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MCL coexpression mm9:649: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002193!1.34e-12!48;UBERON:0002405!1.34e-12!48;UBERON:0002390!9.70e-12!45;UBERON:0003061!9.70e-12!45;UBERON:0002384!1.95e-10!46;UBERON:0003929!2.41e-08!55;UBERON:0000072!4.84e-08!27;UBERON:0004177!1.12e-07!29;UBERON:0005057!1.12e-07!29;UBERON:0000490!1.85e-07!66;UBERON:0000344!3.01e-07!15;UBERON:0002370!4.76e-07!23;UBERON:0000974!4.76e-07!23;UBERON:0004807!4.76e-07!23;UBERON:0005058!4.76e-07!23;UBERON:0003351!4.76e-07!23;UBERON:0009113!4.76e-07!23;UBERON:0003295!4.76e-07!23;UBERON:0009722!4.76e-07!23;UBERON:0005562!4.76e-07!23;UBERON:0007690!4.76e-07!23;UBERON:0003408!9.98e-07!24
|ontology_enrichment_uberon=UBERON:0002193!1.34e-12!48;UBERON:0002405!1.34e-12!48;UBERON:0002390!9.70e-12!45;UBERON:0003061!9.70e-12!45;UBERON:0002384!1.95e-10!46;UBERON:0003929!2.41e-08!55;UBERON:0000072!4.84e-08!27;UBERON:0004177!1.12e-07!29;UBERON:0005057!1.12e-07!29;UBERON:0000490!1.85e-07!66;UBERON:0000344!3.01e-07!15;UBERON:0002370!4.76e-07!23;UBERON:0000974!4.76e-07!23;UBERON:0004807!4.76e-07!23;UBERON:0005058!4.76e-07!23;UBERON:0003351!4.76e-07!23;UBERON:0009113!4.76e-07!23;UBERON:0003295!4.76e-07!23;UBERON:0009722!4.76e-07!23;UBERON:0005562!4.76e-07!23;UBERON:0007690!4.76e-07!23;UBERON:0003408!9.98e-07!24
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.0513547,0.269904,1.58049,0.52369,0.907763,0.425757,0.345089,0.732132,0.208174,0.385334,0.414631,0.703175,0.437133,0.189961,0,0.619876,0.170475,0.096222,0.0448402,0.670854,0.117252,1.11256,0.520732,0.276437,0.4628,0.304017,0.949712,0.213277,0.231659,0.921513,0.717576,0.504188,0.270473,1.06026,0.497128,0.486454,1.0583,0.445168,0.391645,0.173534,0.353696,0.255102,0.191571,0.351346,0.319944,0.543674,0.376103,0.081888,0.215702,0.603113,0.488021,0.0612063,0.855661,0.87275,0.443782,0.634658,0.40287,0.0851299,0.441884,0.698157,0.496904,0.120887,0.592318,0.45416,1.52656,1.00675,1.3527,0.693631,1.20659,0.253722,0.110167,0.549738,0.905636,0.0810502,0.0742951,0.270351,0.532872,0.681539,0.242107,0.110993,0.636582,1.23994,0.101814,0.792744,0.123451,0.291599,0.500771,1.3522,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.404817,0.340672,0.732731,0.543917,1.64097,0.943642,0.717305,0.838603,0.603683,0.602672,0.930972,0.660145,0.372438,0.246223,0.240055,0.781068,0.840348,0.243062,1.01194,1.0825,0.512539,0.170188,0.333247,0.621127,0.158673,0.910937,0.572279,0.464505,1.3176,1.13603,0.685116,0.433317,0.723425,1.00525,0.540802,0.821997,0.323373,0.976125,1.1562,1.10385,0.115066,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,1.66577,0.546641,1.84176,0.302077,0.178088,0.0664621,0.475084,0.857198,1.3356,1.15434,0.93735,0.488969,0.199652,0.290467,0.811219,1.06466,0.791909,0.685546,0.284483,0.593295,1.13944,0.160658,0.413167,0.148813
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.0513547,0.269904,1.58049,0.52369,0.907763,0.425757,0.345089,0.732132,0.208174,0.385334,0.414631,0.703175,0.437133,0.189961,0,0.619876,0.170475,0.096222,0.0448402,0.670854,0.117252,1.11256,0.520732,0.276437,0.4628,0.304017,0.949712,0.213277,0.231659,0.921513,0.717576,0.504188,0.270473,1.06026,0.497128,0.486454,1.0583,0.445168,0.391645,0.173534,0.353696,0.255102,0.191571,0.351346,0.319944,0.543674,0.376103,0.081888,0.215702,0.603113,0.488021,0.0612063,0.855661,0.87275,0.443782,0.634658,0.40287,0.0851299,0.441884,0.698157,0.496904,0.120887,0.592318,0.45416,1.52656,1.00675,1.3527,0.693631,1.20659,0.253722,0.110167,0.549738,0.905636,0.0810502,0.0742951,0.270351,0.532872,0.681539,0.242107,0.110993,0.636582,1.23994,0.101814,0.792744,0.123451,0.291599,0.500771,1.3522,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.404817,0.340672,0.732731,0.543917,1.64097,0.943642,0.717305,0.838603,0.603683,0.602672,0.930972,0.660145,0.372438,0.246223,0.240055,0.781068,0.840348,0.243062,1.01194,1.0825,0.512539,0.170188,0.333247,0.621127,0.158673,0.910937,0.572279,0.464505,1.3176,1.13603,0.685116,0.433317,0.723425,1.00525,0.540802,0.821997,0.323373,0.976125,1.1562,1.10385,0.115066,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,1.66577,0.546641,1.84176,0.302077,0.178088,0.0664621,0.475084,0.857198,1.3356,1.15434,0.93735,0.488969,0.199652,0.290467,0.811219,1.06466,0.791909,0.685546,0.284483,0.593295,1.13944,0.160658,0.413167,0.148813
|tfbs_overrepresentation_jaspar=MA0003.1;0.0832519,MA0004.1;0.330313,MA0006.1;0.547312,MA0007.1;0.316976,MA0009.1;0.743257,MA0014.1;0.144697,MA0017.1;0.207884,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.194782,MA0029.1;0.679737,MA0030.1;0.686088,MA0031.1;0.651724,MA0038.1;0.462726,MA0040.1;0.755433,MA0041.1;0.263922,MA0042.1;0.252679,MA0043.1;0.837621,MA0046.1;0.778239,MA0048.1;0.054097,MA0050.1;0.365212,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;0.0494654,MA0056.1;0,MA0057.1;0.181039,MA0058.1;0.246908,MA0059.1;0.257372,MA0060.1;4.00777,MA0061.1;0.147394,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;0.0500842,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;0.106885,MA0074.1;0.419185,MA0076.1;0.635923,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;0.277253,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.12124,MA0089.1;0,MA0090.1;0.299987,MA0091.1;0.342071,MA0092.1;1.47462,MA0093.1;0.20148,MA0095.1;0,MA0098.1;0,MA0100.1;0.408523,MA0101.1;0.265031,MA0103.1;0.216742,MA0105.1;0.0759118,MA0106.1;0.509454,MA0107.1;0.211681,MA0108.2;2.45353,MA0109.1;0,MA0111.1;0.312463,MA0113.1;1.21288,MA0114.1;0.145642,MA0115.1;0.84036,MA0116.1;0.186271,MA0117.1;0.808813,MA0119.1;0.265536,MA0122.1;0.828211,MA0124.1;1.02871,MA0125.1;0.955734,MA0130.1;0,MA0131.1;0.563262,MA0132.1;0,MA0133.1;0,MA0135.1;0.873285,MA0136.1;0.437601,MA0139.1;0.103495,MA0140.1;1.05203,MA0141.1;0.233109,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.147954,MA0145.1;0.3137,MA0146.1;0.0833862,MA0147.1;0.157258,MA0148.1;0.344843,MA0149.1;0.269772,MA0062.2;0.271822,MA0035.2;1.06146,MA0039.2;0.0799333,MA0138.2;0.555696,MA0002.2;0.105469,MA0137.2;0.230686,MA0104.2;0.11535,MA0047.2;0.46201,MA0112.2;0.0329566,MA0065.2;0.033123,MA0150.1;0.316876,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;0.0529077,MA0155.1;0.154271,MA0156.1;0.222905,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.165031,MA0160.1;0.347545,MA0161.1;0,MA0162.1;0.219632,MA0163.1;0.198448,MA0164.1;0.437937,MA0080.2;0.212408,MA0018.2;0.446948,MA0099.2;0.549696,MA0079.2;0.0743239,MA0102.2;1.45844,MA0258.1;0.135621,MA0259.1;0.455671,MA0442.1;0
}}
}}

