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MCL coexpression mm9:807: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002384!3.41e-22!46;UBERON:0002370!6.61e-15!23;UBERON:0000974!6.61e-15!23;UBERON:0004807!6.61e-15!23;UBERON:0005058!6.61e-15!23;UBERON:0003351!6.61e-15!23;UBERON:0009113!6.61e-15!23;UBERON:0003295!6.61e-15!23;UBERON:0009722!6.61e-15!23;UBERON:0005562!6.61e-15!23;UBERON:0007690!6.61e-15!23;UBERON:0002390!6.92e-15!45;UBERON:0003061!6.92e-15!45;UBERON:0006562!3.36e-14!24;UBERON:0003408!3.36e-14!24;UBERON:0001557!3.36e-14!24;UBERON:0001042!3.36e-14!24;UBERON:0008814!3.36e-14!24;UBERON:0009145!3.36e-14!24;UBERON:0002193!9.36e-14!48;UBERON:0002405!9.36e-14!48;UBERON:0000072!2.14e-12!27;UBERON:0004177!2.11e-11!29;UBERON:0005057!2.11e-11!29;UBERON:0000077!6.80e-11!35;UBERON:0000063!4.23e-09!35;UBERON:0007811!8.60e-09!36;UBERON:0000065!1.78e-07!41;UBERON:0001004!2.98e-07!42;UBERON:0003081!3.85e-07!87;UBERON:0000153!4.89e-07!43
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.0909519,0.330161,0.394491,0.645379,0.40827,0.495658,0.146465,0.154135,0.314043,0.453212,0.484001,0.88117,0.507558,0.680035,0,0.696644,0.22065,0.134657,0.247067,0.296085,0.403891,0.50668,1.20034,0.337218,0.534339,0.801525,0.428336,0.739731,0.0963992,0.414842,0.796599,0.624261,0.113369,0.681042,0.0500417,0.604998,0.480503,0.191662,0.167387,0.224094,0.419787,0.371854,0.244285,0.536558,0.383899,0.618203,0.443479,0.133514,0.271021,0.679429,0.560572,0.633942,0.937018,0.954342,0.514504,0.279148,0.471658,1.25881,0.512521,0.776777,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.460931,0.424998,0.987652,0.116281,0.107966,0.113315,0.607043,0.759798,0.299972,0.152219,0.713779,0.568383,0.858535,0.873141,0.0176817,0.092683,0.0965007,0.623015,1.60001,1.15927,0.878077,1.89585,0.232894,0.188213,0.17334,0.14449,0.812053,0.618454,0.0816605,0.605162,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,1.48974,0.806647,0.348012,0.921485,0.301014,0.458194,1.16629,0.222515,0.265919,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,1.00644,1.05894,0.527782,1.18781,0.177062,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.098204,0.041769,0.938577,0.178329,1.3067,1.01974,0.561556,0.253271,0.928824,0.362302,1.1483,0.872292,0.763895,0.345891,1.60621,0.519673,0.209556,0.482466,0.12239
|tfbs_overrepresentation_jaspar=MA0003.1;0.294637,MA0004.1;0.394951,MA0006.1;0.238555,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.00813637,MA0017.1;1.3362,MA0019.1;0.642876,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.692501,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.0824771,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.221677,MA0056.1;0,MA0057.1;0.0745664,MA0058.1;0.823526,MA0059.1;0.849123,MA0060.1;0.169058,MA0061.1;1.07655,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.954794,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;0.831547,MA0074.1;0.488775,MA0076.1;0.279739,MA0077.1;0.804033,MA0078.1;1.40897,MA0081.1;0.338098,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.413524,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.95209,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;4.25311,MA0103.1;0.748482,MA0105.1;0.720048,MA0106.1;0.582805,MA0107.1;3.79511,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;0.561811,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;2.06044,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.143341,MA0140.1;0.477483,MA0141.1;1.43798,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;0.0543321,MA0146.1;0.148686,MA0147.1;0.205697,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;0.365726,MA0035.2;0.482026,MA0039.2;0.288731,MA0138.2;0.630612,MA0002.2;0.447007,MA0137.2;0.287486,MA0104.2;0.157347,MA0047.2;0.533516,MA0112.2;0.442124,MA0065.2;0.44341,MA0150.1;0.991233,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.276788,MA0155.1;0.226288,MA0156.1;0.763978,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.614411,MA0160.1;1.86992,MA0161.1;0,MA0162.1;0.348617,MA0163.1;0.321031,MA0164.1;0.508398,MA0080.2;0.737531,MA0018.2;2.21977,MA0099.2;1.51239,MA0079.2;0.0340753,MA0102.2;1.5442,MA0258.1;0.533988,MA0259.1;0.196451,MA0442.1;0
}}

Latest revision as of 15:55, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:4914545..4914560,-p5@Ubxn2a
Mm9::chr13:105400705..105400716,-p@chr13:105400705..105400716
-
Mm9::chr13:43364328..43364338,-p@chr13:43364328..43364338
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Mm9::chr1:13152564..13152597,-p@chr1:13152564..13152597
-
Mm9::chr2:127159235..127159246,+p@chr2:127159235..127159246
+
Mm9::chr2:34819390..34819406,+p@chr2:34819390..34819406
+
Mm9::chr8:87186907..87186914,-p3@Ier2
Mm9::chr8:87186926..87186970,-p2@Ier2
Mm9::chr9:20780356..20780371,+p@chr9:20780356..20780371
+


