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MCL coexpression mm9:190: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!1.50e-14!46;UBERON:0002370!3.37e-12!23;UBERON:0000974!3.37e-12!23;UBERON:0004807!3.37e-12!23;UBERON:0005058!3.37e-12!23;UBERON:0003351!3.37e-12!23;UBERON:0009113!3.37e-12!23;UBERON:0003295!3.37e-12!23;UBERON:0009722!3.37e-12!23;UBERON:0005562!3.37e-12!23;UBERON:0007690!3.37e-12!23;UBERON:0006562!1.15e-11!24;UBERON:0003408!1.15e-11!24;UBERON:0001557!1.15e-11!24;UBERON:0001042!1.15e-11!24;UBERON:0008814!1.15e-11!24;UBERON:0009145!1.15e-11!24;UBERON:0000072!2.65e-10!27;UBERON:0004177!1.50e-09!29;UBERON:0005057!1.50e-09!29;UBERON:0000077!8.39e-08!35;UBERON:0000063!8.39e-08!35;UBERON:0002390!1.18e-07!45;UBERON:0003061!1.18e-07!45;UBERON:0007811!1.44e-07!36;UBERON:0002193!4.02e-07!48;UBERON:0002405!4.02e-07!48
|ontology_enrichment_uberon=UBERON:0002384!1.50e-14!46;UBERON:0002370!3.37e-12!23;UBERON:0000974!3.37e-12!23;UBERON:0004807!3.37e-12!23;UBERON:0005058!3.37e-12!23;UBERON:0003351!3.37e-12!23;UBERON:0009113!3.37e-12!23;UBERON:0003295!3.37e-12!23;UBERON:0009722!3.37e-12!23;UBERON:0005562!3.37e-12!23;UBERON:0007690!3.37e-12!23;UBERON:0006562!1.15e-11!24;UBERON:0003408!1.15e-11!24;UBERON:0001557!1.15e-11!24;UBERON:0001042!1.15e-11!24;UBERON:0008814!1.15e-11!24;UBERON:0009145!1.15e-11!24;UBERON:0000072!2.65e-10!27;UBERON:0004177!1.50e-09!29;UBERON:0005057!1.50e-09!29;UBERON:0000077!8.39e-08!35;UBERON:0000063!8.39e-08!35;UBERON:0002390!1.18e-07!45;UBERON:0003061!1.18e-07!45;UBERON:0007811!1.44e-07!36;UBERON:0002193!4.02e-07!48;UBERON:0002405!4.02e-07!48
|tfbs_overrepresentation_for_novel_motifs=0.0707229,0.0152669,0.152081,0.457441,1.09422,0.108349,0.186383,0.138263,0.571334,0.0156619,0.036867,0.394385,0.362386,0.198477,0.90776,0,0.429309,1.34791,0.0241016,0.115853,0.236307,0.26269,0.0534624,0.376491,0.0602981,0.0633797,0.762917,0.296209,0.184769,0.146969,0.814461,0.197802,0.350073,0.211756,0.14249,0.0225549,0.00173006,0.387913,0.262055,0.104675,0.220288,0.282097,0.51481,0.144627,0.0218435,0.0902283,0.0987896,0.0342152,0.461051,0.341728,0.405683,0.0736078,0.309693,0.293909,0.826794,0.0561765,0.204193,0.163017,0.907466,0.0554818,0.1854,0.0773893,0.449842,0.123566,0.217151,0.14508,0.411886,0.714043,1.0291,0.582319,0.0471228,0.149769,0.000586935,0.331647,0.00449212,0.0615039,0.211535,0.0936296,0.519626,0.661863,0.558782,0.14818,0.561258,0.216011,0.248509,4.54189e-06,0.0776395,0.639828,0.331591,0.864265,0.469,0.251923,0.205896,1.13386,0.0270101,0.114972,0.133629,0.207688,0.0989069,0.247465,0.712766,0.574233,0.769467,0.808224,0.405068,0.0281348,0.16203,0.315229,0.121528,0.114076,0.34625,0.282632,0.666227,0.347562,1.19569,0.0471614,0.000122044,0.753388,0.431089,0.182164,0.33573,0.73414,0.22882,0.310511,1.29344,0.525018,0.194386,0.583726,0.410666,0.13117,0.269307,0.440169,1.00541,0.478509,0.493018,0.0101728,0.195082,0.284306,0.451982,1.21737,0.834426,0.415684,0.887948,0.590439,0.396428,0.117838,0.675013,1.1788,0.19821,0.0518572,0.353647,6.49964e-06,0.295048,0.527836,0.476722,0.356288,0.257346,0.070795,0.180979,0.194713,0.459848,0.692649,0.525668,0.0653744,2.50645,1.22128,0.319331,0.173366,0.124497
}}
}}

