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MCL coexpression mm9:2274: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0031957;very-long-chain-fatty-acid-CoA ligase activity;0.00953267955952446;94180!GO:0001948;glycoprotein binding;0.011436082012144;230904!GO:0030433;ER-associated protein catabolic process;0.011436082012144;230904!GO:0000038;very-long-chain fatty acid metabolic process;0.011436082012144;94180!GO:0006515;misfolded or incompletely synthesized protein catabolic process;0.011436082012144;230904!GO:0006516;glycoprotein catabolic process;0.0133362479456937;230904!GO:0004467;long-chain-fatty-acid-CoA ligase activity;0.0133362479456937;94180!GO:0043161;proteasomal ubiquitin-dependent protein catabolic process;0.0133362479456937;230904!GO:0015645;fatty-acid ligase activity;0.0133362479456937;94180!GO:0001676;long-chain fatty acid metabolic process;0.0133362479456937;94180!GO:0016877;ligase activity, forming carbon-sulfur bonds;0.0199079506232692;94180!
|ontology_enrichment_celltype=CL:0000221!1.36e-15!44;CL:0000133!1.36e-15!44;CL:0002319!6.32e-15!43;CL:0000055!3.34e-11!49;CL:0000117!1.50e-09!23;CL:0000337!1.50e-09!23;CL:0000540!6.27e-09!33;CL:0000047!6.27e-09!33;CL:0000031!6.27e-09!33;CL:0000404!6.27e-09!33;CL:0000333!7.55e-08!10;CL:0000095!7.55e-08!10;CL:0000243!7.55e-08!10;CL:0000123!7.55e-08!10;CL:0000125!7.55e-08!10;CL:0000030!7.55e-08!10;CL:0000339!7.55e-08!10;CL:0002453!1.90e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!1.94e-36!75;UBERON:0001017!1.31e-35!73;UBERON:0000073!6.38e-30!54;UBERON:0004121!2.78e-28!95;UBERON:0000924!2.78e-28!95;UBERON:0006601!2.78e-28!95;UBERON:0001049!3.39e-28!52;UBERON:0005068!3.39e-28!52;UBERON:0006241!3.39e-28!52;UBERON:0007135!3.39e-28!52;UBERON:0002346!4.91e-26!64;UBERON:0003075!4.91e-26!64;UBERON:0007284!4.91e-26!64;UBERON:0000955!1.15e-24!47;UBERON:0006238!1.15e-24!47;UBERON:0002616!5.54e-24!46;UBERON:0010371!2.86e-22!73;UBERON:0003080!1.92e-19!40;UBERON:0010314!8.65e-19!92;UBERON:0002780!1.17e-18!39;UBERON:0001890!1.17e-18!39;UBERON:0006240!1.17e-18!39;UBERON:0003056!1.29e-17!49;UBERON:0002020!2.05e-16!34;UBERON:0003528!2.08e-13!29;UBERON:0002791!2.08e-13!29;UBERON:0001893!2.08e-13!29;UBERON:0000956!3.18e-10!21;UBERON:0001869!3.18e-10!21;UBERON:0000203!3.18e-10!21;UBERON:0002619!1.36e-09!17;UBERON:0003076!2.62e-09!12;UBERON:0003057!2.62e-09!12;UBERON:0002021!2.01e-07!10;UBERON:0000411!2.01e-07!10;UBERON:0001950!2.01e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.641384,1.30284,0.612053,0.688265,0.483253,0.704257,0.803568,0.96814,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,2.33178,0.473993,1.65947,0.683591,1.39891,0.57409,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,1.18815,0.854272,0.503207,0.089443,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,1.04032,0.504971,1.10847,0.675898,2.16014,0.744678,0.162985,1.3327,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.864765,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.377699,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,1.4032,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.869142,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.569254,0.650785,1.70963,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,1.03606,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,1.52606,0.993294,0.830321,0.459159,0.788782,0.280875
}}

Latest revision as of 18:16, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:7015918..7016008,-p1@Gpr137
Mm9::chr4:147534740..147534761,+p3@Fbxo2
Mm9::chr4:147534765..147534789,+p2@Fbxo2
Mm9::chr9:54509651..54509662,-p4@Acsbg1


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:0031957very-long-chain-fatty-acid-CoA ligase activity0.00953267955952446
GO:0001948glycoprotein binding0.011436082012144
GO:0030433ER-associated protein catabolic process0.011436082012144
GO:0000038very-long-chain fatty acid metabolic process0.011436082012144
GO:0006515misfolded or incompletely synthesized protein catabolic process0.011436082012144
GO:0006516glycoprotein catabolic process0.0133362479456937
GO:0004467long-chain-fatty-acid-CoA ligase activity0.0133362479456937
GO:0043161proteasomal ubiquitin-dependent protein catabolic process0.0133362479456937
GO:0015645fatty-acid ligase activity0.0133362479456937
GO:0001676long-chain fatty acid metabolic process0.0133362479456937
GO:0016877ligase activity, forming carbon-sulfur bonds0.0199079506232692



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
nervous system1.94e-3675
central nervous system1.31e-3573
regional part of nervous system6.38e-3054
ectoderm-derived structure2.78e-2895
ectoderm2.78e-2895
presumptive ectoderm2.78e-2895
neural tube3.39e-2852
neural rod3.39e-2852
future spinal cord3.39e-2852
neural keel3.39e-2852
neurectoderm4.91e-2664
neural plate4.91e-2664
presumptive neural plate4.91e-2664
brain1.15e-2447
future brain1.15e-2447
regional part of brain5.54e-2446
ecto-epithelium2.86e-2273
anterior neural tube1.92e-1940
structure with developmental contribution from neural crest8.65e-1992
regional part of forebrain1.17e-1839
forebrain1.17e-1839
future forebrain1.17e-1839
pre-chordal neural plate1.29e-1749
gray matter2.05e-1634
brain grey matter2.08e-1329
regional part of telencephalon2.08e-1329
telencephalon2.08e-1329
cerebral cortex3.18e-1021
cerebral hemisphere3.18e-1021
pallium3.18e-1021
regional part of cerebral cortex1.36e-0917
posterior neural tube2.62e-0912
chordal neural plate2.62e-0912
occipital lobe2.01e-0710
visual cortex2.01e-0710
neocortex2.01e-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)
MA0003.11.34944
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.12.62764
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
MA0048.10.266382
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.396346
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.713436
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.18.63716
MA0074.10.795862
MA0076.11.35592
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
MA0105.10.841866
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
MA0119.12.50824
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
MA0145.10.21199
MA0146.10.647546
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.856416
MA0035.20.788288
MA0039.21.91986
MA0138.20.951653
MA0002.20.368961
MA0137.21.37638
MA0104.20.386166
MA0047.20.845655
MA0112.21.14524
MA0065.20.609584
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.230016
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.10667
MA0163.15.18171
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.22.99114
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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