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MCL coexpression mm9:1670: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0060134;prepulse inhibition;0.0351158149807998;14804!GO:0048585;negative regulation of response to stimulus;0.0351158149807998;14804!GO:0032102;negative regulation of response to external stimulus;0.0351158149807998;14804!GO:0032101;regulation of response to external stimulus;0.0351158149807998;14804!GO:0001964;startle response;0.0374507120195016;14804!GO:0005234;extracellular-glutamate-gated ion channel activity;0.0401125708475028;14804!GO:0004970;ionotropic glutamate receptor activity;0.0401125708475028;14804!GO:0003690;double-stranded DNA binding;0.0409415170819246;20683!
|ontology_enrichment_celltype=CL:0000791!7.34e-07!9;CL:0000789!7.34e-07!9;CL:0002420!7.34e-07!9;CL:0002419!7.34e-07!9;CL:0000790!7.34e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001048!1.91e-12!134;UBERON:0004177!6.36e-12!29;UBERON:0005057!6.36e-12!29;UBERON:0000077!6.50e-11!35;UBERON:0000475!7.12e-11!150;UBERON:0001041!1.13e-10!80;UBERON:0001004!2.25e-10!42;UBERON:0000065!3.89e-10!41;UBERON:0003408!2.00e-09!24;UBERON:0002370!3.25e-09!23;UBERON:0000974!3.25e-09!23;UBERON:0004807!3.25e-09!23;UBERON:0005058!3.25e-09!23;UBERON:0003351!3.25e-09!23;UBERON:0009113!3.25e-09!23;UBERON:0003295!3.25e-09!23;UBERON:0009722!3.25e-09!23;UBERON:0005562!3.25e-09!23;UBERON:0007690!3.25e-09!23;UBERON:0000153!4.25e-09!43;UBERON:0006562!8.87e-09!24;UBERON:0001557!8.87e-09!24;UBERON:0001042!8.87e-09!24;UBERON:0008814!8.87e-09!24;UBERON:0009145!8.87e-09!24;UBERON:0000926!1.90e-08!120;UBERON:0004120!1.90e-08!120;UBERON:0006603!1.90e-08!120;UBERON:0003081!5.36e-08!87;UBERON:0007811!7.23e-08!36;UBERON:0005911!8.86e-08!69;UBERON:0002390!9.51e-08!45;UBERON:0003061!9.51e-08!45;UBERON:0002193!2.96e-07!48;UBERON:0002405!2.96e-07!48
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.293744,1.31238,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,1.78433,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.775038,1.0421,0.489529,0.44579,1.72742,0.404661,0.537749,0.757752,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.253145,1.91085,0.791367,1.7724,0.699032,0.360612,0.328675,0.401916,0.631725,0.134724,0.426986,0.4934,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,1.26875,0.30684,2.08316,1.23259,1.31774,1.96909,0.70455,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,1.44773,0.297068,1.20595,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.937248,0.3366,0.297538,1.05152,1.97563,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,1.52669,0.97421,1.5739,3.18917,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,1.03353,1.64321,0.607321,0.932233,0.380707,1.23809,2.03938,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,1.05179,1.21592,3.34092,1.18223,1.62749,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.745913
}}

Latest revision as of 17:18, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:79790473..79790550,-p1@Naa16
Mm9::chr15:102236700..102236764,+p1@Sp1
Mm9::chr1:152240400..152240541,+p1@Tpr
Mm9::chr9:100543991..100544020,+p2@Stag1
Mm9::chr9:100544024..100544045,+p1@Stag1


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:0060134prepulse inhibition0.0351158149807998
GO:0048585negative regulation of response to stimulus0.0351158149807998
GO:0032102negative regulation of response to external stimulus0.0351158149807998
GO:0032101regulation of response to external stimulus0.0351158149807998
GO:0001964startle response0.0374507120195016
GO:0005234extracellular-glutamate-gated ion channel activity0.0401125708475028
GO:0004970ionotropic glutamate receptor activity0.0401125708475028
GO:0003690double-stranded DNA binding0.0409415170819246



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
mature alpha-beta T cell7.34e-079
alpha-beta T cell7.34e-079
immature T cell7.34e-079
mature T cell7.34e-079
immature alpha-beta T cell7.34e-079

Uber Anatomy
Ontology termp-valuen
primordium1.91e-12134
hemopoietic organ6.36e-1229
immune organ6.36e-1229
mixed endoderm/mesoderm-derived structure6.50e-1135
organism subdivision7.12e-11150
foregut1.13e-1080
respiratory system2.25e-1042
respiratory tract3.89e-1041
gland of gut2.00e-0924
thymus3.25e-0923
neck3.25e-0923
respiratory system epithelium3.25e-0923
hemolymphoid system gland3.25e-0923
pharyngeal epithelium3.25e-0923
thymic region3.25e-0923
pharyngeal gland3.25e-0923
entire pharyngeal arch endoderm3.25e-0923
thymus primordium3.25e-0923
early pharyngeal endoderm3.25e-0923
anterior region of body4.25e-0943
pharynx8.87e-0924
upper respiratory tract8.87e-0924
chordate pharynx8.87e-0924
pharyngeal arch system8.87e-0924
pharyngeal region of foregut8.87e-0924
mesoderm1.90e-08120
mesoderm-derived structure1.90e-08120
presumptive mesoderm1.90e-08120
lateral plate mesoderm5.36e-0887
craniocervical region7.23e-0836
endo-epithelium8.86e-0869
hematopoietic system9.51e-0845
blood island9.51e-0845
hemolymphoid system2.96e-0748
immune system2.96e-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)
MA0003.10.989123
MA0004.10.603793
MA0006.11.07705
MA0007.10.587678
MA0009.11.06266
MA0014.11.13011
MA0017.10.449113
MA0019.12.02888
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.11.7574
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.28842
MA0056.10
MA0057.10.562607
MA0058.10.50032
MA0059.10.513699
MA0060.12.4023
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.189951
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.888325
MA0089.10
MA0090.10.566938
MA0091.12.54547
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.11.89733
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.11.30068
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.17.20073
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.11.70396
MA0145.10.476962
MA0146.10.475727
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.706751
MA0035.20.700704
MA0039.20.749235
MA0138.20.861035
MA0002.20.299191
MA0137.21.20517
MA0104.20.845917
MA0047.20.75686
MA0112.20.157681
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.587595
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.526186
MA0163.11.29282
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.21.19329
MA0102.21.79669
MA0258.10.346619
MA0259.10.960816
MA0442.10
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