Revision as of 17:57, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:22026337..22026346,-p@chr10:22026337..22026346
-
Mm9::chr10:43548592..43548596,+p@chr10:43548592..43548596
+
Mm9::chr10:43717170..43717181,-p@chr10:43717170..43717181
-
Mm9::chr10:43717185..43717196,-p@chr10:43717185..43717196
-
Mm9::chr11:107330875..107330898,-p@chr11:107330875..107330898
-
Mm9::chr11:23669810..23669821,+p@chr11:23669810..23669821
+
Mm9::chr11:23670272..23670293,+p@chr11:23670272..23670293
+
Mm9::chr11:33833013..33833018,-p@chr11:33833013..33833018
-
Mm9::chr11:46200322..46200331,+p@chr11:46200322..46200331
+
Mm9::chr11:54336815..54336862,+p@chr11:54336815..54336862
+
Mm9::chr11:68911670..68911709,-p@chr11:68911670..68911709
-
Mm9::chr11:69733412..69733417,+p@chr11:69733412..69733417
+
Mm9::chr12:119615235..119615238,+p@chr12:119615235..119615238
+
Mm9::chr12:15821545..15821558,-p@chr12:15821545..15821558
-
Mm9::chr12:56547913..56547919,+p@chr12:56547913..56547919
+
Mm9::chr14:54817583..54817593,-p@chr14:54817583..54817593
-
Mm9::chr14:61665484..61665494,+p@chr14:61665484..61665494
+
Mm9::chr15:59356178..59356217,-p@chr15:59356178..59356217
-
Mm9::chr15:73006568..73006572,+p@chr15:73006568..73006572
+
Mm9::chr17:27501415..27501432,-p@chr17:27501415..27501432
-
Mm9::chr18:65481793..65481806,-p@chr18:65481793..65481806
-
Mm9::chr19:10806606..10806621,+p@chr19:10806606..10806621
+
Mm9::chr1:138476243..138476250,+p@chr1:138476243..138476250
+
Mm9::chr1:164501526..164501539,-p@chr1:164501526..164501539
-
Mm9::chr1:182286557..182286562,+p@chr1:182286557..182286562
+
Mm9::chr1:82829163..82829172,-p@chr1:82829163..82829172
-
Mm9::chr2:127141035..127141040,-p@chr2:127141035..127141040
-
Mm9::chr2:58013034..58013046,-p10@Cytip
Mm9::chr2:58013062..58013075,-p7@Cytip
Mm9::chr3:126299270..126299290,+p6@Camk2d
Mm9::chr3:68809849..68809868,+p@chr3:68809849..68809868
+
Mm9::chr3:87650806..87650827,-p@chr3:87650806..87650827
-
Mm9::chr4:133188153..133188179,+p@chr4:133188153..133188179
+
Mm9::chr4:155387843..155387856,-p@chr4:155387843..155387856
-
Mm9::chr4:155405070..155405083,+p@chr4:155405070..155405083
+
Mm9::chr4:32327445..32327449,+p@chr4:32327445..32327449
+
Mm9::chr4:32350855..32350868,+p@chr4:32350855..32350868
+
Mm9::chr5:114773355..114773367,+p@chr5:114773355..114773367
+
Mm9::chr5:22892293..22892317,-p@chr5:22892293..22892317
-
Mm9::chr6:108503087..108503091,-p@chr6:108503087..108503091
-
Mm9::chr6:122770872..122770875,-p3@ENSMUST00000112575
Mm9::chr6:125215345..125215360,-p@chr6:125215345..125215360
-
Mm9::chr6:145069654..145069666,+p@chr6:145069654..145069666
+
Mm9::chr6:48656532..48656548,+p@chr6:48656532..48656548
+
Mm9::chr7:29161745..29161757,+p@chr7:29161745..29161757
+
Mm9::chr8:14961880..14961899,+p@chr8:14961880..14961899
+
Mm9::chr8:84022563..84022566,+p@chr8:84022563..84022566
+
Mm9::chr8:84304468..84304473,-p@chr8:84304468..84304473
-
Mm9::chr9:107192291..107192309,+p@chr9:107192291..107192309
+
Mm9::chr9:107237091..107237100,+p@chr9:107237091..107237100
+
Mm9::chr9:108957297..108957310,-p@chr9:108957297..108957310
-
Mm9::chr9:44817346..44817354,-p@chr9:44817346..44817354
-


