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MCL coexpression mm9:2348: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000542!3.48e-09!13;CL:0000051!3.48e-09!13;CL:0000838!1.08e-08!12;CL:0000084!4.83e-08!11;CL:0000827!4.83e-08!11;CL:0000791!4.25e-07!9;CL:0000789!4.25e-07!9;CL:0002420!4.25e-07!9;CL:0002419!4.25e-07!9;CL:0000790!4.25e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!7.47e-11!29;UBERON:0005057!7.47e-11!29;UBERON:0000153!3.20e-10!43;UBERON:0002370!4.62e-09!23;UBERON:0000974!4.62e-09!23;UBERON:0004807!4.62e-09!23;UBERON:0005058!4.62e-09!23;UBERON:0003351!4.62e-09!23;UBERON:0009113!4.62e-09!23;UBERON:0003295!4.62e-09!23;UBERON:0009722!4.62e-09!23;UBERON:0005562!4.62e-09!23;UBERON:0007690!4.62e-09!23;UBERON:0000065!1.12e-08!41;UBERON:0000077!1.26e-08!35;UBERON:0003408!1.59e-08!24;UBERON:0006562!2.28e-08!24;UBERON:0001557!2.28e-08!24;UBERON:0001042!2.28e-08!24;UBERON:0008814!2.28e-08!24;UBERON:0009145!2.28e-08!24;UBERON:0001004!2.42e-08!42;UBERON:0007811!3.42e-08!36;UBERON:0000475!4.52e-08!150;UBERON:0000072!7.14e-08!27;UBERON:0002390!1.30e-07!45;UBERON:0003061!1.30e-07!45;UBERON:0001041!2.12e-07!80;UBERON:0002193!4.90e-07!48;UBERON:0002405!4.90e-07!48
|tfbs_overrepresentation_for_novel_motifs=0.641384,1.30284,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.683591,0.570433,0.57409,0.815872,0.481455,1.50428,0.846564,0.342316,0.727368,1.32554,0.290745,0.711848,1.12823,2.06579,0.318879,0.503207,0.30022,1.16474,0.786577,0.434783,1.03515,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.98374,1.12016,1.32691,2.36634,0.834514,0.318792,0.926147,1.08947,1.40903,0.37865,1.04072,0.884013,0.362446,1.20828,2.44772,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,1.70541,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,1.41174,0.7614,1.51002,0.476467,1.40021,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.569254,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,1.63788,1.27621,1.069,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.589293
}}

Latest revision as of 18:23, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:53050229..53050243,-p2@Prpf40a
Mm9::chr3:152058955..152059023,+p1@Gm8261
p1@Zzz3
Mm9::chr3:157694669..157694738,-p2@Srsf11
Mm9::chr5:52581723..52581763,-p1@Dhx15


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:0008380RNA splicing0.00250756890761273
GO:0006397mRNA processing0.00250756890761273
GO:0016071mRNA metabolic process0.00250756890761273
GO:0006396RNA processing0.00351370644610112
GO:0003724RNA helicase activity0.0119608953170559



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>

Cell Type
Ontology termp-valuen
lymphocyte3.48e-0913
common lymphoid progenitor3.48e-0913
lymphoid lineage restricted progenitor cell1.08e-0812
T cell4.83e-0811
pro-T cell4.83e-0811
mature alpha-beta T cell4.25e-079
alpha-beta T cell4.25e-079
immature T cell4.25e-079
mature T cell4.25e-079
immature alpha-beta T cell4.25e-079

Uber Anatomy
Ontology termp-valuen
hemopoietic organ7.47e-1129
immune organ7.47e-1129
anterior region of body3.20e-1043
thymus4.62e-0923
neck4.62e-0923
respiratory system epithelium4.62e-0923
hemolymphoid system gland4.62e-0923
pharyngeal epithelium4.62e-0923
thymic region4.62e-0923
pharyngeal gland4.62e-0923
entire pharyngeal arch endoderm4.62e-0923
thymus primordium4.62e-0923
early pharyngeal endoderm4.62e-0923
respiratory tract1.12e-0841
mixed endoderm/mesoderm-derived structure1.26e-0835
gland of gut1.59e-0824
pharynx2.28e-0824
upper respiratory tract2.28e-0824
chordate pharynx2.28e-0824
pharyngeal arch system2.28e-0824
pharyngeal region of foregut2.28e-0824
respiratory system2.42e-0842
craniocervical region3.42e-0836
organism subdivision4.52e-08150
segment of respiratory tract7.14e-0827
hematopoietic system1.30e-0745
blood island1.30e-0745
foregut2.12e-0780
hemolymphoid system4.90e-0748
immune system4.90e-0748


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)
MA0003.12.89651
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
MA0028.11.26991
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
MA0048.12.07944
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.396346
MA0056.10
MA0057.11.29714
MA0058.10.581673
MA0059.10.59559
MA0060.11.83511
MA0061.11.11761
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.12.03055
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.552621
MA0074.10.795862
MA0076.11.35592
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.73268
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
MA0107.11.3208
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
MA0139.11.70536
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.608454
MA0146.10.647546
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.21.54479
MA0035.20.788288
MA0039.20.0959929
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.20.211985
MA0065.21.14711
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.11.16288
MA0163.11.64105
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.21.90618
MA0102.21.8929
MA0258.10.419871
MA0259.11.12353
MA0442.10
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