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MCL coexpression mm9:653: Difference between revisions

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{{MCL_coexpression_mm9
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constituent of ribosome;2.14227013399588e-07;20103,66489,22121,27050,67097!GO:0006412;translation;2.14227013399588e-07;73830,20103,55949,66489,22121,27050!GO:0009059;macromolecule biosynthetic process;1.62782180421349e-06;73830,20103,55949,66489,22121,27050!GO:0044249;cellular biosynthetic process;6.19899724867458e-06;73830,20103,55949,66489,22121,27050!GO:0005840;ribosome;7.3803168895522e-06;20103,66489,22121,27050!GO:0030529;ribonucleoprotein complex;7.3803168895522e-06;20103,66489,22121,27050,67097!GO:0032991;macromolecular complex;1.74087010791727e-05;20103,55949,66489,22121,14694,27050,67097!GO:0009058;biosynthetic process;1.8565482700779e-05;73830,20103,55949,66489,22121,27050!GO:0033279;ribosomal subunit;2.34000542491042e-05;20103,22121,27050!GO:0005737;cytoplasm;0.000524415379759629;73830,20103,55949,66489,22121,14694,27050,67097!GO:0015935;small ribosomal subunit;0.000673866954367357;20103,27050!GO:0044267;cellular protein metabolic process;0.00146823999856862;73830,20103,55949,66489,22121,27050!GO:0044260;cellular macromolecule metabolic process;0.00146823999856862;73830,20103,55949,66489,22121,27050!GO:0010467;gene expression;0.00146823999856862;73830,20103,55949,66489,22121,27050!GO:0019538;protein metabolic process;0.00156058478201128;73830,20103,55949,66489,22121,27050!GO:0008135;translation factor activity, nucleic acid binding;0.00697090241983966;73830,55949!GO:0044424;intracellular part;0.0112810809464035;73830,20103,55949,66489,22121,14694,27050,67097!GO:0005853;eukaryotic translation elongation factor 1 complex;0.0112810809464035;55949!GO:0043232;intracellular non-membrane-bound organelle;0.0112810809464035;20103,66489,22121,27050!GO:0043228;non-membrane-bound organelle;0.0112810809464035;20103,66489,22121,27050!GO:0005622;intracellular;0.0127110624320008;73830,20103,55949,66489,22121,14694,27050,67097!GO:0043234;protein complex;0.0127110624320008;20103,55949,14694,27050!GO:0022613;ribonucleoprotein 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|gostat_on_MCL_coexpression=GO:0003735;structural constituent of ribosome;2.14227013399588e-07;20103,66489,22121,27050,67097!GO:0006412;translation;2.14227013399588e-07;73830,20103,55949,66489,22121,27050!GO:0009059;macromolecule biosynthetic process;1.62782180421349e-06;73830,20103,55949,66489,22121,27050!GO:0044249;cellular biosynthetic process;6.19899724867458e-06;73830,20103,55949,66489,22121,27050!GO:0005840;ribosome;7.3803168895522e-06;20103,66489,22121,27050!GO:0030529;ribonucleoprotein complex;7.3803168895522e-06;20103,66489,22121,27050,67097!GO:0032991;macromolecular complex;1.74087010791727e-05;20103,55949,66489,22121,14694,27050,67097!GO:0009058;biosynthetic process;1.8565482700779e-05;73830,20103,55949,66489,22121,27050!GO:0033279;ribosomal subunit;2.34000542491042e-05;20103,22121,27050!GO:0005737;cytoplasm;0.000524415379759629;73830,20103,55949,66489,22121,14694,27050,67097!GO:0015935;small ribosomal subunit;0.000673866954367357;20103,27050!GO:0044267;cellular protein metabolic process;0.00146823999856862;73830,20103,55949,66489,22121,27050!GO:0044260;cellular macromolecule metabolic process;0.00146823999856862;73830,20103,55949,66489,22121,27050!GO:0010467;gene expression;0.00146823999856862;73830,20103,55949,66489,22121,27050!GO:0019538;protein metabolic process;0.00156058478201128;73830,20103,55949,66489,22121,27050!GO:0008135;translation factor activity, nucleic acid binding;0.00697090241983966;73830,55949!GO:0044424;intracellular part;0.0112810809464035;73830,20103,55949,66489,22121,14694,27050,67097!GO:0005853;eukaryotic translation elongation factor 1 complex;0.0112810809464035;55949!GO:0043232;intracellular non-membrane-bound organelle;0.0112810809464035;20103,66489,22121,27050!GO:0043228;non-membrane-bound organelle;0.0112810809464035;20103,66489,22121,27050!GO:0005622;intracellular;0.0127110624320008;73830,20103,55949,66489,22121,14694,27050,67097!GO:0043234;protein complex;0.0127110624320008;20103,55949,14694,27050!GO:0022613;ribonucleoprotein complex biogenesis and assembly;0.0127110624320008;73830,20103!GO:0005080;protein kinase C binding;0.0130239586364739;14694!GO:0044444;cytoplasmic part;0.0192100984712154;20103,55949,66489,22121,27050!GO:0007205;protein kinase C activation;0.0205895928338391;14694!GO:0043170;macromolecule metabolic process;0.036778582067945;73830,20103,55949,66489,22121,27050!GO:0007200;G-protein signaling, coupled to IP3 second messenger (phospholipase C activating);0.0458200732709139;14694!GO:0032147;activation of protein kinase activity;0.0458200732709139;14694!GO:0003746;translation elongation factor activity;0.0458200732709139;55949!GO:0015934;large ribosomal subunit;0.0458200732709139;22121!GO:0005834;heterotrimeric G-protein complex;0.0458200732709139;14694!
