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MCL coexpression mm9:2579: Difference between revisions

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{{MCL_coexpression_mm9
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tautomerase activity;0.00142442338245768;17319!GO:0016862;intramolecular oxidoreductase activity, interconverting keto- and enol-groups;0.00462937599298745;17319!GO:0007569;cell aging;0.00462937599298745;17319!GO:0030330;DNA damage response, signal transduction by p53 class mediator;0.00462937599298745;17319!GO:0007568;aging;0.007976770941763;17319!GO:0042770;DNA damage response, signal transduction;0.00830913639766979;17319!GO:0016860;intramolecular oxidoreductase activity;0.00875002934938288;17319!GO:0016853;isomerase activity;0.0270640442666959;17319!GO:0006954;inflammatory response;0.029675487134535;17319!GO:0005125;cytokine activity;0.029675487134535;17319!GO:0006974;response to DNA damage stimulus;0.029675487134535;17319!GO:0009719;response to endogenous stimulus;0.029675487134535;17319!GO:0009611;response to wounding;0.0315564564729086;17319!GO:0042127;regulation of cell proliferation;0.0322530151599346;17319!GO:0009605;response to external stimulus;0.0411302251684655;17319!GO:0008283;cell proliferation;0.0411302251684655;17319!GO:0005102;receptor 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|gostat_on_MCL_coexpression=GO:0050178;phenylpyruvate tautomerase activity;0.00142442338245768;17319!GO:0016862;intramolecular oxidoreductase activity, interconverting keto- and enol-groups;0.00462937599298745;17319!GO:0007569;cell aging;0.00462937599298745;17319!GO:0030330;DNA damage response, signal transduction by p53 class mediator;0.00462937599298745;17319!GO:0007568;aging;0.007976770941763;17319!GO:0042770;DNA damage response, signal transduction;0.00830913639766979;17319!GO:0016860;intramolecular oxidoreductase activity;0.00875002934938288;17319!GO:0016853;isomerase activity;0.0270640442666959;17319!GO:0006954;inflammatory response;0.029675487134535;17319!GO:0005125;cytokine activity;0.029675487134535;17319!GO:0006974;response to DNA damage stimulus;0.029675487134535;17319!GO:0009719;response to endogenous stimulus;0.029675487134535;17319!GO:0009611;response to wounding;0.0315564564729086;17319!GO:0042127;regulation of cell proliferation;0.0322530151599346;17319!GO:0009605;response to external stimulus;0.0411302251684655;17319!GO:0008283;cell proliferation;0.0411302251684655;17319!GO:0005102;receptor binding;0.0494358703323547;17319!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!2.41e-21!46;UBERON:0002193!1.62e-10!48;UBERON:0002405!1.62e-10!48;UBERON:0002371!1.15e-09!16;UBERON:0002390!6.27e-09!45;UBERON:0003061!6.27e-09!45;UBERON:0000344!6.87e-08!15;UBERON:0003126!4.59e-07!3;UBERON:0001005!4.59e-07!3;UBERON:0007196!4.59e-07!3;UBERON:0001558!4.59e-07!3;UBERON:0000358!8.17e-07!3;UBERON:0000307!8.17e-07!3;UBERON:0007010!8.17e-07!3
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,2.12177,0.467321,0.479531,1.23467,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,2.37023,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.922882,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,2.16561,2.67145,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,1.6706,0.474956,0.284975,1.44925,0.416814,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.535545,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,1.94011,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.609576,1.88801,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,2.14021,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.721422,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
|tfbs_overrepresentation_jaspar=MA0003.1;0.0699972,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;1.33691,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,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;0.353763,MA0050.1;0.845669,MA0051.1;0.973068,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;0.5406,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;0.00834468,MA0074.1;0.911576,MA0076.1;0.657929,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;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,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;0.292366,MA0146.1;0.151124,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;0.0481552,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;0.312898,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.499274,MA0163.1;0.157796,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;0.00937321,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}

Latest revision as of 18:45, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:75322959..75322966,-p2@Mif
Mm9::chr11:29447871..29447878,-p7@Gm8430
p7@Rps27a
Mm9::chr3:91828403..91828446,+p1@ENSMUST00000118636


