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MCL coexpression mm9:178: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002370!1.33e-20!23;UBERON:0000974!1.33e-20!23;UBERON:0004807!1.33e-20!23;UBERON:0005058!1.33e-20!23;UBERON:0003351!1.33e-20!23;UBERON:0009113!1.33e-20!23;UBERON:0003295!1.33e-20!23;UBERON:0009722!1.33e-20!23;UBERON:0005562!1.33e-20!23;UBERON:0007690!1.33e-20!23;UBERON:0006562!9.61e-20!24;UBERON:0003408!9.61e-20!24;UBERON:0001557!9.61e-20!24;UBERON:0001042!9.61e-20!24;UBERON:0008814!9.61e-20!24;UBERON:0009145!9.61e-20!24;UBERON:0000072!1.52e-17!27;UBERON:0004177!2.49e-16!29;UBERON:0005057!2.49e-16!29;UBERON:0000077!1.63e-13!35;UBERON:0000063!1.63e-13!35;UBERON:0007811!3.91e-13!36;UBERON:0000065!1.63e-11!41;UBERON:0001004!3.09e-11!42;UBERON:0000153!5.69e-11!43;UBERON:0002390!1.78e-10!45;UBERON:0003061!1.78e-10!45;UBERON:0002193!8.28e-10!48;UBERON:0002405!8.28e-10!48;UBERON:0003929!1.57e-08!55;UBERON:0002368!8.45e-08!60;UBERON:0002530!3.53e-07!65;UBERON:0000490!4.59e-07!66;UBERON:0005911!9.58e-07!69
|ontology_enrichment_uberon=UBERON:0002370!1.33e-20!23;UBERON:0000974!1.33e-20!23;UBERON:0004807!1.33e-20!23;UBERON:0005058!1.33e-20!23;UBERON:0003351!1.33e-20!23;UBERON:0009113!1.33e-20!23;UBERON:0003295!1.33e-20!23;UBERON:0009722!1.33e-20!23;UBERON:0005562!1.33e-20!23;UBERON:0007690!1.33e-20!23;UBERON:0006562!9.61e-20!24;UBERON:0003408!9.61e-20!24;UBERON:0001557!9.61e-20!24;UBERON:0001042!9.61e-20!24;UBERON:0008814!9.61e-20!24;UBERON:0009145!9.61e-20!24;UBERON:0000072!1.52e-17!27;UBERON:0004177!2.49e-16!29;UBERON:0005057!2.49e-16!29;UBERON:0000077!1.63e-13!35;UBERON:0000063!1.63e-13!35;UBERON:0007811!3.91e-13!36;UBERON:0000065!1.63e-11!41;UBERON:0001004!3.09e-11!42;UBERON:0000153!5.69e-11!43;UBERON:0002390!1.78e-10!45;UBERON:0003061!1.78e-10!45;UBERON:0002193!8.28e-10!48;UBERON:0002405!8.28e-10!48;UBERON:0003929!1.57e-08!55;UBERON:0002368!8.45e-08!60;UBERON:0002530!3.53e-07!65;UBERON:0000490!4.59e-07!66;UBERON:0005911!9.58e-07!69
|tfbs_overrepresentation_for_novel_motifs=0.146567,0.00636313,0.118789,0.384261,1.5126,1.00732,0.155196,0.270766,0.110866,0.0269746,0.119056,0.0364912,0.0964507,0.166142,0.75553,0,0.119925,0.436127,0.136672,0.368967,2.64778,0.114756,0.0429404,0.171431,0.1265,0.426849,0.437326,0.100074,0.141803,0.160069,0.0904807,0.520292,0.156381,0.232812,0.0130875,0.0088637,0.068548,0.0355502,0.903344,0.0319888,1.82095,0.0214762,0.086399,0.35278,0.00226759,0.183419,0.28339,0.269815,0.640961,0.14583,0.111346,0.824909,0.141435,0.267037,0.279316,0.172691,0.701269,0.134193,0.5416,0.68674,0.4916,0.228818,0.131006,0.105975,0.0486964,0.125874,0.381373,0.678485,0.484984,0.548445,0.0345153,0.596798,0.000845264,0.303448,0.00822345,0.0749232,0.828184,0.570522,0.911492,0.346931,0.60382,0.128756,0.492355,1.15897,0.223497,5.30506e-06,0.0237433,0.483918,0.0853783,0.827384,0.437166,0.643288,0.18296,0.316172,0.0174681,1.55224,0.548727,0.184657,0.0834273,0.16899,1.34641,0.175139,0.254967,0.727656,0.72534,0.0213932,0.141674,0.790947,0.0313293,0.00516177,0.138761,0.256193,0.194611,0.0298842,0.442923,0.163895,0.0012246,0.202643,0.767927,0.560911,0.307398,0.318909,0.430184,0.269363,1.22337,0.155933,1.02771,0.178891,0.380184,0.970977,0.243403,0.0726333,1.67666,0.41462,0.460694,0.040681,0.156161,0.0948934,0.420518,1.17879,0.797769,0.385076,0.787631,0.535494,0.350107,0.444986,0.287001,1.14035,0.158909,0.0361124,0.102243,1.87805e-06,0.739242,0.272261,0.727249,0.327312,1.25519,0.229702,0.143819,0.0119463,0.428211,0.634307,0.156184,0.279093,0.345963,0.0469065,0.390556,0.604303,0.00135716
}}
}}

