Personal tools

MCL coexpression mm9:484: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 7: Line 7:
|ontology_enrichment_uberon=UBERON:0002384!1.08e-17!46;UBERON:0000344!9.69e-16!15;UBERON:0001242!8.55e-13!13;UBERON:0000060!8.55e-13!13;UBERON:0001262!8.55e-13!13;UBERON:0004786!8.55e-13!13;UBERON:0000485!2.02e-12!11;UBERON:0003350!9.49e-11!9;UBERON:0004808!9.49e-11!9;UBERON:0001277!9.49e-11!9;UBERON:0004923!1.99e-08!24
|ontology_enrichment_uberon=UBERON:0002384!1.08e-17!46;UBERON:0000344!9.69e-16!15;UBERON:0001242!8.55e-13!13;UBERON:0000060!8.55e-13!13;UBERON:0001262!8.55e-13!13;UBERON:0004786!8.55e-13!13;UBERON:0000485!2.02e-12!11;UBERON:0003350!9.49e-11!9;UBERON:0004808!9.49e-11!9;UBERON:0001277!9.49e-11!9;UBERON:0004923!1.99e-08!24
|tfbs_overrepresentation_for_novel_motifs=0.595185,0.0162298,0.186933,0.238864,0.721878,0.698129,0.324772,0.210111,0.223561,0.820545,0.288187,0.84479,0.210446,0.890651,0.383709,0,0.505674,0.105493,0.0508204,0.0839024,0.939233,0.28295,0.888941,0.109412,0.192505,0.35869,0.401215,0.267095,0.139679,0.297581,0.710801,0.598971,0.104128,0.634402,1.25827,0.0221233,0.667121,0.311629,0.290566,0.0703677,0.710516,0.259911,0.0429639,0.122151,0.147772,0.230148,0.433813,0.279902,0.198601,0.141659,0.48979,0.381972,0.281801,0.732469,0.749094,0.341233,0.147717,0.303999,0.0433654,0.339495,0.580338,0.390204,0.0681609,0.479581,0.925321,0.516415,0.880067,1.22155,0.576002,1.07689,0.515225,0.476117,0.0113485,0.781142,0.158223,0.606791,0.153229,0.423705,0.564426,0.163487,0.479273,0.521544,0.388944,0.443997,0.671442,0.206398,0.602992,0.297913,0.438181,1.38183,0.947651,0.676142,1.48408,0.365956,0.0836626,0.257625,0.206664,0.613539,0.43404,0.469526,0.0985954,0.59871,0.715894,0.490329,0.489372,0.259558,0.543989,0.276621,0.16693,0.161774,0.201092,0.717588,0.493275,0.292444,0.954503,0.346836,0.156262,0.678491,0.506861,0.096357,0.786314,0.46068,0.360259,0.422901,1.00724,0.567849,0.331666,0.60459,0.8786,0.370855,0.699779,1.22651,0.850049,0.352905,0.975524,0.0491355,0.610335,0.261043,0.927716,1.74768,1.35029,0.884624,0.370659,0.608735,0.483498,0.260275,0.436593,1.7082,0.214583,0.726856,0.128142,0.434542,0.733963,0.077277,0.352111,0.81211,0.382849,0.128633,0.204546,0.60983,0.93695,0.670634,0.568261,0.199399,0.480505,0.345769,0.663991,0.313326,1.14539
|tfbs_overrepresentation_for_novel_motifs=0.595185,0.0162298,0.186933,0.238864,0.721878,0.698129,0.324772,0.210111,0.223561,0.820545,0.288187,0.84479,0.210446,0.890651,0.383709,0,0.505674,0.105493,0.0508204,0.0839024,0.939233,0.28295,0.888941,0.109412,0.192505,0.35869,0.401215,0.267095,0.139679,0.297581,0.710801,0.598971,0.104128,0.634402,1.25827,0.0221233,0.667121,0.311629,0.290566,0.0703677,0.710516,0.259911,0.0429639,0.122151,0.147772,0.230148,0.433813,0.279902,0.198601,0.141659,0.48979,0.381972,0.281801,0.732469,0.749094,0.341233,0.147717,0.303999,0.0433654,0.339495,0.580338,0.390204,0.0681609,0.479581,0.925321,0.516415,0.880067,1.22155,0.576002,1.07689,0.515225,0.476117,0.0113485,0.781142,0.158223,0.606791,0.153229,0.423705,0.564426,0.163487,0.479273,0.521544,0.388944,0.443997,0.671442,0.206398,0.602992,0.297913,0.438181,1.38183,0.947651,0.676142,1.48408,0.365956,0.0836626,0.257625,0.206664,0.613539,0.43404,0.469526,0.0985954,0.59871,0.715894,0.490329,0.489372,0.259558,0.543989,0.276621,0.16693,0.161774,0.201092,0.717588,0.493275,0.292444,0.954503,0.346836,0.156262,0.678491,0.506861,0.096357,0.786314,0.46068,0.360259,0.422901,1.00724,0.567849,0.331666,0.60459,0.8786,0.370855,0.699779,1.22651,0.850049,0.352905,0.975524,0.0491355,0.610335,0.261043,0.927716,1.74768,1.35029,0.884624,0.370659,0.608735,0.483498,0.260275,0.436593,1.7082,0.214583,0.726856,0.128142,0.434542,0.733963,0.077277,0.352111,0.81211,0.382849,0.128633,0.204546,0.60983,0.93695,0.670634,0.568261,0.199399,0.480505,0.345769,0.663991,0.313326,1.14539
