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MCL coexpression mm9:1874: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000221!7.09e-13!44;CL:0000133!7.09e-13!44;CL:0002319!1.40e-12!43;CL:0000055!2.27e-11!49;CL:0000117!1.47e-10!23;CL:0000337!1.47e-10!23;CL:0000540!3.28e-10!33;CL:0000047!3.28e-10!33;CL:0000031!3.28e-10!33;CL:0000404!3.28e-10!33;CL:0000393!5.63e-09!39;CL:0000211!5.63e-09!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!4.08e-33!73;UBERON:0001016!7.52e-32!75;UBERON:0002346!1.96e-30!64;UBERON:0003075!1.96e-30!64;UBERON:0007284!1.96e-30!64;UBERON:0004121!1.17e-29!95;UBERON:0000924!1.17e-29!95;UBERON:0006601!1.17e-29!95;UBERON:0000073!1.94e-28!54;UBERON:0001049!2.23e-27!52;UBERON:0005068!2.23e-27!52;UBERON:0006241!2.23e-27!52;UBERON:0007135!2.23e-27!52;UBERON:0010371!3.78e-26!73;UBERON:0000955!1.36e-25!47;UBERON:0006238!1.36e-25!47;UBERON:0003056!4.21e-25!49;UBERON:0002616!7.39e-25!46;UBERON:0010314!1.19e-22!92;UBERON:0003080!8.29e-22!40;UBERON:0002780!4.15e-21!39;UBERON:0001890!4.15e-21!39;UBERON:0006240!4.15e-21!39;UBERON:0002020!1.09e-17!34;UBERON:0003528!7.20e-16!29;UBERON:0002791!7.20e-16!29;UBERON:0001893!7.20e-16!29;UBERON:0000956!1.66e-11!21;UBERON:0001869!1.66e-11!21;UBERON:0000203!1.66e-11!21;UBERON:0002619!5.60e-10!17;UBERON:0000025!9.98e-10!114;UBERON:0004111!1.62e-09!122;UBERON:0002021!3.19e-07!10;UBERON:0000411!3.19e-07!10;UBERON:0001950!3.19e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.57409,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.854272,0.503207,0.089443,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.66772,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.98374,0.205546,1.32691,0.864765,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,1.16494,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.869142,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,2.02497,0.788782,0.280875
}}

Latest revision as of 17:38, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126632769..126632795,-p1@Dtx3
Mm9::chr19:4906598..4906632,-p1@Bbs1
Mm9::chr2:91284786..91284883,-p1@1110051M20Rik
Mm9::chr4:151852285..151852292,+p3@Nphp4


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:0001895retinal homeostasis0.0150643656558385
GO:0035058sensory cilium biogenesis0.0150643656558385
GO:0042384cilium biogenesis0.0281132154888067
GO:0001894tissue homeostasis0.0313158528520386
GO:0048871multicellular organismal homeostasis0.0313158528520386
GO:0016358dendrite development0.0376144828755884
GO:0030031cell projection biogenesis0.0376144828755884
GO:0007219Notch signaling pathway0.0376144828755884
GO:0000226microtubule cytoskeleton organization and biogenesis0.0427804872174396



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 system4.08e-3373
nervous system7.52e-3275
neurectoderm1.96e-3064
neural plate1.96e-3064
presumptive neural plate1.96e-3064
ectoderm-derived structure1.17e-2995
ectoderm1.17e-2995
presumptive ectoderm1.17e-2995
regional part of nervous system1.94e-2854
neural tube2.23e-2752
neural rod2.23e-2752
future spinal cord2.23e-2752
neural keel2.23e-2752
ecto-epithelium3.78e-2673
brain1.36e-2547
future brain1.36e-2547
pre-chordal neural plate4.21e-2549
regional part of brain7.39e-2546
structure with developmental contribution from neural crest1.19e-2292
anterior neural tube8.29e-2240
regional part of forebrain4.15e-2139
forebrain4.15e-2139
future forebrain4.15e-2139
gray matter1.09e-1734
brain grey matter7.20e-1629
regional part of telencephalon7.20e-1629
telencephalon7.20e-1629
cerebral cortex1.66e-1121
cerebral hemisphere1.66e-1121
pallium1.66e-1121
regional part of cerebral cortex5.60e-1017
tube9.98e-10114
anatomical conduit1.62e-09122
occipital lobe3.19e-0710
visual cortex3.19e-0710
neocortex3.19e-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)
MA0003.10.142214
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.276754
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.11.26991
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
MA0048.10.266382
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.125758
MA0056.10
MA0057.11.29714
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
MA0088.10.582815
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
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
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
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.608454
MA0146.11.5929
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.856416
MA0035.20.788288
MA0039.20.731226
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.20.211985
MA0065.20.212467
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
MA0162.10.346529
MA0163.10.672192
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.21.04582
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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