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MCL coexpression mm9:3123: Difference between revisions

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{{MCL_coexpression_mm9
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of transcription from RNA polymerase II promoter in response to stress;0.0130597933285795;13819!GO:0043619;regulation of transcription from RNA polymerase II promoter in response to oxidative stress;0.0130597933285795;13819!GO:0043620;regulation of transcription in response to stress;0.0130597933285795;13819!GO:0048875;chemical homeostasis within a tissue;0.0130597933285795;13819!GO:0043129;surfactant homeostasis;0.0130597933285795;13819!GO:0042415;norepinephrine metabolic process;0.0136035786831511;13819!GO:0002027;regulation of heart rate;0.0224422150894195;13819!GO:0001892;embryonic placenta development;0.0224422150894195;13819!GO:0001974;blood vessel remodeling;0.0244757078470398;13819!GO:0033554;cellular response to stress;0.0244757078470398;13819!GO:0051716;cellular response to stimulus;0.0244757078470398;13819!GO:0003697;single-stranded DNA binding;0.0244757078470398;56878!GO:0001666;response to hypoxia;0.0244757078470398;13819!GO:0003690;double-stranded DNA binding;0.0244757078470398;56878!GO:0001894;tissue homeostasis;0.0248996451830171;13819!GO:0048871;multicellular organismal homeostasis;0.0248996451830171;13819!GO:0001890;placenta development;0.0248996451830171;13819!GO:0018958;phenol metabolic process;0.0248996451830171;13819!GO:0006584;catecholamine metabolic process;0.0248996451830171;13819!GO:0008016;regulation of heart contraction;0.027430425466154;13819!GO:0042133;neurotransmitter metabolic process;0.027430425466154;13819!GO:0030218;erythrocyte differentiation;0.027430425466154;13819!GO:0003015;heart process;0.0293515286077098;13819!GO:0060047;heart contraction;0.0293515286077098;13819!GO:0006979;response to oxidative stress;0.0293515286077098;13819!GO:0043566;structure-specific DNA binding;0.0301016548785821;56878!GO:0046982;protein heterodimerization activity;0.0362215470398131;13819!GO:0030324;lung development;0.0363956629082699;13819!GO:0030323;respiratory tube development;0.0363956629082699;13819!GO:0007005;mitochondrion organization and biogenesis;0.0363956629082699;13819!GO:0006576;biogenic amine metabolic process;0.0376785679627757;13819!GO:0048469;cell maturation;0.0376785679627757;13819!GO:0042445;hormone metabolic process;0.0386746014954127;13819!GO:0006575;amino acid derivative metabolic process;0.0386746014954127;13819!GO:0001505;regulation of neurotransmitter levels;0.0386746014954127;13819!GO:0021700;developmental maturation;0.0386746014954127;13819!GO:0030099;myeloid cell differentiation;0.0386746014954127;13819!GO:0003677;DNA binding;0.0386746014954127;56878,13819!GO:0008015;blood circulation;0.0386746014954127;13819!GO:0003013;circulatory system process;0.0386746014954127;13819!GO:0007601;visual perception;0.0427717939759727;13819!GO:0050953;sensory perception of light stimulus;0.0427717939759727;13819!GO:0006725;aromatic compound metabolic process;0.0427717939759727;13819!GO:0001701;in utero embryonic development;0.0437547144648331;13819!GO:0048771;tissue 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|gostat_on_MCL_coexpression=GO:0043618;regulation of transcription from RNA polymerase II promoter in response to stress;0.0130597933285795;13819!GO:0043619;regulation of transcription from RNA polymerase II promoter in response to oxidative stress;0.0130597933285795;13819!GO:0043620;regulation of transcription in response to stress;0.0130597933285795;13819!GO:0048875;chemical homeostasis within a tissue;0.0130597933285795;13819!GO:0043129;surfactant homeostasis;0.0130597933285795;13819!GO:0042415;norepinephrine metabolic process;0.0136035786831511;13819!GO:0002027;regulation of heart rate;0.0224422150894195;13819!GO:0001892;embryonic placenta development;0.0224422150894195;13819!GO:0001974;blood vessel remodeling;0.0244757078470398;13819!GO:0033554;cellular response to stress;0.0244757078470398;13819!GO:0051716;cellular response to stimulus;0.0244757078470398;13819!GO:0003697;single-stranded