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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=-0.

Latest revision as of 14:51, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:116719441..116719449,-p5@Lyz2
Mm9::chr11:106612556..106612565,+p2@Gm885
Mm9::chr11:70465698..70465709,-p@chr11:70465698..70465709
-
Mm9::chr11:79329880..79329914,-p@chr11:79329880..79329914
-
Mm9::chr11:79344004..79344015,-p8@Evi2b
Mm9::chr12:99497549..99497570,-p1@Galc
Mm9::chr13:20886081..20886092,+p5@Aoah
Mm9::chr15:103140833..103140844,-p2@Gpr84
Mm9::chr15:82861537..82861541,-p@chr15:82861537..82861541
-
Mm9::chr16:23610048..23610085,+p2@Rtp4
Mm9::chr16:23610086..23610118,+p@chr16:23610086..23610118
+
Mm9::chr16:44765845..44765864,+p2@Cd200r1
Mm9::chr16:44765866..44765941,+p1@Cd200r1
Mm9::chr17:35325372..35325391,-p1@Lst1
Mm9::chr17:56092139..56092148,+p4@Ebi3
Mm9::chr17:56092167..56092181,+p2@Ebi3
Mm9::chr17:84525339..84525380,-p@chr17:84525339..84525380
-
Mm9::chr1:154655035..154655046,+p6@Ncf2
Mm9::chr1:173319312..173319328,+p5@Arhgap30
Mm9::chr1:173769846..173769862,+p3@Cd84
Mm9::chr1:37457213..37457217,+p@chr1:37457213..37457217
+
Mm9::chr2:46215961..46215962,-p@chr2:46215961..46215962
-
Mm9::chr2:68699167..68699211,+p3@Lass6
Mm9::chr2:90922519..90922544,+p6@Sfpi1
Mm9::chr2:90922554..90922575,+p4@Sfpi1
Mm9::chr4:132120098..132120125,+p1@Ptafr
Mm9::chr4:3717538..3717542,+p@chr4:3717538..3717542
+
Mm9::chr4:66488733..66488757,+p5@Tlr4
Mm9::chr5:121227637..121227673,-p1@Oas3
Mm9::chr5:76569323..76569342,+p1@Srd5a3
Mm9::chr6:114593128..114593191,+p1@Atg7
p1@LOC100043926
Mm9::chr6:121286818..121286868,+p@chr6:121286818..121286868
+
Mm9::chr6:123073441..123073502,+p3@Clec4a2
Mm9::chr6:123212179..123212203,+p1@Clec4d
Mm9::chr6:123237055..123237057,-p@chr6:123237055..123237057
-
Mm9::chr6:123239835..123239844,-p2@Clec4e
Mm9::chr6:129300221..129300228,+p7@Clec12a
Mm9::chr6:129300300..129300315,+p1@Clec12a
Mm9::chr6:129300327..129300349,+p2@Clec12a
Mm9::chr6:17587059..17587120,+p1@Capza2
Mm9::chr7:128213183..128213188,-p@chr7:128213183..128213188
-
Mm9::chr7:19856925..19856938,-p2@Vasp
Mm9::chr7:3849731..3849744,-p1@Gm14548
p1@Gm15448
p1@Pira11
p1@Pira1
p1@Pira2
p1@Pira4
p1@Pira7
p2@Pira6
Mm9::chr7:87857077..87857081,-p@chr7:87857077..87857081
-
Mm9::chr9:32230510..32230514,-p@chr9:32230510..32230514
-
Mm9::chr9:59414313..59414315,+p@chr9:59414313..59414315
+
Mm9::chr9:66682466..66682484,-p1@Aph1c
Mm9::chrX:103338538..103338553,+p2@Tlr13
Mm9::chrX:103338582..103338641,+p1@Tlr13
Mm9::chrX:163702212..163702223,-p2@Tlr8
Mm9::chrX:9014167..9014180,-p@chrX:9014167..9014180
-


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:0006955immune response0.000339467542868089
GO:0002376immune system process0.000342132608125612
GO:0006954inflammatory response0.00323510684176256
GO:0009605response to external stimulus0.00787571199319539
GO:0009611response to wounding0.00913578151368008
GO:0005529sugar binding0.0181757919188123
GO:0045087innate immune response0.0275297211417301
GO:0030246carbohydrate binding0.0275297211417301
GO:0002274myeloid leukocyte activation0.0275297211417301
GO:0006950response to stress0.0275297211417301
GO:0008064regulation of actin polymerization and/or depolymerization0.0275297211417301
GO:0030832regulation of actin filament length0.0275297211417301
