Personal tools

MCL coexpression mm9:94: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:
{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=-0

Latest revision as of 14:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:115712547..115712560,+p5@Ptprb
Mm9::chr10:126952216..126952224,+p@chr10:126952216..126952224
+
Mm9::chr10:60846080..60846120,-p1@X99384
Mm9::chr10:62128117..62128140,-p@chr10:62128117..62128140
-
Mm9::chr10:92773591..92773623,-p1@Elk3
Mm9::chr11:101107719..101107736,+p1@Ramp2
Mm9::chr11:106243868..106243926,-p1@Icam2
Mm9::chr11:106576565..106576607,-p1@Pecam1
Mm9::chr11:115673450..115673544,-p@chr11:115673450..115673544
-
Mm9::chr11:115674877..115674907,-p1@Caskin2
Mm9::chr11:68770375..68770411,-p1@Arhgef15
Mm9::chr11:68770477..68770496,+p@chr11:68770477..68770496
+
Mm9::chr11:68770947..68770987,-p2@Arhgef15
Mm9::chr11:70043257..70043263,-p1@Bcl6b
Mm9::chr11:78748924..78748935,+p@chr11:78748924..78748935
+
Mm9::chr11:86829486..86829491,+p@chr11:86829486..86829491
+
Mm9::chr11:87029962..87029983,+p@chr11:87029962..87029983
+
Mm9::chr11:95703768..95703797,-p3@Abi3
Mm9::chr11:95704038..95704053,+p4@Gngt2
Mm9::chr12:118896496..118896518,+p@chr12:118896496..118896518
+
Mm9::chr12:59369590..59369620,-p@chr12:59369590..59369620
-
Mm9::chr12:59369827..59369893,-p1@Clec14a
Mm9::chr12:59369917..59369930,-p2@Clec14a
Mm9::chr12:59370149..59370174,-p3@Clec14a
Mm9::chr12:74685221..74685232,+p@chr12:74685221..74685232
+
Mm9::chr13:114584854..114584879,+p3@Arl15
Mm9::chr13:115891766..115891781,-p9@Itga1
Mm9::chr13:115891826..115891864,-p3@Itga1
Mm9::chr13:38442078..38442081,+p@chr13:38442078..38442081
+
Mm9::chr13:99954640..99954681,+p1@Zfp366
Mm9::chr13:99954688..99954710,+p2@Zfp366
Mm9::chr14:102222288..102222307,+p@chr14:102222288..102222307
+
Mm9::chr14:56402844..56402856,-p2@Adcy4
Mm9::chr14:56402864..56402910,-p1@Adcy4
Mm9::chr14:56402955..56403017,+p@chr14:56402955..56403017
+
Mm9::chr14:64562503..64562524,+p1@Sox7
Mm9::chr15:79227251..79227274,-p@chr15:79227251..79227274
-
Mm9::chr15:79227292..79227309,-p@chr15:79227292..79227309
-
Mm9::chr15:83000598..83000616,-p4@Cyb5r3
Mm9::chr15:89328390..89328399,+p@chr15:89328390..89328399
+
Mm9::chr15:89328414..89328425,+p@chr15:89328414..89328425
+
Mm9::chr15:89328433..89328443,+p@chr15:89328433..89328443
+
Mm9::chr15:89328444..89328477,+p@chr15:89328444..89328477
+
Mm9::chr15:89328479..89328500,+p@chr15:89328479..89328500
+
Mm9::chr16:38713118..38713129,-p10@Arhgap31
Mm9::chr16:85550631..85550647,-p1@Cyyr1
Mm9::chr16:85550669..85550677,-p2@Cyyr1
Mm9::chr16:94549999..94550018,+p2@Ripply3
Mm9::chr16:94550031..94550046,+p1@Ripply3
Mm9::chr17:24776906..24776950,+p@chr17:24776906..24776950
+
Mm9::chr17:24781964..24781973,-p5@Slc9a3r2
Mm9::chr17:24787215..24787256,-p1@Slc9a3r2
Mm9::chr17:25218083..25218146,-p1@Tmem204
Mm9::chr17:34701240..34701244,+p5@Notch4
Mm9::chr17:34701245..34701264,+p1@Notch4
Mm9::chr17:34701278..34701288,+p3@Notch4
Mm9::chr17:34701291..34701305,+p2@Notch4
Mm9::chr17:34701318..34701330,+p4@Notch4
Mm9::chr17:43497271..43497285,+p@chr17:43497271..43497285
+
Mm9::chr17:43497335..43497358,+p@chr17:43497335..43497358
+
Mm9::chr17:43497372..43497405,+p@chr17:43497372..43497405
