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MCL coexpression mm9:351: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0042632;cholesterol homeostasis;0.00142028186206366;67470,14385!GO:0055088;lipid homeostasis;0.00142028186206366;67470,14385!GO:0055092;sterol homeostasis;0.00142028186206366;67470,14385!GO:0032642;regulation of chemokine production;0.0163918260012053;14385!GO:0032682;negative regulation of chemokine production;0.0163918260012053;14385!GO:0035166;post-embryonic hemopoiesis;0.018209647453125;14385!GO:0002318;myeloid progenitor cell differentiation;0.018209647453125;14385!GO:0045730;respiratory burst;0.018209647453125;14385!GO:0006089;lactate metabolic process;0.018209647453125;14385!GO:0015760;glucose-6-phosphate transport;0.0245783101549847;14385!GO:0001780;neutrophil homeostasis;0.0297861785229007;14385!GO:0002244;hemopoietic progenitor cell differentiation;0.0338786606807993;14385!GO:0019217;regulation of fatty acid metabolic process;0.0338786606807993;19013!GO:0048569;post-embryonic organ development;0.0338786606807993;14385!GO:0046983;protein dimerization activity;0.0338786606807993;233490,19013!GO:0048878;chemical homeostasis;0.0338786606807993;67470,14385!GO:0032602;chemokine production;0.0338786606807993;14385!GO:0002262;myeloid cell homeostasis;0.0338786606807993;14385!GO:0001818;negative regulation of cytokine production;0.0338786606807993;14385!GO:0032787;monocarboxylic acid metabolic process;0.0338786606807993;14385,19013!GO:0044262;cellular carbohydrate metabolic process;0.0419816813137615;14385,19013!GO:0015914;phospholipid transport;0.0419816813137615;67470!GO:0030593;neutrophil chemotaxis;0.0419816813137615;14385!GO:0016887;ATPase activity;0.0419816813137615;27409,67470!GO:0015918;sterol transport;0.0490436475972099;67470!}}
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homeostasis;0.00142028186206366;67470,14385!GO:0055088;lipid homeostasis;0.00142028186206366;67470,14385!GO:0055092;sterol homeostasis;0.00142028186206366;67470,14385!GO:0032642;regulation of chemokine production;0.0163918260012053;14385!GO:0032682;negative regulation of chemokine production;0.0163918260012053;14385!GO:0035166;post-embryonic hemopoiesis;0.018209647453125;14385!GO:0002318;myeloid progenitor cell differentiation;0.018209647453125;14385!GO:0045730;respiratory burst;0.018209647453125;14385!GO:0006089;lactate metabolic process;0.018209647453125;14385!GO:0015760;glucose-6-phosphate transport;0.0245783101549847;14385!GO:0001780;neutrophil homeostasis;0.0297861785229007;14385!GO:0002244;hemopoietic progenitor cell differentiation;0.0338786606807993;14385!GO:0019217;regulation of fatty acid metabolic process;0.0338786606807993;19013!GO:0048569;post-embryonic organ development;0.0338786606807993;14385!GO:0046983;protein dimerization activity;0.0338786606807993;233490,19013!GO:0048878;chemical