|tfbs_overrepresentation_jaspar=MA0003.1;0.446578,MA0004.1;0.239244,MA0006.1;0.118059,MA0007.1;0.227553,MA0009.1;0.623671,MA0014.1;1.41021,MA0017.1;0.135289,MA0019.1;0.456268,MA0024.1;0.582844,MA0025.1;0.845702,MA0027.1;2.24512,MA0028.1;0.12472,MA0029.1;0.562703,MA0030.1;0.568779,MA0031.1;0.535959,MA0038.1;0.358622,MA0040.1;0.635404,MA0041.1;0.18185,MA0042.1;0.172351,MA0043.1;0.71494,MA0046.1;0.657417,MA0048.1;0.102771,MA0050.1;0.270164,MA0051.1;0.366328,MA0052.1;0.642973,MA0055.1;0.381798,MA0056.1;0,MA0057.1;0.703408,MA0058.1;0.167504,MA0059.1;0.176308,MA0060.1;0.249987,MA0061.1;0.615538,MA0063.1;0,MA0066.1;0.349199,MA0067.1;0.953264,MA0068.1;0.0216542,MA0069.1;0.643292,MA0070.1;0.634186,MA0071.1;0.269487,MA0072.1;0.626238,MA0073.1;0.290179,MA0074.1;0.318792,MA0076.1;0.148159,MA0077.1;0.605975,MA0078.1;0.395048,MA0081.1;0.193203,MA0083.1;0.714187,MA0084.1;1.27474,MA0087.1;0.673355,MA0088.1;0.292366,MA0089.1;0,MA0090.1;0.212772,MA0091.1;0.24961,MA0092.1;0.610874,MA0093.1;0.130107,MA0095.1;0,MA0098.1;0,MA0100.1;0.309116,MA0101.1;0.538493,MA0103.1;0.439015,MA0105.1;0.341877,MA0106.1;0.401864,MA0107.1;0.428571,MA0108.2;0.476838,MA0109.1;0,MA0111.1;0.223614,MA0113.1;0.377232,MA0114.1;0.291992,MA0115.1;0.717599,MA0116.1;0.117928,MA0117.1;0.686999,MA0119.1;0.183219,MA0122.1;0.705806,MA0124.1;0.901619,MA0125.1;0.830088,MA0130.1;0,MA0131.1;1.14691,MA0132.1;0,MA0133.1;0,MA0135.1;0.749615,MA0136.1;0.335579,MA0139.1;0.0558308,MA0140.1;0.30902,MA0141.1;0.155997,MA0142.1;0.522654,MA0143.1;0.391481,MA0144.1;0.0881858,MA0145.1;1.15108,MA0146.1;0.56368,MA0147.1;0.0952713,MA0148.1;0.70223,MA0149.1;0.18682,MA0062.2;0.354916,MA0035.2;0.312946,MA0039.2;0.101713,MA0138.2;0.445088,MA0002.2;0.0572064,MA0137.2;0.153989,MA0104.2;0.0641853,MA0047.2;0.357963,MA0112.2;0.0599393,MA0065.2;0.160972,MA0150.1;0.227466,MA0151.1;0,MA0152.1;1.67957,MA0153.1;0.765498,MA0154.1;0.247047,MA0155.1;0.0729675,MA0156.1;0.885026,MA0157.1;1.23539,MA0158.1;0,MA0159.1;0.101261,MA0160.1;0.254455,MA0161.1;0,MA0162.1;0.903541,MA0163.1;0.150434,MA0164.1;0.335886,MA0080.2;0.13897,MA0018.2;0.344133,MA0099.2;1.1194,MA0079.2;0.0246716,MA0102.2;1.32652,MA0258.1;0.0789466,MA0259.1;0.0890842,MA0442.1;0
}}
}}

Revision as of 11:49, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:94977804..94977814,+p4@Mcg1038069
p4@Ube2n
Mm9::chr11:3024046..3024057,+p3@Pisd-ps3
Mm9::chr15:91537149..91537152,+p@chr15:91537149..91537152
+
Mm9::chr18:35931228..35931253,+p4@Ube2d2
Mm9::chr18:35931264..35931269,+p8@Ube2d2
Mm9::chr19:61242876..61242882,+p@chr19:61242876..61242882
+
Mm9::chr19:9633694..9633738,-p1@ENSMUST00000090527
Mm9::chr1:107352544..107352553,+p1@ENSMUST00000086725
Mm9::chr1:4761175..4761203,+p@chr1:4761175..4761203
+
Mm9::chr3:92493213..92493228,+p@chr3:92493213..92493228
+
Mm9::chr3:92493229..92493259,+p1@ENSMUST00000169025
Mm9::chr4:103235928..103235936,+p1@ENSMUST00000079345
Mm9::chr5:8971911..8971920,+p1@ENSMUST00000104982
Mm9::chr6:46994593..46994618,+p6@Cntnap2
Mm9::chr9:62257059..62257102,+p@chr9:62257059..62257102
