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MCL coexpression mm9:2121: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000117!2.32e-13!23;CL:0000337!2.32e-13!23;CL:0000221!4.68e-12!44;CL:0000133!4.68e-12!44;CL:0002319!6.58e-12!43;CL:0000540!3.00e-11!33;CL:0000047!3.00e-11!33;CL:0000031!3.00e-11!33;CL:0000404!3.00e-11!33;CL:0000055!6.74e-09!49;CL:0000393!6.42e-08!39;CL:0000211!6.42e-08!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.14e-30!73;UBERON:0004121!3.65e-29!95;UBERON:0000924!3.65e-29!95;UBERON:0006601!3.65e-29!95;UBERON:0001016!3.09e-28!75;UBERON:0002346!3.93e-28!64;UBERON:0003075!3.93e-28!64;UBERON:0007284!3.93e-28!64;UBERON:0000073!1.08e-27!54;UBERON:0010371!2.53e-27!73;UBERON:0001049!1.74e-26!52;UBERON:0005068!1.74e-26!52;UBERON:0006241!1.74e-26!52;UBERON:0007135!1.74e-26!52;UBERON:0000955!6.38e-24!47;UBERON:0006238!6.38e-24!47;UBERON:0002616!2.19e-23!46;UBERON:0003056!2.10e-22!49;UBERON:0003080!1.03e-20!40;UBERON:0002780!3.65e-20!39;UBERON:0001890!3.65e-20!39;UBERON:0006240!3.65e-20!39;UBERON:0002020!1.73e-19!34;UBERON:0003528!3.97e-17!29;UBERON:0002791!3.97e-17!29;UBERON:0001893!3.97e-17!29;UBERON:0010314!1.31e-13!92;UBERON:0000956!9.56e-13!21;UBERON:0001869!9.56e-13!21;UBERON:0000203!9.56e-13!21;UBERON:0002619!2.53e-10!17;UBERON:0004111!5.06e-07!122;UBERON:0002021!5.97e-07!10;UBERON:0000411!5.97e-07!10;UBERON:0001950!5.97e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.24402,0.570433,0.197567,0.815872,1.20979,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.089443,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.66772,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,2.03173,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,1.9228,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.593145,1.32691,0.323563,0.834514,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.377699,0.40635,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,1.41174,0.7614,1.51002,0.476467,0.442329,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,1.21803,0.293812,1.03606,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,1.52606,0.993294,0.830321,0.459159,0.788782,0.992915
}}

Latest revision as of 18:02, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:79826217..79826260,+p1@Kbtbd7
Mm9::chr5:65884164..65884209,-p2@1110003E01Rik
Mm9::chr9:121614114..121614159,-p1@Sec22c
Mm9::chr9:26837595..26837699,-p1@Vps26b


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:0030904retromer complex0.0123253901067192
GO:0007034vacuolar transport0.0328443011797946



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 system1.14e-3073
ectoderm-derived structure3.65e-2995
ectoderm3.65e-2995
presumptive ectoderm3.65e-2995
nervous system3.09e-2875
neurectoderm3.93e-2864
neural plate3.93e-2864
presumptive neural plate3.93e-2864
regional part of nervous system1.08e-2754
ecto-epithelium2.53e-2773
neural tube1.74e-2652
neural rod1.74e-2652
future spinal cord1.74e-2652
neural keel1.74e-2652
brain6.38e-2447
future brain6.38e-2447
regional part of brain2.19e-2346
pre-chordal neural plate2.10e-2249
anterior neural tube1.03e-2040
regional part of forebrain3.65e-2039
forebrain3.65e-2039
future forebrain3.65e-2039
gray matter1.73e-1934
brain grey matter3.97e-1729
regional part of telencephalon3.97e-1729
telencephalon3.97e-1729
structure with developmental contribution from neural crest1.31e-1392
cerebral cortex9.56e-1321
cerebral hemisphere9.56e-1321
pallium9.56e-1321
regional part of cerebral cortex2.53e-1017
anatomical conduit5.06e-07122
occipital lobe5.97e-0710
visual cortex5.97e-0710
neocortex5.97e-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)
MA0003.10.942378
MA0004.10.6888
MA0006.11.24418
MA0007.10.672186
MA0009.11.15569
MA0014.10.276754
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
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
MA0055.10.396346
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
MA0073.10.216408
MA0074.10.795862
MA0076.11.35592
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.1032
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
MA0105.10.313353
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
MA0146.10.647546
MA0147.12.0075
MA0148.10.706718
MA0149.10.611881
MA0062.20.856416
MA0035.20.788288
MA0039.20.0959929
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.77707
MA0047.20.845655
MA0112.20.608441
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
MA0162.11.16288
MA0163.10.0996272
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.21.90618
MA0102.21.8929
MA0258.11.07695
MA0259.11.96515
MA0442.10
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