Revision as of 17:56, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128377739..128377750,+p@chr10:128377739..128377750
+
Mm9::chr10:22026200..22026224,-p@chr10:22026200..22026224
-
Mm9::chr10:43549000..43549003,-p@chr10:43549000..43549003
-
Mm9::chr11:100471383..100471386,-p@chr11:100471383..100471386
-
Mm9::chr11:97149062..97149066,-p@chr11:97149062..97149066
-
Mm9::chr14:122329986..122330017,+p@chr14:122329986..122330017
+
Mm9::chr14:53414794..53414801,+p3@ENSMUST00000103582
Mm9::chr14:54565684..54565697,+p1@ENSMUST00000103677
Mm9::chr14:71175978..71175985,+p9@Dok2
Mm9::chr14:71176029..71176038,+p7@Dok2
Mm9::chr17:34084925..34084953,+p@chr17:34084925..34084953
+
Mm9::chr19:57552085..57552092,+p@chr19:57552085..57552092
+
Mm9::chr1:133057843..133057865,+p@chr1:133057843..133057865
+
Mm9::chr1:138477131..138477139,-p@chr1:138477131..138477139
-
Mm9::chr2:101832120..101832141,+p@chr2:101832120..101832141
+
Mm9::chr2:101832319..101832329,+p@chr2:101832319..101832329
+
Mm9::chr2:113669745..113669761,-p5@Scg5
Mm9::chr2:113669769..113669796,-p4@Scg5
Mm9::chr2:113669799..113669833,-p@chr2:113669799..113669833
-
Mm9::chr2:113669834..113669842,-p@chr2:113669834..113669842
-
Mm9::chr2:113972833..113972839,-p@chr2:113972833..113972839
-
Mm9::chr2:165355616..165355619,+p@chr2:165355616..165355619
+
Mm9::chr3:101054539..101054542,-p@chr3:101054539..101054542
-
Mm9::chr3:115677249..115677254,-p@chr3:115677249..115677254
-
Mm9::chr3:39878658..39878665,+p@chr3:39878658..39878665
+
Mm9::chr3:39878699..39878707,+p@chr3:39878699..39878707
+
Mm9::chr3:88992242..88992250,+p@chr3:88992242..88992250
+
Mm9::chr4:116864706..116864725,-p@chr4:116864706..116864725
-
Mm9::chr4:129252879..129252895,+p@chr4:129252879..129252895
+
Mm9::chr4:133674504..133674520,+p@chr4:133674504..133674520
+
Mm9::chr4:154310054..154310101,+p@chr4:154310054..154310101
+
Mm9::chr4:154310687..154310708,-p@chr4:154310687..154310708
-
Mm9::chr4:154310712..154310719,-p@chr4:154310712..154310719
-
Mm9::chr4:154339181..154339210,+p@chr4:154339181..154339210
+
Mm9::chr4:32336248..32336285,+p@chr4:32336248..32336285
+
Mm9::chr5:124713399..124713426,-p4@Mphosph9
Mm9::chr5:150261363..150261373,+p@chr5:150261363..150261373
+
Mm9::chr5:22608195..22608205,+p@chr5:22608195..22608205
+
Mm9::chr5:22608207..22608231,+p@chr5:22608207..22608231
+
Mm9::chr6:146419239..146419243,-p@chr6:146419239..146419243
-
Mm9::chr6:147048074..147048100,+p@chr6:147048074..147048100
+
Mm9::chr6:30252614..30252619,-p@chr6:30252614..30252619
-
Mm9::chr6:48658262..48658273,-p4@Gimap6
Mm9::chr7:104095384..104095412,+p@chr7:104095384..104095412
+
Mm9::chr7:132695647..132695690,-p@chr7:132695647..132695690
-
Mm9::chr7:146420479..146420501,-p@chr7:146420479..146420501
-
Mm9::chr7:75474130..75474170,+p@chr7:75474130..75474170
+
Mm9::chr8:127240594..127240606,-p@chr8:127240594..127240606
-
Mm9::chr8:127240635..127240642,-p@chr8:127240635..127240642
-
Mm9::chr8:14997000..14997016,+p@chr8:14997000..14997016
+
Mm9::chr8:32225510..32225535,+p@chr8:32225510..32225535
+
Mm9::chr8:35209414..35209421,+p@chr8:35209414..35209421
+
Mm9::chr8:35218506..35218510,+p@chr8:35218506..35218510
+
Mm9::chr8:35219934..35219939,+p@chr8:35219934..35219939
+
Mm9::chr9:104756787..104756804,+p@chr9:104756787..104756804
+
Mm9::chr9:44807022..44807033,-p@chr9:44807022..44807033
-
Mm9::chr9:96250310..96250314,-p@chr9:96250310..96250314
-