+
Mm9::chr17:43526385..43526446,+p1@Gpr116
Mm9::chr17:43526450..43526462,+p4@Gpr116
Mm9::chr17:75835226..75835277,+p1@Rasgrp3
Mm9::chr18:32096924..32096942,+p@chr18:32096924..32096942
+
Mm9::chr18:35881965..35881981,-p2@Ecscr
Mm9::chr18:35881984..35882035,-p1@Ecscr
Mm9::chr18:38157182..38157194,-p3@Arap3
Mm9::chr18:38157197..38157223,-p2@Arap3
Mm9::chr18:38444045..38444062,-p1@Pcdh12
Mm9::chr18:44761374..44761391,-p@chr18:44761374..44761391
-
Mm9::chr18:61946290..61946345,-p1@Afap1l1
Mm9::chr1:10983533..10983559,+p2@Prex2
Mm9::chr1:10983563..10983701,+p1@Prex2
Mm9::chr1:4486505..4486527,-p5@Sox17
Mm9::chr1:54035355..54035374,-p@chr1:54035355..54035374
-
Mm9::chr2:119151549..119151553,+p1@Dll4
Mm9::chr2:130953128..130953197,+p1@Hspa12b
Mm9::chr2:145611996..145612010,+p4@Rin2
Mm9::chr2:145612015..145612043,+p3@Rin2
Mm9::chr2:148229675..148229678,-p@chr2:148229675..148229678
-
Mm9::chr2:148233842..148233863,-p1@Thbd
Mm9::chr2:151369692..151369745,+p@chr2:151369692..151369745
+
Mm9::chr2:152891724..152891735,+p1@BC020535
Mm9::chr2:181406327..181406350,-p1@Sox18
Mm9::chr2:26439378..26439394,+p1@Egfl7
Mm9::chr2:32583202..32583232,+p1@Sh2d3c
Mm9::chr2:35288072..35288143,-p3@Ggta1
Mm9::chr2:73559995..73560026,-p@chr2:73559995..73560026
-
Mm9::chr3:121603454..121603482,-p@chr3:121603454..121603482
-
Mm9::chr3:121656244..121656263,+p3@Arhgap29
Mm9::chr3:89635274..89635306,+p1@She
Mm9::chr3:89635317..89635328,+p2@She
Mm9::chr4:118162366..118162382,-p1@Tie1
Mm9::chr4:118162394..118162436,-p2@Tie1
Mm9::chr4:126991224..126991242,-p1@Gja4
Mm9::chr4:133809991..133810043,-p1@Grrp1
Mm9::chr4:137476659..137476676,+p8@Ece1
Mm9::chr4:137476697..137476745,+p2@Ece1
Mm9::chr4:151470845..151470891,+p2@Plekhg5
Mm9::chr4:62280682..62280703,+p10@Rgs3
Mm9::chr4:62280716..62280753,+p3@Rgs3
Mm9::chr4:62280754..62280774,+p6@Rgs3
Mm9::chr4:94405967..94405989,+p3@Tek
Mm9::chr4:94406139..94406146,+p8@Tek
Mm9::chr4:94406153..94406175,+p2@Tek
Mm9::chr5:112717754..112717788,+p2@Tpst2
Mm9::chr5:23870622..23870642,+p1@Nos3
Mm9::chr5:76374472..76374488,-p1@Kdr
Mm9::chr6:17231216..17231227,+p3@Cav2
Mm9::chr6:17231304..17231364,+p1@Cav2
Mm9::chr6:91928951..91928977,+p2@Fgd5
Mm9::chr6:92431158..92431208,-p5@Prickle2
Mm9::chr7:134027479..134027514,-p@chr7:134027479..134027514
-
Mm9::chr7:148647627..148647656,+p2@Efcab4a
Mm9::chr7:150295132..150295160,+p4@Kcnq1
Mm9::chr7:46799790..46799822,+p@chr7:46799790..46799822
+
Mm9::chr7:52882852..52882863,+p2@Rasip1
Mm9::chr7:52882872..52882902,+p1@Rasip1
Mm9::chr8:108137126..108137143,+p@chr8:108137126..108137143
+
Mm9::chr8:108137146..108137166,+p@chr8:108137146..108137166
+
Mm9::chr8:28217914..28217952,-p@chr8:28217914..28217952
-
Mm9::chr8:37676912..37676943,-p3@A730069N07Rik
p3@Dlc1
Mm9::chr8:37676944..37676975,-p1@A730069N07Rik
p1@Dlc1
Mm9::chr8:37676991..37677002,-p6@A730069N07Rik
p6@Dlc1
Mm9::chr8:42127023..42127030,-p8@Mtus1
Mm9::chr8:73919693..73919720,-p1@Ushbp1
Mm9::chr8:73919730..73919739,-p2@Ushbp1
Mm9::chr9:107469198..107469228,-p@chr9:107469198..107469228
-
Mm9::chr9:118515805..118515869,+p1@Itga9
Mm9::chr9:121807527..121807541,+p1@Ccbp2
Mm9::chr9:121807576..121807584,+p2@Ccbp2