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:0000278mitotic cell cycle0.033383528378983
GO:0022403cell cycle phase0.033383528378983
GO:0006583melanin biosynthetic process from tyrosine0.033383528378983
GO:0005954calcium- and calmodulin-dependent protein kinase complex0.033383528378983
GO:0060048cardiac muscle contraction0.033383528378983
GO:0030315T-tubule0.0337504227630374
GO:0006582melanin metabolic process0.0337504227630374
GO:0042438melanin biosynthetic process0.0337504227630374
GO:0006570tyrosine metabolic process0.0337504227630374
GO:0007076mitotic chromosome condensation0.0337504227630374
GO:0004683calmodulin-dependent protein kinase activity0.0337504227630374
GO:0030261chromosome condensation0.0337504227630374
GO:0000070mitotic sister chromatid segregation0.0337504227630374
GO:0000819sister chromatid segregation0.0337504227630374
GO:0000082G1/S transition of mitotic cell cycle0.0383449905330503
GO:0022402cell cycle process0.0383449905330503
GO:0009072aromatic amino acid family metabolic process0.0383449905330503
GO:0046148pigment biosynthetic process0.0383449905330503
GO:0042383sarcolemma0.0383449905330503
GO:0006941striated muscle contraction0.0383449905330503
GO:0048066pigmentation during development0.0383449905330503
GO:0042440pigment metabolic process0.0391198823684918
GO:0046777protein amino acid autophosphorylation0.0394885477758235
GO:0016540protein autoprocessing0.0394885477758235
GO:0007049cell cycle0.0394885477758235
GO:0051325interphase0.0394885477758235
GO:0051329interphase of mitotic cell cycle0.0394885477758235
GO:0019748secondary metabolic process0.0394885477758235
GO:0060047heart contraction0.0394885477758235
GO:0003015heart process0.0394885477758235
GO:0030155regulation of cell adhesion0.0394885477758235
GO:0007059chromosome segregation0.0394885477758235
GO:0005938cell cortex0.0394885477758235



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
mature alpha-beta T cell1.28e-539
alpha-beta T cell1.28e-539
immature T cell1.28e-539
mature T cell1.28e-539
immature alpha-beta T cell1.28e-539
lymphoid lineage restricted progenitor cell3.53e-4912
CD4-positive, alpha-beta T cell9.03e-488
lymphocyte2.53e-4513
common lymphoid progenitor2.53e-4513
T cell9.89e-4411
pro-T cell9.89e-4411
nucleate cell1.21e-3616
thymocyte4.95e-366
double negative thymocyte4.95e-366
naive T cell4.95e-366
double-positive, alpha-beta thymocyte4.95e-366
CD4-positive, alpha-beta thymocyte4.95e-366
naive thymus-derived CD4-positive, alpha-beta T cell4.95e-366
DN4 thymocyte4.95e-366
DN1 thymic pro-T cell4.95e-366
DN2 thymocyte4.95e-366
DN3 thymocyte4.95e-366
immature single positive thymocyte4.95e-366
early T lineage precursor4.95e-366
mature CD4 single-positive thymocyte4.95e-366
resting double-positive thymocyte4.95e-366
double-positive blast4.95e-366
CD69-positive double-positive thymocyte4.95e-366
CD69-positive, CD4-positive single-positive thymocyte4.95e-366
CD4-positive, CD8-intermediate double-positive thymocyte4.95e-366
CD24-positive, CD4 single-positive thymocyte4.95e-366
leukocyte1.99e-3417
nongranular leukocyte1.99e-3417
hematopoietic lineage restricted progenitor cell7.75e-2825
hematopoietic cell1.76e-2132
hematopoietic oligopotent progenitor cell1.76e-2132
hematopoietic stem cell1.76e-2132
angioblastic mesenchymal cell1.76e-2132
hematopoietic multipotent progenitor cell1.76e-2132
connective tissue cell1.50e-1446
mesenchymal cell1.50e-1446
motile cell3.41e-1254
stem cell1.99e-1097
regulatory T cell1.20e-071
CD4-positive, CD25-positive, alpha-beta regulatory T cell1.20e-071
CD8-positive, alpha-beta T cell2.11e-071
lymphocyte of B lineage4.21e-071
B cell4.21e-071
pro-B cell4.21e-071

Uber Anatomy
Ontology termp-valuen
connective tissue1.50e-1446
thymus3.37e-1223
neck3.37e-1223
respiratory system epithelium3.37e-1223
hemolymphoid system gland3.37e-1223
pharyngeal epithelium3.37e-1223
thymic region3.37e-1223
pharyngeal gland3.37e-1223
entire pharyngeal arch endoderm3.37e-1223
thymus primordium3.37e-1223
early pharyngeal endoderm3.37e-1223
pharynx1.15e-1124
gland of gut1.15e-1124
upper respiratory tract1.15e-1124
chordate pharynx1.15e-1124
pharyngeal arch system1.15e-1124
pharyngeal region of foregut1.15e-1124
segment of respiratory tract2.65e-1027
hemopoietic organ1.50e-0929
immune organ1.50e-0929
mixed endoderm/mesoderm-derived structure8.39e-0835
organ segment8.39e-0835
hematopoietic system1.18e-0745
blood island1.18e-0745
craniocervical region1.44e-0736
hemolymphoid system4.02e-0748
immune system4.02e-0748


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)

{{{tfbs_overrepresentation_jaspar}}}

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