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MCL coexpression mm9:296: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002371!2.08e-10!16;UBERON:0002204!7.60e-09!32;UBERON:0001474!1.76e-08!22;UBERON:0004765!1.76e-08!22;UBERON:0001434!1.76e-08!22;UBERON:0002384!4.42e-08!46;UBERON:0002193!7.32e-07!48;UBERON:0002405!7.32e-07!48
|ontology_enrichment_uberon=UBERON:0002371!2.08e-10!16;UBERON:0002204!7.60e-09!32;UBERON:0001474!1.76e-08!22;UBERON:0004765!1.76e-08!22;UBERON:0001434!1.76e-08!22;UBERON:0002384!4.42e-08!46;UBERON:0002193!7.32e-07!48;UBERON:0002405!7.32e-07!48
|tfbs_overrepresentation_for_novel_motifs=0.282271,0.0214946,0.0710623,0.338886,1.2525,0.726757,0.164473,2.27321,0.525465,0.100154,0.137777,0.475202,0.0514803,0.172248,0.59773,0,0.833764,0.28293,0.00830799,0.0862686,0.785128,0.431095,0.17167,0.123801,0.258457,0.556347,0.110597,0.122938,0.0447558,0.147422,0.368848,0.390688,0.278799,0.549502,0.141822,0.0982506,0.107578,0.469672,0.0201911,0.0678345,0.290168,0.117985,0.539272,0.0360344,0.70653,0.0980588,0.697098,0.412087,0.996157,0.174161,0.296304,0.208297,0.135351,0.511069,0.526356,0.176842,0.0489568,0.455754,0.21374,0.175527,1.736,0.61508,0.0648948,0.287721,0.541628,0.318903,0.648538,0.976882,0.968919,0.836509,0.225929,1.10051,0.191772,0.555978,0.199953,0.322721,0.345431,0.241622,0.360359,0.798977,0.304042,0.32329,0.213792,3.1863,0.455476,0.0719933,0.249538,0.147679,0.253413,1.13385,0.712592,0.459726,1.03642,0.308871,0.217255,0.369361,0.137297,0.403591,0.25003,1.35999,2.54456,0.390457,0.495886,0.29676,0.295953,0.117743,0.342607,1.31188,0.0594702,0.206909,0.273137,0.497436,0.211055,0.140823,0.719117,0.11984,0.0686107,0.344114,0.31076,0.479176,0.560777,0.271955,0.19139,0.240971,0.769516,0.363346,0.169628,0.395657,0.647155,1.30148,0.481183,0.328832,0.620289,0.545622,0.739171,0.00363138,0.293295,0.378248,0.693638,1.49553,1.10287,0.652839,0.199449,0.399329,0.291009,0.376878,0.252115,1.45635,0.296414,0.875254,0.0213707,0.142541,0.512441,0.385153,1.03942,0.584782,0.208987,0.634838,0.0817634,0.292926,0.702412,0.454746,0.363706,0.0785906,0.288496,0.532418,0.025066,1.4736,0.196056
|tfbs_overrepresentation_for_novel_motifs=0.282271,0.0214946,0.0710623,0.338886,1.2525,0.726757,0.164473,2.27321,0.525465,0.100154,0.137777,0.475202,0.0514803,0.172248,0.59773,0,0.833764,0.28293,0.00830799,0.0862686,0.785128,0.431095,0.17167,0.123801,0.258457,0.556347,0.110597,0.122938,0.0447558,0.147422,0.368848,0.390688,0.278799,0.549502,0.141822,0.0982506,0.107578,0.469672,0.0201911,0.0678345,0.290168,0.117985,0.539272,0.0360344,0.70653,0.0980588,0.697098,0.412087,0.996157,0.174161,0.296304,0.208297,0.135351,0.511069,0.526356,0.176842,0.0489568,0.455754,0.21374,0.175527,1.736,0.61508,0.0648948,0.287721,0.541628,0.318903,0.648538,0.976882,0.968919,0.836509,0.225929,1.10051,0.191772,0.555978,0.199953,0.322721,0.345431,0.241622,0.360359,0.798977,0.304042,0.32329,0.213792,3.1863,0.455476,0.0719933,0.249538,0.147679,0.253413,1.13385,0.712592,0.459726,1.03642,0.308871,0.217255,0.369361,0.137297,0.403591,0.25003,1.35999,2.54456,0.390457,0.495886,0.29676,0.295953,0.117743,0.342607,1.31188,0.0594702,0.206909,0.273137