Mm9::chr9:37335656..37335733,+p1@Esam
Mm9::chr9:48122507..48122526,+p@chr9:48122507..48122526
+
Mm9::chr9:63862840..63862842,-p@chr9:63862840..63862842
-
Mm9::chrX:6154377..6154412,+p2@Shroom4


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:0001525angiogenesis2.64970444448411e-07
GO:0001568blood vessel development2.64970444448411e-07
GO:0001944vasculature development2.64970444448411e-07
GO:0048514blood vessel morphogenesis7.68267412900292e-07
GO:0048646anatomical structure formation1.15816321019475e-06
GO:0030334regulation of cell migration1.75991235573691e-06
GO:0051270regulation of cell motility3.27871066159407e-06
GO:0040012regulation of locomotion4.28166690385124e-06
GO:0016477cell migration1.73105689814255e-05
GO:0030695GTPase regulator activity2.82126103631599e-05
GO:0006928cell motility5.42941595411039e-05
GO:0051674localization of cell5.42941595411039e-05
GO:0001570vasculogenesis0.000104605505114981
GO:0009887organ morphogenesis0.000208432256221841
GO:0007266Rho protein signal transduction0.000251837197467868
GO:0007265Ras protein signal transduction0.00035974989084525
GO:0030336negative regulation of cell migration0.00039999458665454
GO:0007264small GTPase mediated signal transduction0.00046830674708023
GO:0007242intracellular signaling cascade0.000499921987789595
GO:0005886plasma membrane0.000499921987789595
GO:0051271negative regulation of cell motility0.000719006685210945
GO:0040013negative regulation of locomotion0.000792956971360994
GO:0007165signal transduction0.000792956971360994
GO:0007154cell communication0.000801955348402792
GO:0005085guanyl-nucleotide exchange factor activity0.00112529569665157
GO:0005083small GTPase regulator activity0.00308498417294489
GO:0009653anatomical structure morphogenesis0.00519796578704105
GO:0045446endothelial cell differentiation0.0093711924225644
GO:0048856anatomical structure development0.0119143106461027
GO:0050794regulation of cellular process0.0121106230981079
GO:0051056regulation of small GTPase mediated signal transduction0.0133648339015022
GO:0009966regulation of signal transduction0.0133648339015022
GO:0007275multicellular organismal development0.0133648339015022
GO:0065007biological regulation0.0133648339015022
GO:0035023regulation of Rho protein signal transduction0.0133893416143907
GO:0005100Rho GTPase activator activity0.0146130059143952
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0147484590382442
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0165880198089054
GO:0007160cell-matrix adhesion0.0169306529174035
GO:0048513organ development0.0169465815918363
GO:0050789regulation of biological process0.0182255107439308
GO:0031589cell-substrate adhesion0.0187864104115868
GO:0048731system development0.0194999062713668
GO:0005096GTPase activator activity0.0199902578160445
GO:0019199transmembrane receptor protein kinase activity0.0224436331355046
GO:0042060wound healing0.0275221362160585
GO:0044459plasma membrane part0.0333316775834401
GO:0047276N-acetyllactosaminide 3-alpha-galactosyltransferase activity0.0355733437042172
GO:0045602negative regulation of endothelial cell differentiation0.0355733437042172
GO:0022610biological adhesion0.0355733437042172
