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MCL coexpression mm9:2277: Difference between revisions

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{{MCL_coexpression_mm9
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oxidase activity;1.13461125138868e-05;12861,12868!GO:0016675;oxidoreductase activity, acting on heme group of donors;1.13461125138868e-05;12861,12868!GO:0016676;oxidoreductase activity, acting on heme group of donors, oxygen as acceptor;1.13461125138868e-05;12861,12868!GO:0015002;heme-copper terminal oxidase activity;1.13461125138868e-05;12861,12868!GO:0015078;hydrogen ion transmembrane transporter activity;0.000164248485915314;12861,12868!GO:0015077;monovalent inorganic cation transmembrane transporter activity;0.000164248485915314;12861,12868!GO:0022890;inorganic cation transmembrane transporter activity;0.000262890198791146;12861,12868!GO:0006118;electron transport;0.00132752217867836;12861,12868!GO:0006091;generation of precursor metabolites and energy;0.00200354337292838;12861,12868!GO:0008324;cation transmembrane transporter activity;0.00224199183274404;12861,12868!GO:0015075;ion transmembrane transporter activity;0.00377005286630258;12861,12868!GO:0022891;substrate-specific transmembrane transporter activity;0.00458420765936074;12861,12868!GO:0016491;oxidoreductase activity;0.0047569885881299;12861,12868!GO:0022857;transmembrane transporter activity;0.00527248445609599;12861,12868!GO:0022892;substrate-specific transporter 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|gostat_on_MCL_coexpression=GO:0004129;cytochrome-c oxidase activity;1.13461125138868e-05;12861,12868!GO:0016675;oxidoreductase activity, acting on heme group of donors;1.13461125138868e-05;12861,12868!GO:0016676;oxidoreductase activity, acting on heme group of donors, oxygen as acceptor;1.13461125138868e-05;12861,12868!GO:0015002;heme-copper terminal oxidase activity;1.13461125138868e-05;12861,12868!GO:0015078;hydrogen ion transmembrane transporter activity;0.000164248485915314;12861,12868!GO:0015077;monovalent inorganic cation transmembrane transporter activity;0.000164248485915314;12861,12868!GO:0022890;inorganic cation transmembrane transporter activity;0.000262890198791146;12861,12868!GO:0006118;electron transport;0.00132752217867836;12861,12868!GO:0006091;generation of precursor metabolites and energy;0.00200354337292838;12861,12868!GO:0008324;cation transmembrane transporter activity;0.00224199183274404;12861,12868!GO:0015075;ion transmembrane transporter activity;0.00377005286630258;12861,12868!GO:0022891;substrate-specific transmembrane transporter activity;0.00458420765936074;12861,12868!GO:0016491;oxidoreductase activity;0.0047569885881299;12861,12868!GO:0022857;transmembrane transporter activity;0.00527248445609599;12861,12868!GO:0022892;substrate-specific transporter activity;0.00571006619538157;12861,12868!GO:0005739;mitochondrion;0.00571006619538157;12861,12868!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000344!3.18e-09!15;UBERON:0000160!1.34e-08!31;UBERON:0001242!4.58e-08!13;UBERON:0000060!4.58e-08!13;UBERON:0001262!4.58e-08!13;UBERON:0004786!4.58e-08!13
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,1.48646,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,1.39891,0.57409,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,2.54643,0.471365,0.318879,0.503207,0.30022,1.16474,0.786577,0.434783,1.03515,0.478558,0.717547,0.185353,0.504971,0.66772,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,1.75657,1.32691,0.323563,0.834514,1.54107,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,2.71882,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,2.29566,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,1.79716,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,4.23243,0.293812,0.542121,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,2.61213,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,1.47798
|tfbs_overrepresentation_jaspar=MA0003.1;2.33202,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.276754,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;4.0827,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;6.86461,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;1.97232,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;0.396346,MA0056.1;0,MA0057.1;0.251896,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.256913,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.00221226,MA0074.1;0.795862,MA0076.1;7.18932,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.201215,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;0.783305,MA0101.1;1.47308,MA0103.1;0.540576,MA0105.1;0.313353,MA0106.1;0.899777,MA0107.1;1.3208,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;0.497293,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;1.91256,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;2.36797,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;1.79187,MA0146.1;0.0944145,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;5.25083,MA0035.2;0.788288,MA0039.2;0.0220513,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;1.14524,MA0065.2;1.14711,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.263609,MA0155.1;0.230016,MA0156.1;3.41098,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.10667,MA0163.1;0.327769,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;3.21174,MA0099.2;0.944966,MA0079.2;0.190089,MA0102.2;1.8929,MA0258.1;1.89239,MA0259.1;0.441366,MA0442.1;0
}}

Latest revision as of 18:16, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:7292013..7292018,-p3@Cox8a
p3@LOC100048483
Mm9::chr19:7292019..7292033,-p2@Cox8a
p2@LOC100048483
Mm9::chr19:7292039..7292070,-p1@Cox8a
p1@LOC100048483
Mm9::chr5:115798962..115798968,-p1@Cox6a1


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:0004129cytochrome-c oxidase activity1.13461125138868e-05
GO:0016675oxidoreductase activity, acting on heme group of donors1.13461125138868e-05
GO:0016676oxidoreductase activity, acting on heme group of donors, oxygen as acceptor1.13461125138868e-05
GO:0015002heme-copper terminal oxidase activity1.13461125138868e-05
GO:0015078hydrogen ion transmembrane transporter activity0.000164248485915314
GO:0015077monovalent inorganic cation transmembrane transporter activity0.000164248485915314
GO:0022890inorganic cation transmembrane transporter activity0.000262890198791146
GO:0006118electron transport0.00132752217867836
GO:0006091generation of precursor metabolites and energy0.00200354337292838
GO:0008324cation transmembrane transporter activity0.00224199183274404
GO:0015075ion transmembrane transporter activity0.00377005286630258
GO:0022891substrate-specific transmembrane transporter activity0.00458420765936074
GO:0016491oxidoreductase activity0.0047569885881299
GO:0022857transmembrane transporter activity0.00527248445609599
GO:0022892substrate-specific transporter activity0.00571006619538157
GO:0005739mitochondrion0.00571006619538157



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
mucosa3.18e-0915
intestine1.34e-0831
intestinal mucosa4.58e-0813
anatomical wall4.58e-0813
wall of intestine4.58e-0813
gastrointestinal system mucosa4.58e-0813


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)
MA0003.12.33202
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.276754
MA0017.10.528196
MA0019.10.964875
MA0024.14.0827
MA0025.11.39562
MA0027.12.81824
MA0028.16.86461
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.11.97232
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
MA0055.10.396346
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.00221226
MA0074.10.795862
MA0076.17.18932
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.11.47308
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.11.3208
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
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
MA0136.11.91256
MA0139.10.365453
MA0140.10.78318
MA0141.12.36797
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.11.79187
MA0146.10.0944145
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.25.25083
MA0035.20.788288
MA0039.20.0220513
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.21.14524
MA0065.21.14711
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.230016
MA0156.13.41098
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.10667
MA0163.10.327769
MA0164.10.817786
MA0080.20.534538
MA0018.23.21174
MA0099.20.944966
MA0079.20.190089
MA0102.21.8929
MA0258.11.89239
MA0259.10.441366
MA0442.10
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