homeostasis;0.0338786606807993;67470,14385!GO:0032602;chemokine production;0.0338786606807993;14385!GO:0002262;myeloid cell homeostasis;0.0338786606807993;14385!GO:0001818;negative regulation of cytokine production;0.0338786606807993;14385!GO:0032787;monocarboxylic acid metabolic process;0.0338786606807993;14385,19013!GO:0044262;cellular carbohydrate metabolic process;0.0419816813137615;14385,19013!GO:0015914;phospholipid transport;0.0419816813137615;67470!GO:0030593;neutrophil chemotaxis;0.0419816813137615;14385!GO:0016887;ATPase activity;0.0419816813137615;27409,67470!GO:0015918;sterol transport;0.0490436475972099;67470!|ontology_enrichment_celltype=CL:0002563!1.89e-07!9;CL:0002251!1.89e-07!9;CL:0000066!7.85e-07!25|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000160!4.42e-18!31;UBERON:0005409!3.07e-14!47;UBERON:0009854!1.14e-13!23;UBERON:0009856!1.14e-13!23;UBERON:0002107!3.25e-13!22;UBERON:0007499!3.25e-13!22;UBERON:0006925!3.25e-13!22;UBERON:0009497!3.25e-13!22;UBERON:0000015!3.25e-13!22;UBERON:0002423!3.25e-13!22;UBERON:0006235!3.25e-13!22;UBERON:0008835!3.25e-13!22;UBERON:0003894!3.25e-13!22;UBERON:0004161!3.25e-13!22;UBERON:0008836!3.25e-13!22;UBERON:0002365!3.64e-12!25;UBERON:0002330!3.64e-12!25;UBERON:0000344!1.61e-11!15;UBERON:0005172!2.18e-10!49;UBERON:0005173!2.18e-10!49;UBERON:0002417!2.18e-10!49;UBERON:0000916!2.18e-10!49;UBERON:0001242!3.04e-10!13;UBERON:0000060!3.04e-10!13;UBERON:0001262!3.04e-10!13;UBERON:0004786!3.04e-10!13;UBERON:0001007!1.19e-09!116;UBERON:0001555!1.19e-09!116;UBERON:0007026!1.19e-09!116;UBERON:0004119!2.57e-09!118;UBERON:0000925!2.57e-09!118;UBERON:0006595!2.57e-09!118;UBERON:0004921!8.72e-09!114;UBERON:0005256!1.38e-08!45;UBERON:0003104!1.58e-07!61;UBERON:0009142!1.58e-07!61;UBERON:0003350!1.89e-07!9;UBERON:0004808!1.89e-07!9;UBERON:0001277!1.89e-07!9;UBERON:0004923!6.84e-07!24|tfbs_overrepresentation_for_novel_motifs=0.379825,0.859739,0.341317,0.144583,0.191527,0.15366,0.214952,0.436916,0.465626,0.34075,0.542448,0.206436,0.437632,1.19059,0.211839,0,0.374352,0.182139,1.33193,1.00488,0.0854539,0.321305,0.63467,0.0508498,0.352326,0.243873,0.0728375,0.966722,0.070875,0.25504,0.477864,1.16433,0.40323,0.0585697,1.71431,1.06049,1.05392,0.589223,0.0364629,2.62764,0.186742,0.486105,0.438881,0.0590946,2.74042,0.426921,0.833552,1.00921,0.506887,0.916531,0.359925,0.264025,0.932451,0.586014,0.601849,0.648355,0.0764293,0.573993,0.173818,0.227439,1.127,0.746278,1.16925,0.350689,1.2413,0.384144,0.727642,1.06142,0.438956,0.919268,1.0803,0.240361,2.03698,0.632466,1.5474,0.504764,0.808662,0.300684,0.428247,0.0875778,0.45844,0.388829,0.270104,0.0864064,0.5282,1.51408,3.55416,0.685943,0.313544,1.21975,0.793151,0.532634,0.471416,0.053818,2.87942,0.292027,0.0897681,0.473864,0.309859,0.57641,0.168895,1.16381,0.570262,0.946715,0.359547,0.485402,0.409409,0.174935,1.55184,2.08169,0.744411,0.57187,0.296684,0.187937,0.799811,0.727196,2.26