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:0030375thyroid hormone receptor coactivator activity0.0149012517811746
GO:0030374ligand-dependent nuclear receptor transcription coactivator activity0.018625033901764
GO:0035257nuclear hormone receptor binding0.0193657897706547
GO:0051427hormone receptor binding0.0193657897706547
GO:0030518steroid hormone receptor signaling pathway0.0193657897706547
GO:0030522intracellular receptor-mediated signaling pathway0.0223420803936546



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
hematopoietic cell4.63e-3032
hematopoietic oligopotent progenitor cell4.63e-3032
hematopoietic stem cell4.63e-3032
angioblastic mesenchymal cell4.63e-3032
hematopoietic multipotent progenitor cell4.63e-3032
mature alpha-beta T cell1.08e-299
alpha-beta T cell1.08e-299
immature T cell1.08e-299
mature T cell1.08e-299
immature alpha-beta T cell1.08e-299
lymphoid lineage restricted progenitor cell3.93e-2712
CD4-positive, alpha-beta T cell1.32e-268
lymphocyte6.66e-2513
common lymphoid progenitor6.66e-2513
T cell5.16e-2411
pro-T cell5.16e-2411
connective tissue cell3.41e-2246
mesenchymal cell3.41e-2246
thymocyte1.67e-206
double negative thymocyte1.67e-206
naive T cell1.67e-206
double-positive, alpha-beta thymocyte1.67e-206
CD4-positive, alpha-beta thymocyte1.67e-206
naive thymus-derived CD4-positive, alpha-beta T cell1.67e-206
DN4 thymocyte1.67e-206
DN1 thymic pro-T cell1.67e-206
DN2 thymocyte1.67e-206
DN3 thymocyte1.67e-206
immature single positive thymocyte1.67e-206
early T lineage precursor1.67e-206
mature CD4 single-positive thymocyte1.67e-206
resting double-positive thymocyte1.67e-206
double-positive blast1.67e-206
CD69-positive double-positive thymocyte1.67e-206
CD69-positive, CD4-positive single-positive thymocyte1.67e-206
CD4-positive, CD8-intermediate double-positive thymocyte1.67e-206
CD24-positive, CD4 single-positive thymocyte1.67e-206
nucleate cell6.95e-2016
leukocyte1.32e-1817
nongranular leukocyte1.32e-1817
motile cell2.47e-1854
hematopoietic lineage restricted progenitor cell3.44e-1725
stem cell2.13e-1297
common myeloid progenitor1.77e-0919
somatic stem cell2.65e-0991
multi fate stem cell2.65e-0991

Uber Anatomy
Ontology termp-valuen
connective tissue3.41e-2246
thymus6.61e-1523
neck6.61e-1523
respiratory system epithelium6.61e-1523
hemolymphoid system gland6.61e-1523
pharyngeal epithelium6.61e-1523
thymic region6.61e-1523
pharyngeal gland6.61e-1523
entire pharyngeal arch endoderm6.61e-1523
thymus primordium6.61e-1523
early pharyngeal endoderm6.61e-1523
hematopoietic system6.92e-1545
blood island6.92e-1545
pharynx3.36e-1424
gland of gut3.36e-1424
upper respiratory tract3.36e-1424
chordate pharynx3.36e-1424
pharyngeal arch system3.36e-1424
pharyngeal region of foregut3.36e-1424
hemolymphoid system9.36e-1448
immune system9.36e-1448
segment of respiratory tract2.14e-1227
hemopoietic organ2.11e-1129
immune organ2.11e-1129
mixed endoderm/mesoderm-derived structure6.80e-1135
organ segment4.23e-0935
craniocervical region8.60e-0936
respiratory tract1.78e-0741
respiratory system2.98e-0742
lateral plate mesoderm3.85e-0787
anterior region of body4.89e-0743


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)
MA0003.10.294637
MA0004.10.394951
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.00813637
MA0017.11.3362
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.692501
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.0824771
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.221677
MA0056.10
MA0057.10.0745664
MA0058.10.823526
MA0059.10.849123
MA0060.10.169058
MA0061.11.07655
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.954794
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.831547
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.11.40897
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.413524
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.95209
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.14.25311
MA0103.10.748482
MA0105.10.720048
MA0106.10.582805
MA0107.13.79511
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.10.238371
MA0117.12.06044
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.11.43798
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.0543321
MA0146.10.148686
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.20.365726
MA0035.20.482026
MA0039.20.288731
MA0138.20.630612
MA0002.20.447007
MA0137.20.287486
MA0104.20.157347
MA0047.20.533516
MA0112.20.442124
MA0065.20.44341
MA0150.10.991233
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.276788
MA0155.10.226288
MA0156.10.763978
MA0157.10.683365
MA0158.10
MA0159.10.614411
MA0160.11.86992
MA0161.10
MA0162.10.348617
MA0163.10.321031
MA0164.10.508398
MA0080.20.737531
MA0018.22.21977
MA0099.21.51239
MA0079.20.0340753
MA0102.21.5442
MA0258.10.533988
MA0259.10.196451
MA0442.10
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