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MCL coexpression mm9:2663: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002193!1.07e-22!48;UBERON:0002405!1.07e-22!48;UBERON:0002390!4.17e-20!45;UBERON:0003061!4.17e-20!45;UBERON:0004177!2.16e-18!29;UBERON:0005057!2.16e-18!29;UBERON:0000077!7.25e-17!35;UBERON:0002370!4.72e-15!23;UBERON:0000974!4.72e-15!23;UBERON:0004807!4.72e-15!23;UBERON:0005058!4.72e-15!23;UBERON:0003351!4.72e-15!23;UBERON:0009113!4.72e-15!23;UBERON:0003295!4.72e-15!23;UBERON:0009722!4.72e-15!23;UBERON:0005562!4.72e-15!23;UBERON:0007690!4.72e-15!23;UBERON:0006562!3.53e-14!24;UBERON:0003408!3.53e-14!24;UBERON:0001557!3.53e-14!24;UBERON:0001042!3.53e-14!24;UBERON:0008814!3.53e-14!24;UBERON:0009145!3.53e-14!24;UBERON:0000072!5.84e-12!27;UBERON:0000065!1.19e-11!41;UBERON:0001004!3.35e-11!42;UBERON:0003081!6.46e-09!87;UBERON:0002384!8.67e-09!46;UBERON:0000063!5.60e-08!35;UBERON:0000926!6.81e-08!120;UBERON:0004120!6.81e-08!120;UBERON:0006603!6.81e-08!120;UBERON:0007811!1.30e-07!36
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,1.38557,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.922882,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.568545,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,1.95046
|tfbs_overrepresentation_jaspar=MA0003.1;0.526413,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.416365,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;1.49373,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.932001,MA0050.1;1.97065,MA0051.1;2.23119,MA0052.1;1.29825,MA0055.1;0.190475,MA0056.1;0,MA0057.1;0.337566,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;0.502699,MA0061.1;1.33581,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;0.343188,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;0.121346,MA0074.1;0.911576,MA0076.1;1.58243,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.27999,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;0.62555,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;1.70277,MA0103.1;0.647985,MA0105.1;2.75918,MA0106.1;1.01755,MA0107.1;1.54626,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;0.537669,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;0.462282,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.794492,MA0146.1;1.44443,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;2.79231,MA0035.2;0.903829,MA0039.2;1.10518,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;0.48458,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;0.292912,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.35067,MA0155.1;0.840842,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.166722,MA0163.1;0.157796,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;1.16605,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}

Latest revision as of 18:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:34596624..34596637,-p@chr11:34596624..34596637
-
Mm9::chr12:81216836..81216923,+p@chr12:81216836..81216923
+
Mm9::chr4:128709945..128709974,-p@chr4:128709945..128709974
-


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
lymphoid lineage restricted progenitor cell6.31e-1612
hematopoietic cell1.05e-1532
hematopoietic oligopotent progenitor cell1.05e-1532
hematopoietic stem cell1.05e-1532
angioblastic mesenchymal cell1.05e-1532
hematopoietic multipotent progenitor cell1.05e-1532
T cell1.11e-1411
pro-T cell1.11e-1411
lymphocyte2.15e-1413
common lymphoid progenitor2.15e-1413
mature alpha-beta T cell6.12e-139
alpha-beta T cell6.12e-139
immature T cell6.12e-139
mature T cell6.12e-139
immature alpha-beta T cell6.12e-139
hematopoietic lineage restricted progenitor cell1.03e-1225
CD4-positive, alpha-beta T cell9.81e-128
nucleate cell5.76e-1116
leukocyte4.24e-1017
nongranular leukocyte4.24e-1017
thymocyte3.79e-096
double negative thymocyte3.79e-096
naive T cell3.79e-096
double-positive, alpha-beta thymocyte3.79e-096
CD4-positive, alpha-beta thymocyte3.79e-096
naive thymus-derived CD4-positive, alpha-beta T cell3.79e-096
DN4 thymocyte3.79e-096
DN1 thymic pro-T cell3.79e-096
DN2 thymocyte3.79e-096
DN3 thymocyte3.79e-096
immature single positive thymocyte3.79e-096
early T lineage precursor3.79e-096
mature CD4 single-positive thymocyte3.79e-096
resting double-positive thymocyte3.79e-096
double-positive blast3.79e-096
CD69-positive double-positive thymocyte3.79e-096
CD69-positive, CD4-positive single-positive thymocyte3.79e-096
CD4-positive, CD8-intermediate double-positive thymocyte3.79e-096
CD24-positive, CD4 single-positive thymocyte3.79e-096
connective tissue cell8.67e-0946
mesenchymal cell8.67e-0946

Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.07e-2248
immune system1.07e-2248
hematopoietic system4.17e-2045
blood island4.17e-2045
hemopoietic organ2.16e-1829
immune organ2.16e-1829
mixed endoderm/mesoderm-derived structure7.25e-1735
thymus4.72e-1523
neck4.72e-1523
respiratory system epithelium4.72e-1523
hemolymphoid system gland4.72e-1523
pharyngeal epithelium4.72e-1523
thymic region4.72e-1523
pharyngeal gland4.72e-1523
entire pharyngeal arch endoderm4.72e-1523
thymus primordium4.72e-1523
early pharyngeal endoderm4.72e-1523
pharynx3.53e-1424
gland of gut3.53e-1424
upper respiratory tract3.53e-1424
chordate pharynx3.53e-1424
pharyngeal arch system3.53e-1424
pharyngeal region of foregut3.53e-1424
segment of respiratory tract5.84e-1227
respiratory tract1.19e-1141
respiratory system3.35e-1142
lateral plate mesoderm6.46e-0987
connective tissue8.67e-0946
organ segment5.60e-0835
mesoderm6.81e-08120
mesoderm-derived structure6.81e-08120
presumptive mesoderm6.81e-08120
craniocervical region1.30e-0736


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)
MA0003.10.526413
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.416365
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.11.49373
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.932001
MA0050.11.97065
MA0051.12.23119
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.11.33581
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.121346
MA0074.10.911576
MA0076.11.58243
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.11.70277
MA0103.10.647985
MA0105.12.75918
MA0106.11.01755
MA0107.11.54626
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.794492
MA0146.11.44443
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.22.79231
MA0035.20.903829
MA0039.21.10518
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.21.16605
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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