GO:0032535regulation of cellular component size0.0275297211417301
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0275297211417301
GO:0051493regulation of cytoskeleton organization and biogenesis0.0275297211417301
GO:0033043regulation of organelle organization and biogenesis0.0275297211417301
GO:0042222interleukin-1 biosynthetic process0.0275297211417301
GO:0050528acyloxyacyl hydrolase activity0.0275297211417301
GO:0006683galactosylceramide catabolic process0.0275297211417301
GO:0045360regulation of interleukin-1 biosynthetic process0.0275297211417301
GO:0045368positive regulation of interleukin-13 biosynthetic process0.0275297211417301
GO:0004336galactosylceramidase activity0.0275297211417301
GO:0042989sequestering of actin monomers0.0275297211417301
GO:0045362positive regulation of interleukin-1 biosynthetic process0.0275297211417301
GO:0030837negative regulation of actin filament polymerization0.0275297211417301
GO:0045366regulation of interleukin-13 biosynthetic process0.0275297211417301
GO:0004992platelet activating factor receptor activity0.0275297211417301
GO:0019376galactolipid catabolic process0.0275297211417301
GO:0008154actin polymerization and/or depolymerization0.031627873146193
GO:0030036actin cytoskeleton organization and biogenesis0.031627873146193
GO:0001843neural tube closure0.0342124694877948
GO:0030029actin filament-based process0.0351636572778514
GO:0014020primary neural tube formation0.0351636572778514
GO:0004872receptor activity0.0394984521570506
GO:0045523interleukin-27 receptor binding0.0394984521570506
GO:0042231interleukin-13 biosynthetic process0.0394984521570506
GO:0032616interleukin-13 production0.0394984521570506
GO:0046477glycosylceramide catabolic process0.0394984521570506
GO:0032612interleukin-1 production0.0394984521570506
GO:0051128regulation of cellular component organization and biogenesis0.0398073138868076
GO:0001841neural tube formation0.0398073138868076
GO:0001839neural plate morphogenesis0.0398073138868076
GO:0001840neural plate development0.0398073138868076
GO:0001838embryonic epithelial tube formation0.0398073138868076
GO:0031175neurite development0.0398073138868076
GO:0044425membrane part0.0398073138868076
GO:0006952defense response0.0398073138868076
GO:0016021integral to membrane0.0398073138868076
GO:0031224intrinsic to membrane0.0398073138868076
GO:0016337cell-cell adhesion0.0398073138868076
GO:0021860pyramidal neuron development0.0398073138868076
GO:0019374galactolipid metabolic process0.0398073138868076
GO:0006681galactosylceramide metabolic process0.0398073138868076
GO:0019364pyridine nucleotide catabolic process0.0398073138868076
GO:0006742NADP catabolic process0.0398073138868076
GO:0021859pyramidal neuron differentiation0.0398073138868076
GO:0042365water-soluble vitamin catabolic process0.0398073138868076
GO:0009111vitamin catabolic process0.0398073138868076
GO:0021915neural tube development0.0404889957359714
GO:0048666neuron development0.0420419331167892
GO:0051248negative regulation of protein metabolic process0.0426313595960248
GO:0004871signal transducer activity0.0426313595960248
GO:0060089molecular transducer activity0.0426313595960248
GO:0051246regulation of protein metabolic process0.0439426826011918
GO:0016331morphogenesis of embryonic epithelium0.0439426826011918
GO:0046521sphingoid catabolic process0.0439426826011918