Revision as of 12:05, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:17805943..17805945,+p@chr11:17805943..17805945
+
Mm9::chr13:117839387..117839413,+p@chr13:117839387..117839413
+
Mm9::chr13:21826924..21826939,+p8@Hist1h4c
p8@Hist1h4d
p8@Hist1h4f
p8@Hist1h4h
p8@Hist1h4i
p8@Hist1h4j
p8@Hist1h4k
p8@Hist1h4m
p8@Hist1h4n
p9@Hist1h4a
p9@Hist1h4b
p9@Hist2h4
p9@Hist4h4
Mm9::chr13:21902297..21902311,+p7@Hist1h2ap
Mm9::chr13:21903606..21903623,+p6@Hist1h4c
p6@Hist1h4d
p6@Hist1h4f
p6@Hist1h4h
p6@Hist1h4i
p6@Hist1h4j
p6@Hist1h4k
p6@Hist1h4m
p6@Hist1h4n
p7@Hist1h4a
p7@Hist1h4b
p7@Hist2h4
p7@Hist4h4
Mm9::chr13:21925605..21925620,+p1@Hist1h2bq
p1@Hist1h2br
p5@Hist1h2bf
p5@Hist1h2bj
p5@Hist1h2bl
p5@Hist1h2bn
Mm9::chr17:17026218..17026227,+p@chr17:17026218..17026227
+
Mm9::chr1:129690056..129690058,+p@chr1:129690056..129690058
+
Mm9::chr3:96049453..96049469,+p1@Hist2h2aa1
p1@Hist2h2aa2
Mm9::chr3:96050759..96050773,+p4@Hist2h3c1
Mm9::chr5:74733727..74733734,+p@chr5:74733727..74733734
+