|ontology_enrichment_celltype=CL:0000219!4.65e-16!54;CL:0002320!2.90e-15!46;CL:0000134!2.90e-15!46;CL:0000988!3.03e-15!32;CL:0002032!3.03e-15!32;CL:0000037!3.03e-15!32;CL:0000566!3.03e-15!32;CL:0000837!3.03e-15!32;CL:0000034!2.78e-13!97;CL:0002371!1.60e-12!118;CL:0000548!2.89e-12!115;CL:0000255!2.89e-12!115;CL:0000723!1.34e-11!91;CL:0000048!1.34e-11!91;CL:0002031!3.48e-11!25;CL:0002242!1.11e-08!16;CL:0000542!1.71e-08!13;CL:0000051!1.71e-08!13;CL:0000738!1.90e-08!17;CL:0002087!1.90e-08!17;CL:0000838!2.22e-08!12;CL:0000049!4.54e-08!19;CL:0000084!7.43e-08!11;CL:0000827!7.43e-08!11;CL:0000791!8.03e-07!9;CL:0000789!8.03e-07!9;CL:0002420!8.03e-07!9;CL:0002419!8.03e-07!9;CL:0000790!8.03e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!2.90e-15!46;UBERON:0002193!7.36e-08!48;UBERON:0002405!7.36e-08!48;UBERON:0002390!1.11e-07!45;UBERON:0003061!1.11e-07!45;UBERON:0002371!4.66e-07!16
|tfbs_overrepresentation_for_novel_motifs=0.795069,0.286791,0.269904,0.878892,0.176699,0.342839,0.425757,0.345089,0.362206,0.208174,0.385334,0.414631,0.703175,1.11437,0.189961,0,1.50287,0.170475,0.318616,0.387499,0.238546,0.117252,1.94803,0.175485,0.276437,0.4628,0.630402,0.361771,0.611503,0.231659,0.921513,0.717576,0.168723,0.270473,0.556756,2.09375,0.94339,1.8632,0.144953,1.27598,0.173534,0.353696,0.104243,0.191571,0.195622,0.856658,0.543674,0.376103,0.081888,0.61724,0.603113,1.22385,0.829247,0.855661,0.87275,0.443782,0.634658,1.03993,0.0851299,1.12465,0.698157,0.496904,0.383763,0.592318,1.15114,0.631188,1.00675,1.3527,0.693631,1.20659,1.30396,0.355763,0.126035,0.905636,1.46454,0.258161,0.0786324,0.532872,0.681539,0.679143,0.357936,0.636582,0.495545,1.13,0.792744,0.444993,0.291599,0.0651072,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.437593,0.404817,1.14799,0.732731,0.543917,0.0534645,0.161581,0.717305,0.838603,0.603683,0.602672,0.930972,2.681,0.372438,1.27588,2.72214,0.286453,0.840348,0.243062,0.390066,2.45372,0.512539,1.19449,0.886406,1.50549,0.158673,0.910937,0.572279,1.17341,0.532013,1.13603,0.685116,1.10612,0.723425,1.00525,0.183744,0.821997,0.323373,0.976125,0.456508,1.10385,0.821605,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,0.527071,0.235808,0.103135,0.857198,1.3356,0.455644,0.93735,0.488969,0.57908,0.290467,0.299755,1.06466,0.791909,0.685546,0.284483,0.593295,0.448733,0.160658,0.413167,0.0207556
|tfbs_overrepresentation_jaspar=MA0003.1;0.156602,MA0004.1;0.879856,MA0006.1;0.547312,MA0007.1;0.316976,MA0009.1;0.743257,MA0014.1;0.44164,MA0017.1;0.598706,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;2.40463,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;0.440822,MA0050.1;0.95731,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;0.136328,MA0056.1;0,MA0057.1;0.71676,MA0058.1;1.9784,MA0059.1;0.714494,MA0060.1;0.789184,MA0061.1;0.147394,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;0.187364,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.955636,MA0072.1;0.745922,MA0073.1;0.672958,MA0074.1;1.07546,MA0076.1;3.43847,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;0.760108,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.849797,MA0089.1;0,MA0090.1;0.299987,MA0091.1;0.342071,MA0092.1;0.300264,MA0093.1;1.73415,MA0095.1;0,MA0098.1;0,MA0100.1;0.408523,MA0101.1;0.73212