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:0005069transmembrane receptor protein tyrosine kinase docking protein activity0.0164352041704131
GO:0016486peptide hormone processing0.0219100036200702
GO:0005066transmembrane receptor protein tyrosine kinase signaling protein activity0.0219100036200702
GO:0005158insulin receptor binding0.02669915869116
GO:0046883regulation of hormone secretion0.0328541996086636
GO:0030141secretory granule0.0474144436780716
GO:0046879hormone secretion0.0474144436780716
GO:0032403protein complex binding0.0474144436780716
GO:0051046regulation of secretion0.0474144436780716



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
CD4-positive, alpha-beta T cell4.06e-318
mature alpha-beta T cell1.06e-279
alpha-beta T cell1.06e-279
immature T cell1.06e-279
mature T cell1.06e-279
immature alpha-beta T cell1.06e-279
thymocyte9.31e-276
double negative thymocyte9.31e-276
naive T cell9.31e-276
double-positive, alpha-beta thymocyte9.31e-276
CD4-positive, alpha-beta thymocyte9.31e-276
naive thymus-derived CD4-positive, alpha-beta T cell9.31e-276
DN4 thymocyte9.31e-276
DN1 thymic pro-T cell9.31e-276
DN2 thymocyte9.31e-276
DN3 thymocyte9.31e-276
immature single positive thymocyte9.31e-276
early T lineage precursor9.31e-276
mature CD4 single-positive thymocyte9.31e-276
resting double-positive thymocyte9.31e-276
double-positive blast9.31e-276
CD69-positive double-positive thymocyte9.31e-276
CD69-positive, CD4-positive single-positive thymocyte9.31e-276
CD4-positive, CD8-intermediate double-positive thymocyte9.31e-276
CD24-positive, CD4 single-positive thymocyte9.31e-276
T cell1.01e-2211
pro-T cell1.01e-2211
lymphoid lineage restricted progenitor cell7.46e-2112
lymphocyte2.86e-1913
common lymphoid progenitor2.86e-1913
nucleate cell1.06e-1516
leukocyte8.61e-1517
nongranular leukocyte8.61e-1517
regulatory T cell2.31e-111
CD4-positive, CD25-positive, alpha-beta regulatory T cell2.31e-111
hematopoietic lineage restricted progenitor cell4.14e-1025
hematopoietic cell6.42e-0832
hematopoietic oligopotent progenitor cell6.42e-0832
hematopoietic stem cell6.42e-0832
angioblastic mesenchymal cell6.42e-0832
hematopoietic multipotent progenitor cell6.42e-0832

Uber Anatomy
Ontology termp-valuen
thymus1.33e-2023
neck1.33e-2023
respiratory system epithelium1.33e-2023
hemolymphoid system gland1.33e-2023
pharyngeal epithelium1.33e-2023
thymic region1.33e-2023
pharyngeal gland1.33e-2023
entire pharyngeal arch endoderm1.33e-2023
thymus primordium1.33e-2023
early pharyngeal endoderm1.33e-2023
pharynx9.61e-2024
gland of gut9.61e-2024
upper respiratory tract9.61e-2024
chordate pharynx9.61e-2024
pharyngeal arch system9.61e-2024
pharyngeal region of foregut9.61e-2024
segment of respiratory tract1.52e-1727
hemopoietic organ2.49e-1629
immune organ2.49e-1629
mixed endoderm/mesoderm-derived structure1.63e-1335
organ segment1.63e-1335
craniocervical region3.91e-1336
respiratory tract1.63e-1141
respiratory system3.09e-1142
anterior region of body5.69e-1143
hematopoietic system1.78e-1045
blood island1.78e-1045
hemolymphoid system8.28e-1048
immune system8.28e-1048
gut epithelium1.57e-0855
endocrine gland8.45e-0860
gland3.53e-0765
unilaminar epithelium4.59e-0766
endo-epithelium9.58e-0769


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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