DNA binding;0.0244757078470398;56878!GO:0001666;response to hypoxia;0.0244757078470398;13819!GO:0003690;double-stranded DNA binding;0.0244757078470398;56878!GO:0001894;tissue homeostasis;0.0248996451830171;13819!GO:0048871;multicellular organismal homeostasis;0.0248996451830171;13819!GO:0001890;placenta development;0.0248996451830171;13819!GO:0018958;phenol metabolic process;0.0248996451830171;13819!GO:0006584;catecholamine metabolic process;0.0248996451830171;13819!GO:0008016;regulation of heart contraction;0.027430425466154;13819!GO:0042133;neurotransmitter metabolic process;0.027430425466154;13819!GO:0030218;erythrocyte differentiation;0.027430425466154;13819!GO:0003015;heart process;0.0293515286077098;13819!GO:0060047;heart contraction;0.0293515286077098;13819!GO:0006979;response to oxidative stress;0.0293515286077098;13819!GO:0043566;structure-specific DNA binding;0.0301016548785821;56878!GO:0046982;protein heterodimerization activity;0.0362215470398131;13819!GO:0030324;lung development;0.0363956629082699;13819!GO:0030323;respiratory tube development;0.0363956629082699;13819!GO:0007005;mitochondrion organization and biogenesis;0.0363956629082699;13819!GO:0006576;biogenic amine metabolic process;0.0376785679627757;13819!GO:0048469;cell maturation;0.0376785679627757;13819!GO:0042445;hormone metabolic process;0.0386746014954127;13819!GO:0006575;amino acid derivative metabolic process;0.0386746014954127;13819!GO:0001505;regulation of neurotransmitter levels;0.0386746014954127;13819!GO:0021700;developmental maturation;0.0386746014954127;13819!GO:0030099;myeloid cell differentiation;0.0386746014954127;13819!GO:0003677;DNA binding;0.0386746014954127;56878,13819!GO:0008015;blood circulation;0.0386746014954127;13819!GO:0003013;circulatory system process;0.0386746014954127;13819!GO:0007601;visual perception;0.0427717939759727;13819!GO:0050953;sensory perception of light stimulus;0.0427717939759727;13819!GO:0006725;aromatic compound metabolic process;0.0427717939759727;13819!GO:0001701;in utero embryonic development;0.0437547144648331;13819!GO:0048771;tissue remodeling;0.0437547144648331;13819!GO:0006260;DNA replication;0.046721929108951;56878!GO:0001525;angiogenesis;0.046721929108951;13819!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000025!4.01e-13!114;UBERON:0004111!2.70e-12!122;UBERON:0005177!9.96e-11!79;UBERON:0009569!1.00e-10!66;UBERON:0002100!1.34e-09!90;UBERON:0000468!3.80e-08!333;UBERON:0003914!6.39e-08!47;UBERON:0000479!1.04e-07!349;UBERON:0005172!1.27e-07!49;UBERON:0005173!1.27e-07!49;UBERON:0002417!1.27e-07!49;UBERON:0000916!1.27e-07!49;UBERON:0000062!3.67e-07!266
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.07244,0.722405,0.801166,1.43553,0.81763,0.919454,0.467321,0.479531,1.23467,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.876292,0.679146,0.275782,0.932027,0.585919,0.731217,2.21138,0.437236,0.841386,0.64294,0.99159,0.825437,1.24901,0.575271,0.411696,0.608816,6.04797,0.563758,0.902078,0.536514,3.19233,0.582863,0.831295,0.261619,0.610669,1.47707,0.788421,1.05665,0.859154,0.235354,1.55852,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,1.07031,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,1.62246,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,2.8238,1.05692,0.928366,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,4.21798,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.721422,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.833542
|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;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;1.06076,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;0.439282,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;1.16863,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;1.33779,MA0145.1;0.292366,MA0146.1;0.46063,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;0.71803,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;1.52001,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;1.53682,MA0163.1;0.157796,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;1.81944,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}

