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MCL coexpression mm9:2223: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003081!3.45e-16!87;UBERON:0002390!1.22e-15!45;UBERON:0003061!1.22e-15!45;UBERON:0002193!1.88e-15!48;UBERON:0002405!1.88e-15!48;UBERON:0002384!3.46e-15!46;UBERON:0000926!1.92e-14!120;UBERON:0004120!1.92e-14!120;UBERON:0006603!1.92e-14!120;UBERON:0002371!7.77e-10!16;UBERON:0002204!2.64e-09!32;UBERON:0001474!4.31e-09!22;UBERON:0004765!4.31e-09!22;UBERON:0001434!4.31e-09!22;UBERON:0001041!1.38e-07!80;UBERON:0004177!1.95e-07!29;UBERON:0005057!1.95e-07!29;UBERON:0000077!2.76e-07!35
|ontology_enrichment_uberon=UBERON:0003081!3.45e-16!87;UBERON:0002390!1.22e-15!45;UBERON:0003061!1.22e-15!45;UBERON:0002193!1.88e-15!48;UBERON:0002405!1.88e-15!48;UBERON:0002384!3.46e-15!46;UBERON:0000926!1.92e-14!120;UBERON:0004120!1.92e-14!120;UBERON:0006603!1.92e-14!120;UBERON:0002371!7.77e-10!16;UBERON:0002204!2.64e-09!32;UBERON:0001474!4.31e-09!22;UBERON:0004765!4.31e-09!22;UBERON:0001434!4.31e-09!22;UBERON:0001041!1.38e-07!80;UBERON:0004177!1.95e-07!29;UBERON:0005057!1.95e-07!29;UBERON:0000077!2.76e-07!35
|tfbs_overrepresentation_for_novel_motifs=0.641384,2.54893,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.993085,0.489964,0.755749,0.790506,0.96877,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.57409,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,1.18815,0.318879,0.503207,2.11901,0.460474,0.786577,0.434783,1.82692,0.478558,0.717547,0.185353,0.504971,0.0986756,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,1.44172,0.377213,1.12016,1.32691,0.864765,1.50994,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.951203,1.20828,1.24129,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,1.2358,1.23918,0.680176,1.40022,0.839311,1.53196,0.569254,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,1.21803,0.293812,0.542121,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,1.56687,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,2.65001
|tfbs_overrepresentation_for_novel_motifs=0.641384,2.54893,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.993085,0.489964,0.755749,0.790506,0.96877,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.57409,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,1.18815,0.318879,0.503207,2.11901,0.460474,0.786577,0.434783,1.82692,0.478558,0.717547,0.185353,0.504971,0.0986756,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,1.44172,0.377213,1.12016,1.32691,0.864765,1.50994,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.951203,1.20828,1.24129,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,1.2358,1.23918,0.680176,1.40022,0.839311,1.53196,0.569254,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,1.21803,0.293812,0.542121,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,1.56687,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,2.65001
|tfbs_overrepresentation_jaspar=MA0003.1;4.15047,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.981995,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.266382,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.790894,MA0056.1;0,MA0057.1;1.29714,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;2.91229,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.713436,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.0140887,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;1.5065,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.582815,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;1.84237,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;5.19185,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;1.24367,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.957842,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;1.79187,MA0146.1;2.17792,MA0147.1;1.15069,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;2.95164,MA0138.2;0.951653,MA0002.2;0.965577,MA0137.2;0.559766,MA0104.2;1.0034,MA0047.2;0.845655,MA0112.2;0.608441,MA0065.2;1.14711,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.728853,MA0155.1;2.6534,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;2.99359,MA0163.1;1.64105,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;10.3152,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}
}}

Revision as of 14:32, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr17:71202091..71202110,+p@chr17:71202091..71202110
+
Mm9::chr5:122286819..122286854,-p1@Sh2b3
Mm9::chr7:26472013..26472031,+p1@Tgfb1