GO:0007155cell adhesion0.0355733437042172
GO:0032502developmental process0.0398278839144057
GO:0045765regulation of angiogenesis0.0456072135681949
GO:0046578regulation of Ras protein signal transduction0.0456072135681949
GO:0008047enzyme activator activity0.0456072135681949
GO:0016337cell-cell adhesion0.049659269781546



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
trunk region element2.07e-1279
subdivision of trunk2.70e-1066
multi-cellular organism2.83e-10333
lung1.70e-0914
respiratory tube1.70e-0914
respiration organ1.70e-0914
pair of lungs1.70e-0914
lung primordium1.70e-0914
lung bud1.70e-0914
epithelial bud1.09e-0817
trunk2.08e-0890
compound organ1.36e-0743
primary circulatory organ2.70e-0718
heart2.70e-0718
primitive heart tube2.70e-0718
primary heart field2.70e-0718
anterior lateral plate mesoderm2.70e-0718
heart tube2.70e-0718
heart primordium2.70e-0718
cardiac mesoderm2.70e-0718
cardiogenic plate2.70e-0718
heart rudiment2.70e-0718
splanchnic layer of lateral plate mesoderm7.49e-0733


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)
MA0003.10.600676
MA0004.10.00158433
MA0006.10.00464364
MA0007.11.70768
MA0009.10.629859
MA0014.10.199952
MA0017.11.00611
MA0019.10.261892
MA0024.10.028807
MA0025.10.390807
MA0027.11.29761
MA0028.10.0300996
MA0029.10.481102
MA0030.10.109202
MA0031.10.219683
MA0038.10.223481
MA0040.10.0418392
MA0041.10.00150853
MA0042.10.00413342
MA0043.10.238085
MA0046.10.0481838
MA0048.10.46876
MA0050.10.0132847
MA0051.10.0164631
MA0052.10.168514
MA0055.10.064206
MA0056.10
MA0057.12.11941
MA0058.10.000917649
MA0059.10.00125306
MA0060.10.0108912
MA0061.14.90318
MA0063.10
MA0066.10.105542
MA0067.10.182337
MA0068.11.66883
MA0069.10.168797
MA0070.10.160809
MA0071.10.155767
MA0072.10.153993
MA0073.12.71312
MA0074.11.10196
MA0076.10.00556072
MA0077.10.585157
MA0078.10.485861
MA0081.11.83577
MA0083.10.237299
MA0084.10.408533
MA0087.10.196506
MA0088.10.431234
MA0089.10
MA0090.10.0315507
MA0091.10.470619
MA0092.10.444952
MA0093.10.000183051
MA0095.10
MA0098.10
MA0100.10.00685885
MA0101.11.68045
MA0103.10.0262539
MA0105.11.43753
MA0106.10.508183
MA0107.12.61413
MA0108.20.510373
MA0109.10
MA0111.11.11501
MA0113.11.53144
MA0114.10.971512
MA0115.10.240867
MA0116.10.268082
MA0117.10.209741
MA0119.10.125749
MA0122.10.851741
MA0124.10.152851
MA0125.10.115971
MA0130.10
MA0131.10.122523
MA0132.10
MA0133.10
MA0135.10.27548
MA0136.10.936345
MA0139.10.262439
MA0140.14.63903
MA0141.10.038307
MA0142.10.017424
MA0143.10.0226832
MA0144.11.83896
MA0145.12.62341
MA0146.10.187015
MA0147.10.00922086
MA0148.10.124018
MA0149.11.74031
MA0062.20.0762592
MA0035.23.72224
MA0039.23.36499
MA0138.20.943749
MA0002.20.359927
MA0137.20.183623
MA0104.20.00126107
MA0047.20.0488019
MA0112.20.971407
MA0065.24.80491
MA0150.10.247441
MA0151.10
MA0152.10.0488552
MA0153.10.086951
MA0154.10.535995
MA0155.10.401593
MA0156.13.1833
MA0157.10.84219
MA0158.10
MA0159.10.720861
MA0160.10.0288367
MA0161.10
MA0162.10.0323715
MA0163.10.0251398
MA0164.10.938189
MA0080.23.29447
MA0018.20.0120387
MA0099.20.638028
MA0079.27.43744
MA0102.20.450252
MA0258.10.251981
MA0259.10.0793914
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:94&oldid=3072093"