,0.497436,0.211055,0.140823,0.719117,0.11984,0.0686107,0.344114,0.31076,0.479176,0.560777,0.271955,0.19139,0.240971,0.769516,0.363346,0.169628,0.395657,0.647155,1.30148,0.481183,0.328832,0.620289,0.545622,0.739171,0.00363138,0.293295,0.378248,0.693638,1.49553,1.10287,0.652839,0.199449,0.399329,0.291009,0.376878,0.252115,1.45635,0.296414,0.875254,0.0213707,0.142541,0.512441,0.385153,1.03942,0.584782,0.208987,0.634838,0.0817634,0.292926,0.702412,0.454746,0.363706,0.0785906,0.288496,0.532418,0.025066,1.4736,0.196056
|tfbs_overrepresentation_jaspar=MA0003.1;0.136408,MA0004.1;0.339556,MA0006.1;0.321056,MA0007.1;0.319014,MA0009.1;0.412602,MA0014.1;0.122564,MA0017.1;0.373582,MA0019.1;0.268299,MA0024.1;0.37648,MA0025.1;0.616209,MA0027.1;1.99083,MA0028.1;0.0372733,MA0029.1;0.358857,MA0030.1;0.364159,MA0031.1;0.335674,MA0038.1;0.556221,MA0040.1;1.08391,MA0041.1;0.2404,MA0042.1;0.0625496,MA0043.1;1.2388,MA0046.1;0.442826,MA0048.1;0.0477447,MA0050.1;1.86378,MA0051.1;0.196084,MA0052.1;0.429851,MA0055.1;0.0200406,MA0056.1;0,MA0057.1;0.187973,MA0058.1;0.216391,MA0059.1;0.0648268,MA0060.1;0.593514,MA0061.1;2.89759,MA0063.1;0,MA0066.1;0.182901,MA0067.1;0.717937,MA0068.1;0.10147,MA0069.1;0.430137,MA0070.1;0.421986,MA0071.1;0.785781,MA0072.1;0.414891,MA0073.1;0.0070517,MA0074.1;0.160032,MA0076.1;0.184645,MA0077.1;1.02686,MA0078.1;0.218627,MA0081.1;1.40189,MA0083.1;0.494326,MA0084.1;1.02883,MA0087.1;0.457205,MA0088.1;0.0452858,MA0089.1;0,MA0090.1;0.0869074,MA0091.1;0.357896,MA0092.1;0.29369,MA0093.1;0.357759,MA0095.1;0,MA0098.1;0,MA0100.1;0.152909,MA0101.1;1.85544,MA0103.1;0.395656,MA0105.1;1.39891,MA0106.1;1.19178,MA0107.1;3.14334,MA0108.2;0.778724,MA0109.1;0,MA0111.1;0.312128,MA0113.1;0.20458,MA0114.1;0.0900443,MA0115.1;0.497446,MA0116.1;1.31901,MA0117.1;0.469566,MA0119.1;0.0688632,MA0122.1;0.486676,MA0124.1;0.668899,MA0125.1;0.601578,MA0130.1;0,MA0131.1;0.264933,MA0132.1;0,MA0133.1;0,MA0135.1;0.526836,MA0136.1;1.5708,MA0139.1;0.0490456,MA0140.1;0.152839,MA0141.1;0.43696,MA0142.1;0.866283,MA0143.1;0.215799,MA0144.1;0.230788,MA0145.1;0.0542189,MA0146.1;0.503601,MA0147.1;0.102772,MA0148.1;0.362249,MA0149.1;0.0709954,MA0062.2;1.1053,MA0035.2;0.472078,MA0039.2;0.0151214,MA0138.2;0.259078,MA0002.2;0.487389,MA0137.2;0.430805,MA0104.2;0.159629,MA0047.2;0.18962,MA0112.2;0.114958,MA0065.2;0.115736,MA0150.1;0.318861,MA0151.1;0,MA0152.1;0.189691,MA0153.1;0.541494,MA0154.1;0.109874,MA0155.1;0.0278048,MA0156.1;2.65609,MA0157.1;0.299365,MA0158.1;0,MA0159.1;1.17099,MA0160.1;1.21328,MA0161.1;0,MA0162.1;1.22543,MA0163.1;0.203588,MA0164.1;0.514179,MA0080.2;3.15178,MA0018.2;0.179043,MA0099.2;0.254459,MA0079.2;2.47133e-05,MA0102.2;1.07954,MA0258.1;0.017528,MA0259.1;0.233481,MA0442.1;0
}}
}}

Revision as of 11:31, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:111432947..111432958,-p7@Glipr1
Mm9::chr10:111433688..111433699,-p@chr10:111433688..111433699
-
Mm9::chr10:119638520..119638539,-p4@Irak3
Mm9::chr11:100488216..100488234,+p@chr11:100488216..100488234
+
Mm9::chr11:16899725..16899729,-p@chr11:16899725..16899729
-
Mm9::chr11:59356203..59356228,+p2@Nlrp3
Mm9::chr11:59356232..59356249,+p3@Nlrp3
Mm9::chr11:59356250..59356277,+p4@Nlrp3