,MA0103.1;0.216742,MA0105.1;0.556739,MA0106.1;0.509454,MA0107.1;0.607721,MA0108.2;1.4389,MA0109.1;0,MA0111.1;0.312463,MA0113.1;0.482899,MA0114.1;0.876865,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;1.11539,MA0139.1;0.338099,MA0140.1;0.408417,MA0141.1;0.233109,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.88666,MA0145.1;0.3137,MA0146.1;0.529624,MA0147.1;0.925698,MA0148.1;0.344843,MA0149.1;0.269772,MA0062.2;3.97393,MA0035.2;0.412747,MA0039.2;0.0387728,MA0138.2;0.555696,MA0002.2;0.105469,MA0137.2;0.652494,MA0104.2;1.22043,MA0047.2;0.46201,MA0112.2;0.0329566,MA0065.2;0.905908,MA0150.1;0.316876,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;0.0529077,MA0155.1;0.0394399,MA0156.1;2.60418,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.495113,MA0160.1;0.347545,MA0161.1;0,MA0162.1;0.388731,MA0163.1;0.00559554,MA0164.1;1.95358,MA0080.2;1.14688,MA0018.2;0.446948,MA0099.2;0.549696,MA0079.2;0.534138,MA0102.2;1.45844,MA0258.1;0.135621,MA0259.1;0.455671,MA0442.1;0
}}

Latest revision as of 15:40, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:48613859..48613871,+p1@Gnb2l1
Mm9::chr17:27772183..27772212,-p1@Rps10
Mm9::chr1:63223693..63223719,+p1@Eef1b2
Mm9::chr2:38860646..38860665,-p1@Rpl35
Mm9::chr6:115758754..115758772,-p1@Gm6251
p1@LOC100504872
p1@Rpl32
Mm9::chr7:106632155..106632164,-p1@Rps3
Mm9::chr7:13507664..13507669,+p1@Rps5
Mm9::chr7:148364406..148364417,-p@chr7:148364406..148364417
-
Mm9::chr7:29766806..29766840,-p1@Eif3k
Mm9::chr7:31270201..31270202,-p@chr7:31270201..31270202
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Mm9::chr7:52384095..52384117,-p1@Rpl13a


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:0003735structural constituent of ribosome2.14227013399588e-07
GO:0006412translation2.14227013399588e-07
GO:0009059macromolecule biosynthetic process1.62782180421349e-06
GO:0044249cellular biosynthetic process6.19899724867458e-06
GO:0005840ribosome7.3803168895522e-06
GO:0030529ribonucleoprotein complex7.3803168895522e-06
GO:0032991macromolecular complex1.74087010791727e-05
GO:0009058biosynthetic process1.8565482700779e-05
GO:0033279ribosomal subunit2.34000542491042e-05
GO:0005737cytoplasm0.000524415379759629
GO:0015935small ribosomal subunit0.000673866954367357
GO:0044267cellular protein metabolic process0.00146823999856862
GO:0044260cellular macromolecule metabolic process0.00146823999856862
GO:0010467gene expression0.00146823999856862
GO:0019538protein metabolic process0.00156058478201128
GO:0008135translation factor activity, nucleic acid binding0.00697090241983966
GO:0044424intracellular part0.0112810809464035
GO:0005853eukaryotic translation elongation factor 1 complex0.0112810809464035
GO:0043232intracellular non-membrane-bound organelle0.0112810809464035
GO:0043228non-membrane-bound organelle0.0112810809464035
GO:0005622intracellular0.0127110624320008
GO:0043234protein complex0.0127110624320008
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0127110624320008
GO:0005080protein kinase C binding0.0130239586364739
GO:0044444cytoplasmic part0.0192100984712154
GO:0007205protein kinase C activation0.0205895928338391
GO:0043170macromolecule metabolic process0.036778582067945
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0458200732709139
