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MCL coexpression mm9:1640: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!1.73e-19!46;UBERON:0002193!2.61e-13!48;UBERON:0002405!2.61e-13!48;UBERON:0002370!3.52e-13!23;UBERON:0000974!3.52e-13!23;UBERON:0004807!3.52e-13!23;UBERON:0005058!3.52e-13!23;UBERON:0003351!3.52e-13!23;UBERON:0009113!3.52e-13!23;UBERON:0003295!3.52e-13!23;UBERON:0009722!3.52e-13!23;UBERON:0005562!3.52e-13!23;UBERON:0007690!3.52e-13!23;UBERON:0006562!1.47e-12!24;UBERON:0003408!1.47e-12!24;UBERON:0001557!1.47e-12!24;UBERON:0001042!1.47e-12!24;UBERON:0008814!1.47e-12!24;UBERON:0009145!1.47e-12!24;UBERON:0002390!2.17e-12!45;UBERON:0003061!2.17e-12!45;UBERON:0000072!5.63e-11!27;UBERON:0004177!4.21e-10!29;UBERON:0005057!4.21e-10!29;UBERON:0000077!6.54e-10!35;UBERON:0000063!4.42e-08!35;UBERON:0007811!8.24e-08!36
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.612204,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.115752,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.775038,0.185796,0.489529,0.44579,0.727684,1.04384,0.537749,0.757752,0.274609,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,0.253145,0.425309,0.20704,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,0.4934,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.827208,2.08316,1.23259,0.257421,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.796301,1.1148,0.0793594,0.618102,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.328405,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.44142,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,2.6072,1.18223,0.343194,0.749664,1.26545,0.787153,1.11626,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.745913
}}

Latest revision as of 17:15, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:30878237..30878249,+p@chr13:30878237..30878249
+
Mm9::chr14:122328651..122328669,-p@chr14:122328651..122328669
-
Mm9::chr1:161983227..161983241,-p@chr1:161983227..161983241
-
Mm9::chr5:122669837..122669864,+p@chr5:122669837..122669864
+
Mm9::chr7:6107402..6107413,+p@chr7:6107402..6107413
+


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

no results for this coexpression

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 cell8.24e-329
alpha-beta T cell8.24e-329
immature T cell8.24e-329
mature T cell8.24e-329
immature alpha-beta T cell8.24e-329
lymphoid lineage restricted progenitor cell3.21e-2912
CD4-positive, alpha-beta T cell3.45e-288
lymphocyte7.75e-2713
common lymphoid progenitor7.75e-2713
hematopoietic lineage restricted progenitor cell4.62e-2625
hematopoietic cell6.25e-2632
hematopoietic oligopotent progenitor cell6.25e-2632
hematopoietic stem cell6.25e-2632
angioblastic mesenchymal cell6.25e-2632
hematopoietic multipotent progenitor cell6.25e-2632
T cell9.25e-2611
pro-T cell9.25e-2611
nucleate cell1.80e-2116
thymocyte2.64e-216
double negative thymocyte2.64e-216
naive T cell2.64e-216
double-positive, alpha-beta thymocyte2.64e-216
CD4-positive, alpha-beta thymocyte2.64e-216
naive thymus-derived CD4-positive, alpha-beta T cell2.64e-216
DN4 thymocyte2.64e-216
DN1 thymic pro-T cell2.64e-216
DN2 thymocyte2.64e-216
DN3 thymocyte2.64e-216
immature single positive thymocyte2.64e-216
early T lineage precursor2.64e-216
mature CD4 single-positive thymocyte2.64e-216
resting double-positive thymocyte2.64e-216
double-positive blast2.64e-216
CD69-positive double-positive thymocyte2.64e-216
CD69-positive, CD4-positive single-positive thymocyte2.64e-216
CD4-positive, CD8-intermediate double-positive thymocyte2.64e-216
CD24-positive, CD4 single-positive thymocyte2.64e-216
leukocyte4.21e-2017
nongranular leukocyte4.21e-2017
connective tissue cell1.73e-1946
mesenchymal cell1.73e-1946
motile cell4.20e-1654
stem cell6.11e-1197
megakaryocyte progenitor cell1.06e-096
megakaryocyte1.06e-096
somatic stem cell3.53e-0891
multi fate stem cell3.53e-0891

Uber Anatomy
Ontology termp-valuen
connective tissue1.73e-1946
hemolymphoid system2.61e-1348
immune system2.61e-1348
thymus3.52e-1323
neck3.52e-1323
respiratory system epithelium3.52e-1323
hemolymphoid system gland3.52e-1323
pharyngeal epithelium3.52e-1323
thymic region3.52e-1323
pharyngeal gland3.52e-1323
entire pharyngeal arch endoderm3.52e-1323
thymus primordium3.52e-1323
early pharyngeal endoderm3.52e-1323
pharynx1.47e-1224
gland of gut1.47e-1224
upper respiratory tract1.47e-1224
chordate pharynx1.47e-1224
pharyngeal arch system1.47e-1224
pharyngeal region of foregut1.47e-1224
hematopoietic system2.17e-1245
blood island2.17e-1245
segment of respiratory tract5.63e-1127
hemopoietic organ4.21e-1029
immune organ4.21e-1029
mixed endoderm/mesoderm-derived structure6.54e-1035
organ segment4.42e-0835
craniocervical region8.24e-0836


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)
MA0003.10.406907
MA0004.10.603793
MA0006.11.07705
MA0007.10.587678
MA0009.11.06266
MA0014.10.418772
MA0017.10.449113
MA0019.10.874061
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
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.12.39011
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
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
MA0073.111.9602
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.11.33193
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.11.39153
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
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
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.11.73051
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.11.48363
MA0146.10.21827
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.21.67146
MA0039.20.489701
MA0138.20.861035
MA0002.20.809945
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.22.12679
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.173445
MA0156.12.05819
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.11.87338
MA0163.10.230013
MA0164.10.729558
MA0080.22.98824
MA0018.20.739807
MA0099.20.854449
MA0079.23.38617
MA0102.21.79669
MA0258.10.346619
MA0259.10.960816
MA0442.10
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