Mm9::chr7:26472296..26472360,+p2@Tgfb1


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:0030097hemopoiesis0.00745062589058729
GO:0048534hemopoietic or lymphoid organ development0.00745062589058729
GO:0002520immune system development0.00745062589058729
GO:0048298positive regulation of isotype switching to IgA isotypes0.00745062589058729
GO:0048296regulation of isotype switching to IgA isotypes0.00745062589058729
GO:0048290isotype switching to IgA isotypes0.00745062589058729
GO:0045066regulatory T cell differentiation0.00838172450320505
GO:0002513tolerance induction to self antigen0.00838172450320505
GO:0002507tolerance induction0.00993362356088819
GO:0035162embryonic hemopoiesis0.0111747141761175
GO:0005160transforming growth factor beta receptor binding0.0111747141761175
GO:0008354germ cell migration0.0111747141761175
GO:0045830positive regulation of isotype switching0.0117615679119517
GO:0042306regulation of protein import into nucleus0.0117615679119517
GO:0033157regulation of intracellular protein transport0.0117615679119517
GO:0030279negative regulation of ossification0.0117615679119517
GO:0032386regulation of intracellular transport0.0117615679119517
GO:0043029T cell homeostasis0.0117615679119517
GO:0051101regulation of DNA binding0.0117615679119517
GO:0051223regulation of protein transport0.0121036186066592
GO:0045191regulation of isotype switching0.0121036186066592
GO:0046822regulation of nucleocytoplasmic transport0.0121036186066592
GO:0016202regulation of striated muscle development0.0121036186066592
GO:0046851negative regulation of bone remodeling0.0121036186066592
GO:0042130negative regulation of T cell proliferation0.012124272964592
GO:0002376immune system process0.012124272964592
GO:0048535lymph node development0.0132830238819138
GO:0050868negative regulation of T cell activation0.0132830238819138
GO:0002260lymphocyte homeostasis0.0132830238819138
GO:0050672negative regulation of lymphocyte proliferation0.0132830238819138
GO:0032945negative regulation of mononuclear cell proliferation0.0132830238819138
GO:0051098regulation of binding0.0132830238819138
GO:0002208somatic diversification of immunoglobulins during immune response0.0132830238819138
GO:0002204somatic recombination of immunoglobulin genes during immune response0.0132830238819138
GO:0045190isotype switching0.0132830238819138
GO:0002381immunoglobulin production during immune response0.0132830238819138
GO:0030879mammary gland development0.0132830238819138
GO:0030278regulation of ossification0.0137813829400792
GO:0051250negative regulation of lymphocyte activation0.0137813829400792
GO:0001776leukocyte homeostasis0.0137813829400792
GO:0050871positive regulation of B cell activation0.0137813829400792
GO:0016447somatic recombination of immunoglobulin gene segments0.0137813829400792
GO:0048872homeostasis of number of cells0.0137813829400792
GO:0051241negative regulation of multicellular organismal process0.0137813829400792
GO:0046850regulation of bone remodeling0.0137813829400792
GO:0016444somatic cell DNA recombination0.0137813829400792
GO:0002562somatic diversification of immune receptors via germline recombination within a single locus0.0137813829400792
GO:0016445somatic diversification of immunoglobulins0.0139592077719214
GO:0002200somatic diversification of immune receptors0.0145851479348968
GO:0050864regulation of B cell activation0.0162005197383997
GO:0048568embryonic organ development0.0162005197383997
GO:0002377immunoglobulin production0.0167469160996042
GO:0002440production of molecular mediator of immune response0.0168517804801941
GO:0042129regulation of T cell proliferation0.0173657434817174
GO:0007179transforming growth factor beta receptor signaling pathway0.0186717639494633
GO:0048513organ development0.0191244399477819
GO:0050670regulation of lymphocyte proliferation0.0203964549816058
GO:0032944regulation of mononuclear cell proliferation0.0203964549816058
GO:0042098T cell proliferation0.0208062428871481
GO:0006606protein import into nucleus0.0208308910676066
GO:0051170nuclear import0.0208547110346113
GO:0051251positive regulation of lymphocyte activation0.0216073136941783
GO:0030217T cell differentiation0.0216073136941783
GO:0050863regulation of T cell activation0.0219658610872752
GO:0017038protein import0.0219706222464948
GO:0016064immunoglobulin mediated immune response0.0229274507513982
GO:0019724B cell mediated immunity0.0229274507513982
GO:0048731system development0.0229274507513982