GO:0032147activation of protein kinase activity0.0458200732709139
GO:0003746translation elongation factor activity0.0458200732709139
GO:0015934large ribosomal subunit0.0458200732709139
GO:0005834heterotrimeric G-protein complex0.0458200732709139



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
motile cell4.65e-1654
connective tissue cell2.90e-1546
mesenchymal cell2.90e-1546
hematopoietic cell3.03e-1532
hematopoietic oligopotent progenitor cell3.03e-1532
hematopoietic stem cell3.03e-1532
angioblastic mesenchymal cell3.03e-1532
hematopoietic multipotent progenitor cell3.03e-1532
stem cell2.78e-1397
somatic cell1.60e-12118
animal cell2.89e-12115
eukaryotic cell2.89e-12115
somatic stem cell1.34e-1191
multi fate stem cell1.34e-1191
hematopoietic lineage restricted progenitor cell3.48e-1125
nucleate cell1.11e-0816
lymphocyte1.71e-0813
common lymphoid progenitor1.71e-0813
leukocyte1.90e-0817
nongranular leukocyte1.90e-0817
lymphoid lineage restricted progenitor cell2.22e-0812
common myeloid progenitor4.54e-0819
T cell7.43e-0811
pro-T cell7.43e-0811
mature alpha-beta T cell8.03e-079
alpha-beta T cell8.03e-079
immature T cell8.03e-079
mature T cell8.03e-079
immature alpha-beta T cell8.03e-079

Uber Anatomy
Ontology termp-valuen
connective tissue2.90e-1546
hemolymphoid system7.36e-0848
immune system7.36e-0848
hematopoietic system1.11e-0745
blood island1.11e-0745
bone marrow4.66e-0716


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)
MA0003.10.156602
MA0004.10.879856
MA0006.10.547312
MA0007.10.316976
MA0009.10.743257
MA0014.10.44164
MA0017.10.598706
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.12.40463
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
MA0048.10.440822
MA0050.10.95731
MA0051.10.471092
MA0052.10.76328
MA0055.10.136328
MA0056.10
MA0057.10.71676
MA0058.11.9784
MA0059.10.714494
MA0060.10.789184
MA0061.10.147394
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.187364
MA0069.10.76361
MA0070.10.75417
MA0071.10.955636
MA0072.10.745922
MA0073.10.672958
MA0074.11.07546
MA0076.13.43847
MA0077.10.724865
MA0078.10.502121
MA0081.10.760108
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.849797
MA0089.10
MA0090.10.299987
MA0091.10.342071
MA0092.10.300264
MA0093.11.73415
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.73212
MA0103.10.216742
MA0105.10.556739
MA0106.10.509454
MA0107.10.607721
MA0108.21.4389
MA0109.10
MA0111.10.312463
MA0113.10.482899
MA0114.10.876865
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
MA0136.11.11539
MA0139.10.338099
MA0140.10.408417
MA0141.10.233109
MA0142.10.63775
MA0143.10.49828
MA0144.10.88666
MA0145.10.3137
MA0146.10.529624
MA0147.10.925698
MA0148.10.344843
MA0149.10.269772
MA0062.23.97393
MA0035.20.412747
MA0039.20.0387728
MA0138.20.555696
MA0002.20.105469
MA0137.20.652494
MA0104.21.22043
MA0047.20.46201
MA0112.20.0329566
MA0065.20.905908
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.0529077
MA0155.10.0394399
MA0156.12.60418
MA0157.10.606944
MA0158.10
MA0159.10.495113
MA0160.10.347545
MA0161.10
MA0162.10.388731
MA0163.10.00559554
MA0164.11.95358
MA0080.21.14688
MA0018.20.446948
MA0099.20.549696
MA0079.20.534138
MA0102.21.45844
MA0258.10.135621
MA0259.10.455671
MA0442.10
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