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MCL coexpression mm9:169: Difference between revisions

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{{MCL_coexpression_mm9
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invagination;0.00968472649411227;56715,107817,13660!GO:0006897;endocytosis;0.00968472649411227;56715,107817,13660!GO:0016044;membrane organization and biogenesis;0.0169885790271681;56715,107817,13660!GO:0016070;RNA metabolic process;0.0239212496634755;67197,240263,12455,231386,12393,53317!GO:0043654;recognition of apoptotic cell;0.0242151975017805;107817!GO:0016192;vesicle-mediated transport;0.0345675601230205;56715,107817,13660!GO:0010467;gene expression;0.0345675601230205;67197,240263,12455,231386,12393,53317!GO:0003676;nucleic acid binding;0.0345675601230205;56715,67197,240263,12455,231386,12393!GO:0043283;biopolymer metabolic process;0.0345675601230205;56715,67197,240263,12455,231386,12393,53317!GO:0003677;DNA binding;0.0345675601230205;56715,240263,12455,231386,12393!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0345675601230205;67197,240263,12455,231386,12393,53317!GO:0043277;apoptotic cell clearance;0.0345675601230205;107817!GO:0045879;negative regulation of smoothened signaling pathway;0.0345675601230205;12393!GO:0040036;regulation of fibroblast growth factor receptor signaling pathway;0.0345675601230205;12393!GO:0005681;spliceosome;0.0355754810325557;67197,53317!GO:0042487;regulation of odontogenesis of dentine-containing teeth;0.0355754810325557;12393!GO:0017069;snRNA binding;0.0355754810325557;12455!GO:0005768;endosome;0.041610011908597;56715,13660!GO:0043231;intracellular membrane-bound organelle;0.041610011908597;56715,12455,13660,12393,67197,107817,231386,53317!GO:0043227;membrane-bound organelle;0.041610011908597;56715,12455,13660,12393,67197,107817,231386,53317!GO:0008380;RNA splicing;0.041610011908597;67197,53317!GO:0042116;macrophage activation;0.0439517138307661;107817!GO:0060041;retina development in camera-type eye;0.0453140336107808;107817!GO:0048821;erythrocyte 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|gostat_on_MCL_coexpression=GO:0010324;membrane invagination;0.00968472649411227;56715,107817,13660!GO:0006897;endocytosis;0.00968472649411227;56715,107817,13660!GO:0016044;membrane organization and biogenesis;0.0169885790271681;56715,107817,13660!GO:0016070;RNA metabolic process;0.0239212496634755;67197,240263,12455,231386,12393,53317!GO:0043654;recognition of apoptotic cell;0.0242151975017805;107817!GO:0016192;vesicle-mediated transport;0.0345675601230205;56715,107817,13660!GO:0010467;gene expression;0.0345675601230205;67197,240263,12455,231386,12393,53317!GO:0003676;nucleic acid binding;0.0345675601230205;56715,67197,240263,12455,231386,12393!GO:0043283;biopolymer metabolic process;0.0345675601230205;56715,67197,240263,12455,231386,12393,53317!GO:0003677;DNA binding;0.0345675601230205;56715,240263,12455,231386,12393!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0345675601230205;67197,240263,12455,231386,12393,53317!GO:0043277;apoptotic cell clearance;0.0345675601230205;107817!GO:0045879;negative regulation of smoothened signaling pathway;0.0345675601230205;12393!GO:0040036;regulation of fibroblast growth factor receptor signaling pathway;0.0345675601230205;12393!GO:0005681;spliceosome;0.0355754810325557;67197,53317!GO:0042487;regulation of odontogenesis of dentine-containing teeth;0.0355754810325557;12393!GO:0017069;snRNA binding;0.0355754810325557;12455!GO:0005768;endosome;0.041610011908597;56715,13660!GO:0043231;intracellular membrane-bound organelle;0.041610011908597;56715,12455,13660,12393,67197,107817,231386,53317!GO:0043227;membrane-bound organelle;0.041610011908597;56715,12455,13660,12393,67197,107817,231386,53317!GO:0008380;RNA splicing;0.041610011908597;67197,53317!GO:0042116;macrophage activation;0.0439517138307661;107817!GO:0060041;retina development in camera-type eye;0.0453140336107808;107817!GO:0048821;erythrocyte development;0.0453140336107808;107817!