GO:0032943mononuclear cell proliferation0.0229274507513982
GO:0006310DNA recombination0.0229274507513982
GO:0048732gland development0.0229274507513982
GO:0046651lymphocyte proliferation0.0229274507513982
GO:0048869cellular developmental process0.0232573811711488
GO:0030154cell differentiation0.0232573811711488
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0234943137786506
GO:0051249regulation of lymphocyte activation0.0237979600484555
GO:0051049regulation of transport0.0237979600484555
GO:0042113B cell activation0.0237979600484555
GO:0050865regulation of cell activation0.0237979600484555
GO:0002250adaptive immune response0.0237979600484555
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0237979600484555
GO:0030098lymphocyte differentiation0.0237979600484555
GO:0006913nucleocytoplasmic transport0.0237979600484555
GO:0002449lymphocyte mediated immunity0.0237979600484555
GO:0001503ossification0.0237979600484555
GO:0051169nuclear transport0.0237979600484555
GO:0016049cell growth0.0237979600484555
GO:0031214biomineral formation0.0237979600484555
GO:0007519skeletal muscle development0.0237979600484555
GO:0002443leukocyte mediated immunity0.0243809033882287
GO:0048856anatomical structure development0.0243809033882287
GO:0046849bone remodeling0.0249551449177405
GO:0008361regulation of cell size0.0256427030608344
GO:0042110T cell activation0.0276751578299701
GO:0008285negative regulation of cell proliferation0.0276751578299701
GO:0048771tissue remodeling0.0280202532627508
GO:0014706striated muscle development0.0280202532627508
GO:0007275multicellular organismal development0.028361058193276
GO:0002521leukocyte differentiation0.0285754315903206
GO:0002252immune effector process0.030065091026619
GO:0008083growth factor activity0.0328417615019168
GO:0007517muscle development0.0362131531844413
GO:0008284positive regulation of cell proliferation0.0380114415527461
GO:0016563transcription activator activity0.0380716457215351
GO:0001501skeletal development0.0381306564905467
GO:0006605protein targeting0.0392790963079813
GO:0046649lymphocyte activation0.0392790963079813
GO:0045321leukocyte activation0.0423958726799473
GO:0006954inflammatory response0.0424124169261955
GO:0032502developmental process0.0437515935107479
GO:0001775cell activation0.0442353946983323
GO:0045893positive regulation of transcription, DNA-dependent0.0467966770102563
GO:0007276gamete generation0.0491150881882739



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
lateral plate mesoderm3.45e-1687
hematopoietic system1.22e-1545
blood island1.22e-1545
hemolymphoid system1.88e-1548
immune system1.88e-1548
connective tissue3.46e-1546
mesoderm1.92e-14120
mesoderm-derived structure1.92e-14120
presumptive mesoderm1.92e-14120
bone marrow7.77e-1016
musculoskeletal system2.64e-0932
bone element4.31e-0922
skeletal element4.31e-0922
skeletal system4.31e-0922
foregut1.38e-0780
hemopoietic organ1.95e-0729
immune organ1.95e-0729
mixed endoderm/mesoderm-derived structure2.76e-0735


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)
MA0003.14.15047
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.981995
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
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
MA0048.10.266382
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.790894
MA0056.10
MA0057.11.29714
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.12.91229
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.713436
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.0140887
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.11.5065
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.582815
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.11.84237
MA0101.10.605676
MA0103.10.540576
MA0105.15.19185
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.11.24367
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
MA0139.10.957842
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.11.79187
MA0146.12.17792
MA0147.11.15069
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.22.95164
MA0138.20.951653
MA0002.20.965577
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.20.608441
MA0065.21.14711
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.728853
MA0155.12.6534
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.12.99359
MA0163.11.64105
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.210.3152
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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