242,0.146927,0.375433,0.0427125,0.637418,0.333667,0.686386,0.299972,0.851175,0.43141,0.220786,0.465518,0.726225,0.0550287,0.554981,0.432886,0.698665,0.238902,0.820264,0.183848,0.124253,0.488358,0.773792,1.58317,1.18855,0.732048,0.254204,0.469382,0.933035,0.161672,0.839116,1.54387,0.125637,2.14869,0.698441,3.41698,1.43474,1.27075,0.238221,0.662158,0.264789,0.847,0.376149,1.85552,0.782756,0.527439,0.431791,0.738623,0.351524,0.232792,0.167532,1.11929,1.98409|tfbs_overrepresentation_jaspar=MA0003.1;4.60906,MA0004.1;0.444991,MA0006.1;0.789557,MA0007.1;0.135697,MA0009.1;0.483331,MA0014.1;0.732965,MA0017.1;1.32958,MA0019.1;0.329708,MA0024.1;0.445298,MA0025.1;0.694475,MA0027.1;2.07936,MA0028.1;1.25253,MA0029.1;1.09168,MA0030.1;0.43227,MA0031.1;1.03811,MA0038.1;0.243815,MA0040.1;0.494317,MA0041.1;0.10094,MA0042.1;0.0939798,MA0043.1;0.569356,MA0046.1;0.514989,MA0048.1;0.582467,MA0050.1;0.169675,MA0051.1;0.250459,MA0052.1;0.501416,MA0055.1;0.114275,MA0056.1;0,MA0057.1;0.180412,MA0058.1;0.303016,MA0059.1;0.320353,MA0060.1;2.11912,MA0061.1;0.968084,MA0063.1;0,MA0066.1;0.235725,MA0067.1;0.798606,MA0068.1;0.0867743,MA0069.1;0.501715,MA0070.1;0.493176,MA0071.1;0.169125,MA0072.1;0.485733,MA0073.1;0.0340283,MA0074.1;0.209912,MA0076.1;0.0767377,MA0077.1;0.466808,MA0078.1;0.755969,MA0081.1;0.717402,MA0083.1;0.568641,MA0084.1;1.11388,MA0087.1;0.530004,MA0088.1;2.80461,MA0089.1;0,MA0090.1;1.27796,MA0091.1;0.153118,MA0092.1;0.124428,MA0093.1;0.496926,MA0095.1;0,MA0098.1;0,MA0100.1;0.201797,MA0101.1;0.101635,MA0103.1;0.253989,MA0105.1;0.515449,MA0106.1;0.769607,MA0107.1;0.526347,MA0108.2;0.348212,MA0109.1;0,MA0111.1;0.132626,MA0113.1;1.32697,MA0114.1;4.19335,MA0115.1;0.571881,MA0116.1;0.788841,MA0117.1;0.542889,MA0119.1;0.333984,MA0122.1;0.560692,MA0124.1;0.748494,MA0125.1;0.67944,MA0130.1;0,MA0131.1;0.326061,MA0132.1;0,MA0133.1;0,MA0135.1;0.602346,MA0136.1;0.224107,MA0139.1;1.02435,MA0140.1;0.201717,MA0141.1;0.280405,MA0142.1;0.389844,MA0143.1;0.27232,MA0144.1;0.0377982,MA0145.1;0.799315,MA0146.1;1.96294,MA0147.1;1.9513,MA0148.1;0.470482,MA0149.1;0.104621,MA0062.2;0.15838,MA0035.2;1.75359,MA0039.2;2.4645,MA0138.2;1.54433,MA0002.2;0.020674,MA0137.2;0.080825,MA0104.2;2.50372,MA0047.2;0.243248,MA0112.2;1.38655,MA0065.2;2.12205,MA0150.1;0.421594,MA0151.1;0,MA0152.1;0.243327,MA0153.1;0.617506,MA0154.1;0.360977,MA0155.1;0.913852,MA0156.1;0.0763253,MA0157.1;0.952896,MA0158.1;0,MA0159.1;1.52077,MA0160.1;0.924598,MA0161.1;0,MA0162.1;4.18474,MA0163.1;0.583427,MA0164.1;0.224368,MA0080.2;0.0703895,MA0018.2;0.654151,MA0099.2;0.314682,MA0079.2;0.60142,MA0102.2;1.16504,MA0258.1;0.310208,MA0259.1;1.39654,MA0442.1;0}}

Latest revision as of 15:09, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:102007554..102007574,-p1@ENSMUST00000123060
Mm9::chr11:53236625..53236637,-p1@Leap2
Mm9::chr11:98448507..98448567,-p1@Ormdl3
Mm9::chr13:96661836..96661857,-p2@Iqgap2