Mm9::chr11:67377978..67377989,+p@chr11:67377978..67377989
+
Mm9::chr12:32634451..32634474,+p@chr12:32634451..32634474
+
Mm9::chr12:70548695..70548699,+p@chr12:70548695..70548699
+
Mm9::chr13:51741105..51741116,+p@chr13:51741105..51741116
+
Mm9::chr14:28192677..28192680,+p@chr14:28192677..28192680
+
Mm9::chr14:28192716..28192779,+p@chr14:28192716..28192779
+
Mm9::chr14:28192780..28192801,+p@chr14:28192780..28192801
+
Mm9::chr14:28192831..28192847,+p@chr14:28192831..28192847
+
Mm9::chr14:28192852..28192868,+p@chr14:28192852..28192868
+
Mm9::chr1:52557492..52557495,+p@chr1:52557492..52557495
+
Mm9::chr2:102705692..102705695,-p@chr2:102705692..102705695
-
Mm9::chr2:127880698..127880703,-p@chr2:127880698..127880703
-
Mm9::chr2:127888836..127888845,+p@chr2:127888836..127888845
+
Mm9::chr2:13335211..13335224,-p@chr2:13335211..13335224
-
Mm9::chr3:83645477..83645490,-p2@Tlr2
Mm9::chr5:136722449..136722468,-p@chr5:136722449..136722468
-
Mm9::chr6:54767639..54767644,-p@chr6:54767639..54767644
-
Mm9::chr7:35841771..35841778,+p@chr7:35841771..35841778
+
Mm9::chrX:9048152..9048155,-p@chrX:9048152..9048155
-


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:0042892chloramphenicol transport0.00701254588286857
GO:0042891antibiotic transport0.00701254588286857
GO:0043244regulation of protein complex disassembly0.00701254588286857
GO:0002755MyD88-dependent toll-like receptor signaling pathway0.00841459401106075
GO:0002752cell surface pattern recognition receptor signaling pathway0.00841459401106075
GO:0002238response to molecule of fungal origin0.0105176662244004
GO:0002220innate immune response activating cell surface receptor signaling pathway0.0120195313783155
GO:0002224toll-like receptor signaling pathway0.0131456421358788
GO:0002221pattern recognition receptor signaling pathway0.0140181770504761
GO:0032760positive regulation of tumor necrosis factor production0.0140181770504761
GO:0002218activation of innate immune response0.0140181770504761
GO:0002758innate immune response-activating signal transduction0.0140181770504761
GO:0032680regulation of tumor necrosis factor production0.0140181770504761
GO:0045088regulation of innate immune response0.0140181770504761
GO:0045089positive regulation of innate immune response0.0140181770504761
GO:0009620response to fungus0.0151838620381715
GO:0043241protein complex disassembly0.0151838620381715
GO:0015893drug transport0.0151838620381715
GO:0032984macromolecular complex disassembly0.0154903787390998
GO:0032640tumor necrosis factor production0.0157661285899398
GO:0006915apoptosis0.0177806043039439
GO:0001819positive regulation of cytokine production0.0177806043039439
GO:0012501programmed cell death0.0177806043039439
GO:0008219cell death0.0177806043039439
GO:0016265death0.0177806043039439
GO:0022411cellular component disassembly0.0177806043039439
GO:0001817regulation of cytokine production0.0225045307870591
GO:0042493response to drug0.0225045307870591
GO:0002429immune response-activating cell surface receptor signaling pathway0.0231745390088081
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0237995731722582
GO:0002757immune response-activating signal transduction0.024383985638227