+


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:0004842ubiquitin-protein ligase activity0.00128265225111418
GO:0008639small protein conjugating enzyme activity0.00128265225111418
GO:0019787small conjugating protein ligase activity0.00128265225111418
GO:0006511ubiquitin-dependent protein catabolic process0.00128265225111418
GO:0043632modification-dependent macromolecule catabolic process0.00128265225111418
GO:0019941modification-dependent protein catabolic process0.00128265225111418
GO:0051603proteolysis involved in cellular protein catabolic process0.00128265225111418
GO:0044257cellular protein catabolic process0.00128265225111418
GO:0016881acid-amino acid ligase activity0.00128265225111418
GO:0016879ligase activity, forming carbon-nitrogen bonds0.00175439577964413
GO:0030163protein catabolic process0.00193202443631754
GO:0044265cellular macromolecule catabolic process0.00284655464124699
GO:0043285biopolymer catabolic process0.00284655464124699
GO:0009057macromolecule catabolic process0.0042178770412939
GO:0016874ligase activity0.00481300063153218
GO:0044248cellular catabolic process0.00718152715250053
GO:0006512ubiquitin cycle0.00774700785183523
GO:0051092activation of NF-kappaB transcription factor0.0099638634077022
GO:0009056catabolic process0.010013119315629
GO:0050852T cell receptor signaling pathway0.0115270861488087
GO:0006508proteolysis0.0116422451271434
GO:0051091positive regulation of transcription factor activity0.0116422451271434
GO:0051090regulation of transcription factor activity0.0139162613497778
GO:0050851antigen receptor-mediated signaling pathway0.0144017515599351
GO:0002429immune response-activating cell surface receptor signaling pathway0.0163815022618512
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0167340748867441
GO:0002757immune response-activating signal transduction0.017060323285079
GO:0002764immune response-regulating signal transduction0.0173630679316928
GO:0002253activation of immune response0.0338972660671632
GO:0043687post-translational protein modification0.0346689203717076
GO:0050778positive regulation of immune response0.0390523850299093
GO:0002684positive regulation of immune system process0.0390523850299093
GO:0006464protein modification process0.0392211885276638
GO:0005515protein binding0.0392211885276638
GO:0050776regulation of immune response0.0392211885276638
GO:0002682regulation of immune system process0.0392211885276638
GO:0043412biopolymer modification0.0392211885276638
GO:0051240positive regulation of multicellular organismal process0.0392211885276638



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
somatic cell3.88e-24118
animal cell1.31e-21115
eukaryotic cell1.31e-21115
hematopoietic cell3.73e-2032
hematopoietic oligopotent progenitor cell3.73e-2032
hematopoietic stem cell3.73e-2032
angioblastic mesenchymal cell3.73e-2032
hematopoietic multipotent progenitor cell3.73e-2032
connective tissue cell1.08e-1746
mesenchymal cell1.08e-1746
hematopoietic lineage restricted progenitor cell2.64e-1725
epithelial cell3.50e-1725
motile cell1.20e-1654
endo-epithelial cell2.14e-1515
lymphoid lineage restricted progenitor cell9.88e-1412
stem cell1.62e-1397
leukocyte6.09e-1317
nongranular leukocyte6.09e-1317
endodermal cell1.51e-1220
lymphocyte1.93e-1213
common lymphoid progenitor1.93e-1213
mature alpha-beta T cell2.30e-129
alpha-beta T cell2.30e-129
immature T cell2.30e-129
