0.717547,0.185353,0.504971,1.10847,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.98374,2.48198,1.32691,1.55806,0.310084,0.318792,0.926147,1.08947,1.40903,0.37865,1.04072,0.884013,0.362446,1.20828,6.45377,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.731844,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,1.42067,1.4032,0.633483,1.25851,1.41174,0.7614,1.51002,0.476467,3.46168,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.569254,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.79777,1.63788,1.27621,1.069,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,1.52606,0.993294,0.830321,0.459159,0.788782,2.03331
|tfbs_overrepresentation_jaspar=MA0003.1;5.5495,MA0004.1;0.6888,MA0006.1;1.24418,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.981995,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.735223,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.790894,MA0056.1;0,MA0057.1;2.00447,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.256913,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.783927,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;1.1032,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;1.52164,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;1.24367,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;1.70536,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;1.14526,MA0146.1;1.07887,MA0147.1;2.0075,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;1.91986,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;1.0034,MA0047.2;0.845655,MA0112.2;0.608441,MA0065.2;0.609584,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.263609,MA0155.1;1.21457,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;6.19111,MA0163.1;1.64105,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;5.22387,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}

Latest revision as of 18:11, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr17:51952537..51952552,-p15@Satb1
Mm9::chr17:51972332..51972342,+p@chr17:51972332..51972342
+
Mm9::chr17:51972345..51972362,+p@chr17:51972345..51972362
+
Mm9::chr18:39679035..39679049,-p@chr18:39679035..39679049
-


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:0016571histone methylation0.0162712978688435
GO:0005720nuclear heterochromatin0.0162712978688435
GO:0008213protein amino acid alkylation0.0162712978688435
GO:0006479protein amino acid methylation0.0162712978688435
GO:0000790nuclear chromatin0.0162712978688435
GO:0016570histone modification0.0162712978688435
GO:0000792heterochromatin0.0162712978688435
GO:0016569covalent chromatin modification0.0162712978688435
GO:0043414biopolymer methylation0.0162712978688435
GO:0032259methylation0.0162712978688435
GO:0044454nuclear chromosome part0.0216950638251246
GO:0006730one-carbon compound metabolic process0.0216950638251246
GO:0000228nuclear chromosome0.0216950638251246
GO:0016568chromatin modification0.0426153039422091
GO:0000785chromatin0.0465238590916562



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
hemopoietic organ8.37e-1429
immune organ8.37e-1429
thymus1.51e-1223
neck1.51e-1223
respiratory system epithelium1.51e-1223
hemolymphoid system gland1.51e-1223
pharyngeal epithelium1.51e-1223
thymic region1.51e-1223
pharyngeal gland1.51e-1223
entire pharyngeal arch endoderm1.51e-1223
thymus primordium1.51e-1223
early pharyngeal endoderm1.51e-1223
organ part6.27e-1299
pharynx1.20e-1124
gland of gut1.20e-1124
upper respiratory tract1.20e-1124
chordate pharynx1.20e-1124
pharyngeal arch system1.20e-1124
pharyngeal region of foregut1.20e-1124
mixed endoderm/mesoderm-derived structure8.49e-1135
anterior region of body1.14e-1043
craniocervical region1.80e-0936
segment of respiratory tract2.18e-0927
hematopoietic system2.78e-0945
blood island2.78e-0945
brain grey matter2.86e-0929
regional part of telencephalon2.86e-0929
telencephalon2.86e-0929
occipital lobe3.19e-0910
visual cortex3.19e-0910
neocortex3.19e-0910
hemolymphoid system5.39e-0948
immune system5.39e-0948
gray matter5.67e-0934
anterior neural tube9.48e-0940
regional part of forebrain2.31e-0839
forebrain2.31e-0839
future forebrain2.31e-0839
neural tube4.58e-0852
neural rod4.58e-0852
future spinal cord4.58e-0852
neural keel4.58e-0852
brain4.95e-0847
future brain4.95e-0847
cerebral cortex5.04e-0821
cerebral hemisphere5.04e-0821
pallium5.04e-0821
pre-chordal neural plate8.61e-0849
regional part of nervous system9.51e-0854
regional part of brain1.33e-0746
regional part of cerebral cortex1.88e-0717
ecto-epithelium6.15e-0773
organ segment8.55e-0735


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)
MA0003.15.5495
MA0004.10.6888
MA0006.11.24418
MA0007.10.672186
MA0009.11.15569
MA0014.10.981995
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.735223
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.790894
MA0056.10
MA0057.12.00447
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.783927
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.1032
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.11.52164
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.11.24367
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.11.70536
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.11.14526
MA0146.11.07887
MA0147.12.0075
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.21.91986
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.20.608441
MA0065.20.609584
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.11.21457
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.16.19111
MA0163.11.64105
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.25.22387
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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