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:0006334nucleosome assembly1.36092384170213e-08
GO:0000786nucleosome1.36092384170213e-08
GO:0031497chromatin assembly1.36092384170213e-08
GO:0065004protein-DNA complex assembly1.68781729974058e-08
GO:0006333chromatin assembly or disassembly1.92589973053561e-08
GO:0000785chromatin7.6750922537972e-08
GO:0006325establishment and/or maintenance of chromatin architecture2.39504771253207e-07
GO:0006323DNA packaging2.39504771253207e-07
GO:0044427chromosomal part3.02073060572191e-07
GO:0065003macromolecular complex assembly3.30771804293327e-07
GO:0005694chromosome4.86122415955161e-07
GO:0022607cellular component assembly5.29295570108079e-07
GO:0051276chromosome organization and biogenesis5.29295570108079e-07
GO:0006259DNA metabolic process3.3315282502706e-06
GO:0006996organelle organization and biogenesis3.31219047587105e-05
GO:0043232intracellular non-membrane-bound organelle9.19041659126887e-05
GO:0043228non-membrane-bound organelle9.19041659126887e-05
GO:0043234protein complex0.000111663926635138
GO:0003677DNA binding0.000208617178318726
GO:0032991macromolecular complex0.000253461686821122
GO:0044446intracellular organelle part0.000425046946605353
GO:0044422organelle part0.000425046946605353
GO:0016043cellular component organization and biogenesis0.000425046946605353
GO:0003676nucleic acid binding0.00077584897085914
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00100471602029284
GO:0005634nucleus0.00314665442940148
GO:0043283biopolymer metabolic process0.00342409833126973
GO:0043170macromolecule metabolic process0.00983723022032124
GO:0044238primary metabolic process0.01592009323515
GO:0044237cellular metabolic process0.01592009323515
GO:0043231intracellular membrane-bound organelle0.01592009323515
GO:0043227membrane-bound organelle0.01592009323515
GO:0043229intracellular organelle0.0246068068402387
GO:0043226organelle0.0246068068402387
GO:0044424intracellular part0.0490728166954524



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>

Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.34e-1248
immune system1.34e-1248
hematopoietic system9.70e-1245
blood island9.70e-1245
connective tissue1.95e-1046
gut epithelium2.41e-0855
segment of respiratory tract4.84e-0827
hemopoietic organ1.12e-0729
immune organ1.12e-0729
unilaminar epithelium1.85e-0766
mucosa3.01e-0715
thymus4.76e-0723
neck4.76e-0723
respiratory system epithelium4.76e-0723
hemolymphoid system gland4.76e-0723
pharyngeal epithelium4.76e-0723
thymic region4.76e-0723
pharyngeal gland4.76e-0723
entire pharyngeal arch endoderm4.76e-0723
thymus primordium4.76e-0723
early pharyngeal endoderm4.76e-0723
gland of gut9.98e-0724


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)
MA0003.10.0832519
MA0004.10.330313
MA0006.10.547312
MA0007.10.316976
MA0009.10.743257
MA0014.10.144697
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.10.263922
MA0042.10.252679
MA0043.10.837621
MA0046.10.778239
MA0048.10.054097
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.10.0494654
MA0056.10
MA0057.10.181039
MA0058.10.246908
MA0059.10.257372
MA0060.14.00777
MA0061.10.147394
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.0500842
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.10.106885
MA0074.10.419185
MA0076.10.635923
MA0077.10.724865
MA0078.10.502121
MA0081.10.277253
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.12124
MA0089.10
MA0090.10.299987
MA0091.10.342071
MA0092.11.47462
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.265031
MA0103.10.216742
MA0105.10.0759118
MA0106.10.509454
MA0107.10.211681
MA0108.22.45353
MA0109.10
MA0111.10.312463
MA0113.11.21288
MA0114.10.145642
MA0115.10.84036
MA0116.10.186271
MA0117.10.808813
MA0119.10.265536
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.10.103495
MA0140.11.05203
MA0141.10.233109
MA0142.10.63775
MA0143.10.49828
MA0144.10.147954
MA0145.10.3137
MA0146.10.0833862
MA0147.10.157258
MA0148.10.344843
MA0149.10.269772
MA0062.20.271822
MA0035.21.06146
MA0039.20.0799333
MA0138.20.555696
MA0002.20.105469
MA0137.20.230686
MA0104.20.11535
MA0047.20.46201
MA0112.20.0329566
MA0065.20.033123
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.0529077
MA0155.10.154271
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.10.165031
MA0160.10.347545
MA0161.10
MA0162.10.219632
MA0163.10.198448
MA0164.10.437937
MA0080.20.212408
MA0018.20.446948
MA0099.20.549696
MA0079.20.0743239
MA0102.21.45844
MA0258.10.135621
MA0259.10.455671
MA0442.10
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