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:0050178phenylpyruvate tautomerase activity0.00142442338245768
GO:0016862intramolecular oxidoreductase activity, interconverting keto- and enol-groups0.00462937599298745
GO:0007569cell aging0.00462937599298745
GO:0030330DNA damage response, signal transduction by p53 class mediator0.00462937599298745
GO:0007568aging0.007976770941763
GO:0042770DNA damage response, signal transduction0.00830913639766979
GO:0016860intramolecular oxidoreductase activity0.00875002934938288
GO:0016853isomerase activity0.0270640442666959
GO:0006954inflammatory response0.029675487134535
GO:0005125cytokine activity0.029675487134535
GO:0006974response to DNA damage stimulus0.029675487134535
GO:0009719response to endogenous stimulus0.029675487134535
GO:0009611response to wounding0.0315564564729086
GO:0042127regulation of cell proliferation0.0322530151599346
GO:0009605response to external stimulus0.0411302251684655
GO:0008283cell proliferation0.0411302251684655
GO:0005102receptor binding0.0494358703323547



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 cell2.09e-2532
hematopoietic oligopotent progenitor cell2.09e-2532
hematopoietic stem cell2.09e-2532
angioblastic mesenchymal cell2.09e-2532
hematopoietic multipotent progenitor cell2.09e-2532
connective tissue cell2.41e-2146
mesenchymal cell2.41e-2146
motile cell1.34e-2054
hematopoietic lineage restricted progenitor cell1.98e-2025
animal cell2.88e-17115
eukaryotic cell2.88e-17115
somatic cell1.41e-16118
lymphoid lineage restricted progenitor cell4.08e-1412
leukocyte6.20e-1417
nongranular leukocyte6.20e-1417
common myeloid progenitor1.52e-1319
stem cell4.88e-1397
lymphocyte7.46e-1313
common lymphoid progenitor7.46e-1313
T cell8.52e-1311
pro-T cell8.52e-1311
mature alpha-beta T cell1.89e-129
alpha-beta T cell1.89e-129
immature T cell1.89e-129
mature T cell1.89e-129
immature alpha-beta T cell1.89e-129
nucleate cell3.26e-1216
thymocyte1.69e-116
double negative thymocyte1.69e-116
naive T cell1.69e-116
double-positive, alpha-beta thymocyte1.69e-116
CD4-positive, alpha-beta thymocyte1.69e-116
naive thymus-derived CD4-positive, alpha-beta T cell1.69e-116
DN4 thymocyte1.69e-116
DN1 thymic pro-T cell1.69e-116
DN2 thymocyte1.69e-116
DN3 thymocyte1.69e-116
immature single positive thymocyte1.69e-116
early T lineage precursor1.69e-116
mature CD4 single-positive thymocyte1.69e-116
resting double-positive thymocyte1.69e-116
double-positive blast1.69e-116
CD69-positive double-positive thymocyte1.69e-116
CD69-positive, CD4-positive single-positive thymocyte1.69e-116
CD4-positive, CD8-intermediate double-positive thymocyte1.69e-116
CD24-positive, CD4 single-positive thymocyte1.69e-116
CD4-positive, alpha-beta T cell4.15e-118
somatic stem cell4.54e-1091
multi fate stem cell4.54e-1091
myeloid cell6.95e-1016
myeloid lineage restricted progenitor cell4.36e-0813
megakaryocyte progenitor cell1.90e-076
megakaryocyte1.90e-076
duct epithelial cell4.59e-073
epithelial cell of tracheobronchial tree4.59e-073
branched duct epithelial cell4.59e-073
epithelial cell of lower respiratory tract4.59e-073
respiratory epithelial cell4.59e-073
tracheal epithelial cell4.59e-073
tracheoblast4.59e-073
extraembryonic cell8.17e-073
trophoblast cell8.17e-073
megakaryocyte-erythroid progenitor cell8.92e-079

Uber Anatomy
Ontology termp-valuen
connective tissue2.41e-2146
hemolymphoid system1.62e-1048
immune system1.62e-1048
bone marrow1.15e-0916
hematopoietic system6.27e-0945
blood island6.27e-0945
mucosa6.87e-0815
trachea4.59e-073
respiratory airway4.59e-073
tracheobronchial tree4.59e-073
lower respiratory tract4.59e-073
blastocyst8.17e-073
blastula8.17e-073
cleaving embryo8.17e-073


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)
MA0003.10.0699972
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.11.33691
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
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
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.00834468
MA0074.10.911576
MA0076.10.657929
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
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
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
MA0145.10.292366
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.0481552
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
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.499274
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.00937321
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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