Latest revision as of 19:37, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr17:87153028..87153049,+p2@Epas1
Mm9::chr17:87153240..87153254,+p1@Epas1
Mm9::chr2:60800858..60800878,-p6@Rbms1


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:0043618regulation of transcription from RNA polymerase II promoter in response to stress0.0130597933285795
GO:0043619regulation of transcription from RNA polymerase II promoter in response to oxidative stress0.0130597933285795
GO:0043620regulation of transcription in response to stress0.0130597933285795
GO:0048875chemical homeostasis within a tissue0.0130597933285795
GO:0043129surfactant homeostasis0.0130597933285795
GO:0042415norepinephrine metabolic process0.0136035786831511
GO:0002027regulation of heart rate0.0224422150894195
GO:0001892embryonic placenta development0.0224422150894195
GO:0001974blood vessel remodeling0.0244757078470398
GO:0033554cellular response to stress0.0244757078470398
GO:0051716cellular response to stimulus0.0244757078470398
GO:0003697single-stranded DNA binding0.0244757078470398
GO:0001666response to hypoxia0.0244757078470398
GO:0003690double-stranded DNA binding0.0244757078470398
GO:0001894tissue homeostasis0.0248996451830171
GO:0048871multicellular organismal homeostasis0.0248996451830171
GO:0001890placenta development0.0248996451830171
GO:0018958phenol metabolic process0.0248996451830171
GO:0006584catecholamine metabolic process0.0248996451830171
GO:0008016regulation of heart contraction0.027430425466154
GO:0042133neurotransmitter metabolic process0.027430425466154
GO:0030218erythrocyte differentiation0.027430425466154
GO:0003015heart process0.0293515286077098
GO:0060047heart contraction0.0293515286077098
GO:0006979response to oxidative stress0.0293515286077098
GO:0043566structure-specific DNA binding0.0301016548785821
GO:0046982protein heterodimerization activity0.0362215470398131
GO:0030324lung development0.0363956629082699
GO:0030323respiratory tube development0.0363956629082699
GO:0007005mitochondrion organization and biogenesis0.0363956629082699
GO:0006576biogenic amine metabolic process0.0376785679627757
GO:0048469cell maturation0.0376785679627757
GO:0042445hormone metabolic process0.0386746014954127
GO:0006575amino acid derivative metabolic process0.0386746014954127
GO:0001505regulation of neurotransmitter levels0.0386746014954127
GO:0021700developmental maturation0.0386746014954127
GO:0030099myeloid cell differentiation0.0386746014954127
GO:0003677DNA binding0.0386746014954127
GO:0008015blood circulation0.0386746014954127
GO:0003013circulatory system process0.0386746014954127
GO:0007601visual perception0.0427717939759727
GO:0050953sensory perception of light stimulus0.0427717939759727
GO:0006725aromatic compound metabolic process0.0427717939759727
GO:0001701in utero embryonic development0.0437547144648331
GO:0048771tissue remodeling0.0437547144648331
GO:0006260DNA replication0.046721929108951
GO:0001525angiogenesis0.046721929108951



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
tube4.01e-13114
anatomical conduit2.70e-12122
trunk region element9.96e-1179
subdivision of trunk1.00e-1066
trunk1.34e-0990
multi-cellular organism3.80e-08333
epithelial tube6.39e-0847
tissue1.04e-07349
abdomen element1.27e-0749
abdominal segment element1.27e-0749
abdominal segment of trunk1.27e-0749
abdomen1.27e-0749
organ3.67e-07266


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
MA0014.11.33691
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
MA0055.11.06076
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
MA0073.10.439282
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
MA0139.11.16863
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.11.33779
MA0145.10.292366
MA0146.10.46063
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.71803
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
MA0155.11.52001
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.11.53682
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.21.81944
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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