GO:0031401positive regulation of protein modification process0.0439426826011918
GO:0016175superoxide-generating NADPH oxidase activity0.0439426826011918
GO:0050664oxidoreductase activity, acting on NADH or NADPH, with oxygen as acceptor0.0439426826011918
GO:0046514ceramide catabolic process0.0439426826011918
GO:0003779actin binding0.0473986571630735
GO:0019903protein phosphatase binding0.0486320536389916
GO:0019377glycolipid catabolic process0.0486320536389916
GO:0006677glycosylceramide metabolic process0.0486320536389916
GO:0021884forebrain neuron development0.0486320536389916
GO:0007250activation of NF-kappaB-inducing kinase0.0486320536389916
GO:0031396regulation of protein ubiquitination0.0486320536389916
GO:0004839ubiquitin activating enzyme activity0.0486320536389916
GO:0008290F-actin capping protein complex0.0486320536389916



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
bone element9.43e-1022
skeletal element9.43e-1022
skeletal system9.43e-1022
bone marrow1.76e-0916
musculoskeletal system1.46e-0832
hemolymphoid system2.30e-0848
immune system2.30e-0848
hematopoietic system2.76e-0845
blood island2.76e-0845


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)
MA0003.10.00594608
MA0004.10.103083
MA0006.10.0630352
MA0007.10.230767
MA0009.10.626825
MA0014.10.00109387
MA0017.10.333164
MA0019.10.366735
MA0024.10.191846
MA0025.10.389923
MA0027.11.7166
MA0028.10.159126
MA0029.10.178556
MA0030.10.537862
MA0031.10.486239
MA0038.10.505651
MA0040.10.646226
MA0041.10.789433
MA0042.11.04388
MA0043.10.286348
MA0046.10.243748
MA0048.10.11092
MA0050.12.25681
MA0051.11.86627
MA0052.10.233385
MA0055.10.00834441
MA0056.10
MA0057.10.0474366
MA0058.10.266397
MA0059.10.758219
MA0060.10.115486
MA0061.10.646624
MA0063.10
MA0066.10.222826
MA0067.10.480655
MA0068.10.00367073
MA0069.10.233612
MA0070.10.644206
MA0071.10.570233
MA0072.10.221558
MA0073.19.59247e-05
MA0074.10.416262
MA0076.10.0346709
MA0077.10.597811
MA0078.10.590813
MA0081.13.5587
MA0083.10.285777
MA0084.10.771136
MA0087.10.255344
MA0088.10.0140065
MA0089.10
MA0090.10.203942
MA0091.12.60031
MA0092.11.3376
MA0093.10.0773728
MA0095.10
MA0098.10
MA0100.10.175296
MA0101.10.308279
MA0103.10.360915
MA0105.10.461948
MA0106.10.0860259
MA0107.10.344976
MA0108.20.125899
MA0109.10
MA0111.10.089074
MA0113.10.932684
MA0114.10.160957
MA0115.10.785414
MA0116.10.0197865
MA0117.10.2654
MA0119.10.153729
MA0122.10.765119
MA0124.10.436557
MA0125.10.377128
MA0130.10
MA0131.10.36088
MA0132.10
MA0133.10
MA0135.10.312969
MA0136.11.20246
MA0139.10.0326105
MA0140.11.07988
MA0141.10.644982
MA0142.10.465684
MA0143.10.276987
MA0144.10.166521
MA0145.10.0381028
MA0146.10.000540238
MA0147.10.189638
MA0148.10.115196
MA0149.10.817527
MA0062.20.140963
MA0035.20.403512
MA0039.20.000723977
MA0138.20.108256
MA0002.20.97155
MA0137.20.0380226
MA0104.20.176484
MA0047.20.233733
MA0112.20.176376
MA0065.20.115284
MA0150.10.713794
MA0151.10
MA0152.10.0657833
MA0153.10.325381
MA0154.10.858671
MA0155.10.0135555
MA0156.11.53643
MA0157.10.421328
MA0158.10
MA0159.11.33859
MA0160.10.117517
MA0161.10
MA0162.10.000165977
MA0163.10.0157091
MA0164.10.206602
MA0080.20.804628
MA0018.20.0598662
MA0099.20.698339
MA0079.23.54578e-10
MA0102.23.18521
MA0258.10.137714
MA0259.10.0339619
MA0442.10
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