Mm9::chr14:56178830..56178841,+p4@Dcaf11
Mm9::chr15:85565338..85565355,+p7@Ppara
Mm9::chr15:85566051..85566080,+p4@Ppara
Mm9::chr16:21826090..21826118,+p@chr16:21826090..21826118
+
Mm9::chr17:85082272..85082284,-p2@Abcg5
Mm9::chr17:85082473..85082481,+p4@Abcg8
Mm9::chr17:85082530..85082533,+p8@Abcg8
Mm9::chr1:159456258..159456284,+p2@Sec16b
Mm9::chr2:27282009..27282055,-p3@Vav2
Mm9::chr2:27282056..27282083,-p2@Vav2
Mm9::chr3:104621398..104621422,-p3@Mov10
Mm9::chr3:40753703..40753736,+p@chr3:40753703..40753736
+
Mm9::chr3:40753740..40753774,+p@chr3:40753740..40753774
+
Mm9::chr4:149594810..149594830,-p@chr4:149594810..149594830
-
Mm9::chr5:89022703..89022738,+p@chr5:89022703..89022738
+
Mm9::chr7:97591412..97591431,+p2@Crebzf
Mm9::chr8:124900800..124900829,+p@chr8:124900800..124900829
+
Mm9::chr9:44205228..44205237,+p8@Slc37a4


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:0042632cholesterol homeostasis0.00142028186206366
GO:0055088lipid homeostasis0.00142028186206366
GO:0055092sterol homeostasis0.00142028186206366
GO:0032642regulation of chemokine production0.0163918260012053
GO:0032682negative regulation of chemokine production0.0163918260012053
GO:0035166post-embryonic hemopoiesis0.018209647453125
GO:0002318myeloid progenitor cell differentiation0.018209647453125
GO:0045730respiratory burst0.018209647453125
GO:0006089lactate metabolic process0.018209647453125
GO:0015760glucose-6-phosphate transport0.0245783101549847
GO:0001780neutrophil homeostasis0.0297861785229007
GO:0002244hemopoietic progenitor cell differentiation0.0338786606807993
GO:0019217regulation of fatty acid metabolic process0.0338786606807993
GO:0048569post-embryonic organ development0.0338786606807993
GO:0046983protein dimerization activity0.0338786606807993
GO:0048878chemical homeostasis0.0338786606807993
GO:0032602chemokine production0.0338786606807993
GO:0002262myeloid cell homeostasis0.0338786606807993
GO:0001818negative regulation of cytokine production0.0338786606807993
GO:0032787monocarboxylic acid metabolic process0.0338786606807993
GO:0044262cellular carbohydrate metabolic process0.0419816813137615
GO:0015914phospholipid transport0.0419816813137615
GO:0030593neutrophil chemotaxis0.0419816813137615
GO:0016887ATPase activity0.0419816813137615
GO:0015918sterol transport0.0490436475972099



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
intestinal epithelial cell1.89e-079
epithelial cell of alimentary canal1.89e-079
epithelial cell7.85e-0725

Uber Anatomy
Ontology termp-valuen
intestine4.42e-1831
gastrointestinal system3.07e-1447
digestive tract diverticulum1.14e-1323
sac1.14e-1323
liver3.25e-1322
epithelial sac3.25e-1322
digestive gland3.25e-1322
epithelium of foregut-midgut junction3.25e-1322
anatomical boundary3.25e-1322
hepatobiliary system3.25e-1322
foregut-midgut junction3.25e-1322
hepatic diverticulum3.25e-1322
liver primordium3.25e-1322
septum transversum3.25e-1322