mature T cell2.30e-129
immature alpha-beta T cell2.30e-129
T cell2.70e-1211
pro-T cell2.70e-1211
CD4-positive, alpha-beta T cell3.96e-118
nucleate cell4.23e-1116
intestinal epithelial cell9.49e-119
epithelial cell of alimentary canal9.49e-119
somatic stem cell1.20e-0991
multi fate stem cell1.20e-0991
columnar/cuboidal epithelial cell1.69e-097
common myeloid progenitor2.67e-0919
thymocyte5.71e-096
double negative thymocyte5.71e-096
naive T cell5.71e-096
double-positive, alpha-beta thymocyte5.71e-096
CD4-positive, alpha-beta thymocyte5.71e-096
naive thymus-derived CD4-positive, alpha-beta T cell5.71e-096
DN4 thymocyte5.71e-096
DN1 thymic pro-T cell5.71e-096
DN2 thymocyte5.71e-096
DN3 thymocyte5.71e-096
immature single positive thymocyte5.71e-096
early T lineage precursor5.71e-096
mature CD4 single-positive thymocyte5.71e-096
resting double-positive thymocyte5.71e-096
double-positive blast5.71e-096
CD69-positive double-positive thymocyte5.71e-096
CD69-positive, CD4-positive single-positive thymocyte5.71e-096
CD4-positive, CD8-intermediate double-positive thymocyte5.71e-096
CD24-positive, CD4 single-positive thymocyte5.71e-096
brush border epithelial cell1.23e-086
gut absorptive cell1.23e-086
absorptive cell1.23e-086
enterocyte1.23e-086
myeloid cell4.95e-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)
MA0003.10.446578
MA0004.10.239244
MA0006.10.118059
MA0007.10.227553
MA0009.10.623671
MA0014.11.41021
MA0017.10.135289
MA0019.10.456268
MA0024.10.582844
MA0025.10.845702
MA0027.12.24512
MA0028.10.12472
MA0029.10.562703
MA0030.10.568779
MA0031.10.535959
MA0038.10.358622
MA0040.10.635404
MA0041.10.18185
MA0042.10.172351
MA0043.10.71494
MA0046.10.657417
MA0048.10.102771
MA0050.10.270164
MA0051.10.366328
MA0052.10.642973
MA0055.10.381798
MA0056.10
MA0057.10.703408
MA0058.10.167504
MA0059.10.176308
MA0060.10.249987
MA0061.10.615538
MA0063.10
MA0066.10.349199
MA0067.10.953264
MA0068.10.0216542
MA0069.10.643292
MA0070.10.634186
MA0071.10.269487
MA0072.10.626238
MA0073.10.290179
MA0074.10.318792
MA0076.10.148159
MA0077.10.605975
MA0078.10.395048
MA0081.10.193203
MA0083.10.714187
MA0084.11.27474
MA0087.10.673355
MA0088.10.292366
MA0089.10
MA0090.10.212772
MA0091.10.24961
MA0092.10.610874
MA0093.10.130107
MA0095.10
MA0098.10
MA0100.10.309116
MA0101.10.538493
MA0103.10.439015
MA0105.10.341877
MA0106.10.401864
MA0107.10.428571
MA0108.20.476838
MA0109.10
MA0111.10.223614
MA0113.10.377232
MA0114.10.291992
MA0115.10.717599
MA0116.10.117928
MA0117.10.686999
MA0119.10.183219
MA0122.10.705806
MA0124.10.901619
MA0125.10.830088
MA0130.10
MA0131.11.14691
MA0132.10
MA0133.10
MA0135.10.749615
MA0136.10.335579
MA0139.10.0558308
MA0140.10.30902
MA0141.10.155997
MA0142.10.522654
MA0143.10.391481
MA0144.10.0881858
MA0145.11.15108
MA0146.10.56368
MA0147.10.0952713
MA0148.10.70223
MA0149.10.18682
MA0062.20.354916
MA0035.20.312946
MA0039.20.101713
MA0138.20.445088
MA0002.20.0572064
MA0137.20.153989
MA0104.20.0641853
MA0047.20.357963
MA0112.20.0599393
MA0065.20.160972
MA0150.10.227466
MA0151.10
MA0152.11.67957
MA0153.10.765498
MA0154.10.247047
MA0155.10.0729675
MA0156.10.885026
MA0157.11.23539
MA0158.10
MA0159.10.101261
MA0160.10.254455
MA0161.10
MA0162.10.903541
MA0163.10.150434
MA0164.10.335886
MA0080.20.13897
MA0018.20.344133
MA0099.21.1194
MA0079.20.0246716
MA0102.21.32652
MA0258.10.0789466
MA0259.10.0890842
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:484&oldid=2573879"