GO:0002764immune response-regulating signal transduction0.0249315847224307
GO:0019221cytokine and chemokine mediated signaling pathway0.0286185847577295
GO:0048468cell development0.039830640220822
GO:0002253activation of immune response0.0460903485865604
GO:0005524ATP binding0.0462014597936259
GO:0032559adenyl ribonucleotide binding0.0462014597936259
GO:0045087innate immune response0.048186354519928
GO:0030554adenyl nucleotide binding0.048186354519928
GO:0050778positive regulation of immune response0.0493229335703659
GO:0002684positive regulation of immune system process0.0493229335703659
GO:0001816cytokine production0.0493229335703659



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
bone marrow2.08e-1016
musculoskeletal system7.60e-0932
bone element1.76e-0822
skeletal element1.76e-0822
skeletal system1.76e-0822
connective tissue4.42e-0846
hemolymphoid system7.32e-0748
immune system7.32e-0748

Disease
Ontology termp-valuen
musculoskeletal system cancer8.02e-073
muscle cancer8.02e-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)
MA0003.10.136408
MA0004.10.339556
MA0006.10.321056
MA0007.10.319014
MA0009.10.412602
MA0014.10.122564
MA0017.10.373582
MA0019.10.268299
MA0024.10.37648
MA0025.10.616209
MA0027.11.99083
MA0028.10.0372733
MA0029.10.358857
MA0030.10.364159
MA0031.10.335674
MA0038.10.556221
MA0040.11.08391
MA0041.10.2404
MA0042.10.0625496
MA0043.11.2388
MA0046.10.442826
MA0048.10.0477447
MA0050.11.86378
MA0051.10.196084
MA0052.10.429851
MA0055.10.0200406
MA0056.10
MA0057.10.187973
MA0058.10.216391
MA0059.10.0648268
MA0060.10.593514
MA0061.12.89759
MA0063.10
MA0066.10.182901
MA0067.10.717937
MA0068.10.10147
MA0069.10.430137
MA0070.10.421986
MA0071.10.785781
MA0072.10.414891
MA0073.10.0070517
MA0074.10.160032
MA0076.10.184645
MA0077.11.02686
MA0078.10.218627
MA0081.11.40189
MA0083.10.494326
MA0084.11.02883
MA0087.10.457205
MA0088.10.0452858
MA0089.10
MA0090.10.0869074
MA0091.10.357896
MA0092.10.29369
MA0093.10.357759
MA0095.10
MA0098.10
MA0100.10.152909
MA0101.11.85544
MA0103.10.395656
MA0105.11.39891
MA0106.11.19178
MA0107.13.14334
MA0108.20.778724
MA0109.10
MA0111.10.312128
MA0113.10.20458
MA0114.10.0900443
MA0115.10.497446
MA0116.11.31901
MA0117.10.469566
MA0119.10.0688632
MA0122.10.486676
MA0124.10.668899
MA0125.10.601578
MA0130.10
MA0131.10.264933
MA0132.10
MA0133.10
MA0135.10.526836
MA0136.11.5708
MA0139.10.0490456
MA0140.10.152839
MA0141.10.43696
MA0142.10.866283
MA0143.10.215799
MA0144.10.230788
MA0145.10.0542189
MA0146.10.503601
MA0147.10.102772
MA0148.10.362249
MA0149.10.0709954
MA0062.21.1053
MA0035.20.472078
MA0039.20.0151214
MA0138.20.259078
MA0002.20.487389
MA0137.20.430805
MA0104.20.159629
MA0047.20.18962
MA0112.20.114958
MA0065.20.115736
MA0150.10.318861
MA0151.10
MA0152.10.189691
MA0153.10.541494
MA0154.10.109874
MA0155.10.0278048
MA0156.12.65609
MA0157.10.299365
MA0158.10
MA0159.11.17099
MA0160.11.21328
MA0161.10
MA0162.11.22543
MA0163.10.203588
MA0164.10.514179
MA0080.23.15178
MA0018.20.179043
MA0099.20.254459
MA0079.22.47133e-05
MA0102.21.07954
MA0258.10.017528
MA0259.10.233481
MA0442.10
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