liver bud3.25e-1322
exocrine gland3.64e-1225
exocrine system3.64e-1225
mucosa1.61e-1115
abdomen element2.18e-1049
abdominal segment element2.18e-1049
abdominal segment of trunk2.18e-1049
abdomen2.18e-1049
intestinal mucosa3.04e-1013
anatomical wall3.04e-1013
wall of intestine3.04e-1013
gastrointestinal system mucosa3.04e-1013
digestive system1.19e-09116
digestive tract1.19e-09116
primitive gut1.19e-09116
endoderm-derived structure2.57e-09118
endoderm2.57e-09118
presumptive endoderm2.57e-09118
subdivision of digestive tract8.72e-09114
trunk mesenchyme1.38e-0845
mesenchyme1.58e-0761
entire embryonic mesenchyme1.58e-0761
epithelium of mucosa1.89e-079
gastrointestinal system epithelium1.89e-079
intestinal epithelium1.89e-079
organ component layer6.84e-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)
MA0003.14.60906
MA0004.10.444991
MA0006.10.789557
MA0007.10.135697
MA0009.10.483331
MA0014.10.732965
MA0017.11.32958
MA0019.10.329708
MA0024.10.445298
MA0025.10.694475
MA0027.12.07936
MA0028.11.25253
MA0029.11.09168
MA0030.10.43227
MA0031.11.03811
MA0038.10.243815
MA0040.10.494317
MA0041.10.10094
MA0042.10.0939798
MA0043.10.569356
MA0046.10.514989
MA0048.10.582467
MA0050.10.169675
MA0051.10.250459
MA0052.10.501416
MA0055.10.114275
MA0056.10
MA0057.10.180412
MA0058.10.303016
MA0059.10.320353
MA0060.12.11912
MA0061.10.968084
MA0063.10
MA0066.10.235725
MA0067.10.798606
MA0068.10.0867743
MA0069.10.501715
MA0070.10.493176
MA0071.10.169125
MA0072.10.485733
MA0073.10.0340283
MA0074.10.209912
MA0076.10.0767377
MA0077.10.466808
MA0078.10.755969
MA0081.10.717402
MA0083.10.568641
MA0084.11.11388
MA0087.10.530004
MA0088.12.80461
MA0089.10
MA0090.11.27796
MA0091.10.153118
MA0092.10.124428
MA0093.10.496926
MA0095.10
MA0098.10
MA0100.10.201797
MA0101.10.101635
MA0103.10.253989
MA0105.10.515449
MA0106.10.769607
MA0107.10.526347
MA0108.20.348212
MA0109.10
MA0111.10.132626
MA0113.11.32697
MA0114.14.19335
MA0115.10.571881
MA0116.10.788841
MA0117.10.542889
MA0119.10.333984
MA0122.10.560692
MA0124.10.748494
MA0125.10.67944
MA0130.10
MA0131.10.326061
MA0132.10
MA0133.10
MA0135.10.602346
MA0136.10.224107
MA0139.11.02435
MA0140.10.201717
MA0141.10.280405
MA0142.10.389844
MA0143.10.27232
MA0144.10.0377982
MA0145.10.799315
MA0146.11.96294
MA0147.11.9513
MA0148.10.470482
MA0149.10.104621
MA0062.20.15838
MA0035.21.75359
MA0039.22.4645
MA0138.21.54433
MA0002.20.020674
MA0137.20.080825
MA0104.22.50372
MA0047.20.243248
MA0112.21.38655
MA0065.22.12205
MA0150.10.421594
MA0151.10
MA0152.10.243327
MA0153.10.617506
MA0154.10.360977
MA0155.10.913852
MA0156.10.0763253
MA0157.10.952896
MA0158.10
MA0159.11.52077
MA0160.10.924598
MA0161.10
MA0162.14.18474
MA0163.10.583427
MA0164.10.224368
MA0080.20.0703895
MA0018.20.654151
MA0099.20.314682
MA0079.20.60142
MA0102.21.16504
MA0258.10.310208
MA0259.11.39654
MA0442.10
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