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|ontology_enrichment_disease=DOID:0060100!1.10e-10!3;DOID:4045!1.10e-10!3
|ontology_enrichment_uberon=UBERON:0002384!2.00e-19!46
|tfbs_overrepresentation_for_novel_motifs=0.384457,0.050764,0.320797,0.497367,0.489945,0.318861,0.279401,0.0989363,0.191818,0.464989,0.681877,0.261624,0.0993275,0.547811,0.778225,0,0.317024,1.72511,0.314801,0.212242,0.126517,0.670783,0.124734,0.483517,0.187556,0.341878,0.28104,0.0151834,0.182492,0.414581,0.332498,0.4463,0.448156,0.135055,0.780931,0.041612,0.411396,0.480873,0.0636301,0.00500589,0.193883,0.342915,0.441818,0.244923,0.172939,0.270396,0.85033,0.203886,0.368089,0.320305,0.296491,0.38712,0.810015,0.651961,0.242015,0.893506,1.01555,0.243357,0.354757,0.560425,0.134763,0.179677,0.339502,0.283549,0.326871,0.100898,0.339144,0.628317,0.132335,0.50094,0.0209132,0.281504,0.00192321,0.264819,0.0229629,0.0173117,0.0804452,0.472455,0.125943,0.248986,0.957822,0.103457,0.178345,0.238905,0.555368,0.610478,0.0121857,0.415454,0.864392,0.775114,0.39287,0.562663,0.152396,0.346956,0.0598046,0.161221,0.252149,0.911885,0.494355,0.52521,0.270484,0.875212,0.625341,0.0883318,1.03261,0.0655268,0.114988,0.198718,0.137983,0.243974,0.579188,0.220281,0.0575553,0.698409,0.398434,0.310401,0.128014,0.0541975,0.0962078,0.0826641,0.268562,0.552073,0.621713,0.215585,0.441909,0.127819,0.12228,0.148677,0.338003,0.222181,0.208313,0.731795,0.847831,0.142018,0.415628,0.412566,0.633998,0.34578,0.376801,1.12381,0.745855,0.907449,0.653,0.15111,0.288491,0.575763,0.499807,1.08557,0.23484,0.333795,0.430172,0.00475197,0.231489,0.174379,0.32943,0.287477,0.0450698,0.615872,0.212864,0.109005,0.384222,0.554117,0.800957,0.2019,0.284712,0.135244,0.407061,0.780706,0.310387
|tfbs_overrepresentation_jaspar=MA0003.1;0.382646,MA0004.1;0.291955,MA0006.1;0.367556,MA0007.1;0.264348,MA0009.1;0.482714,MA0014.1;0.183094,MA0017.1;0.0855882,MA0019.1;0.254769,MA0024.1;0.136175,MA0025.1;0.840394,MA0027.1;1.61241,MA0028.1;0.811934,MA0029.1;0.787566,MA0030.1;0.128331,MA0031.1;0.110801,MA0038.1;0.341749,MA0040.1;0.167138,MA0041.1;0.0241609,MA0042.1;0.147987,MA0043.1;0.623818,MA0046.1;0.180835,MA0048.1;0.0907375,MA0050.1;0.612884,MA0051.1;0.356522,MA0052.1;0.985598,MA0055.1;0.139639,MA0056.1;0,MA0057.1;0.110069,MA0058.1;0.640728,MA0059.1;0.466773,MA0060.1;0.0166702,MA0061.1;2.7916,MA0063.1;0,MA0066.1;0.323968,MA0067.1;0.397426,MA0068.1;2.08096,MA0069.1;0.171998,MA0070.1;0.498463,MA0071.1;0.610326,MA0072.1;0.161558,MA0073.1;1.40865,MA0074.1;0.110954,MA0076.1;0.755089,MA0077.1;0.45654,MA0078.1;0.184832,MA0081.1;1.80401,MA0083.1;1.8244,MA0084.1;0.676467,MA0087.1;0.558334,MA0088.1;0.0330858,MA0089.1;0,MA0090.1;0.230817,MA0091.1;0.158194,MA0092.1;0.635077,MA0093.1;0.431087,MA0095.1;0,MA0098.1;0,MA0100.1;0.023969,MA0101.1;1.33174,MA0103.1;0.190019,MA0105.1;0.535708,MA0106.1;0.427153,MA0107.1;2.27124,MA0108.2;0.990877,MA0109.1;0,MA0111.1;0.443356,MA0113.1;1.04309,MA0114.1;0.125162,MA0115.1;0.220288,MA0116.1;0.229425,MA0117.1;0.199875,MA0119.1;0.168873,MA0122.1;1.79376,MA0124.1;0.35604,MA0125.1;0.300895,MA0130.1;0,MA0131.1;0.909841,MA0132.1;0,MA0133.1;0,MA0135.1;0.24238,MA0136.1;2.19346,MA0139.1;0.671048,MA0140.1;0.76358,MA0141.1;0.0503163,MA0142.1;0.339483,MA0143.1;0.406106,MA0144.1;0.0294811,MA0145.1;0.114255,MA0146.1;0.383724,MA0147.1;0.254714,MA0148.1;0.32325,MA0149.1;0.00459441,MA0062.2;2.51332,MA0035.2;0.77919,MA0039.2;1.40988,MA0138.2;0.241368,MA0002.2;0.375398,MA0137.2;0.370774,MA0104.2;0.309103,MA0047.2;0.0371401,MA0112.2;0.419552,MA0065.2;0.823415,MA0150.1;3.14294,MA0151.1;0,MA0152.1;0.146996,MA0153.1;0.705792,MA0154.1;0.516824,MA0155.1;0.547511,MA0156.1;3.30852,MA0157.1;0.0897789,MA0158.1;0,MA0159.1;1.98864,MA0160.1;0.554176,MA0161.1;0,MA0162.1;0.770118,MA0163.1;0.0481976,MA0164.1;0.299399,MA0080.2;3.60276,MA0018.2;0.573973,MA0099.2;5.16563,MA0079.2;2.41527,MA0102.2;0.723908,MA0258.1;1.01576,MA0259.1;0.226086,MA0442.1;0
}}

Latest revision as of 14:49, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:116704465..116704476,-p10@Jmjd6
Mm9::chr11:118073291..118073298,+p@chr11:118073291..118073298
+
Mm9::chr11:59355103..59355117,+p5@Nlrp3
Mm9::chr11:86391025..86391039,+p@chr11:86391025..86391039
+
Mm9::chr11:86400692..86400711,+p@chr11:86400692..86400711
+
Mm9::chr11:86400731..86400756,+p@chr11:86400731..86400756
+
Mm9::chr12:109688622..109688625,+p@chr12:109688622..109688625
+
Mm9::chr12:79962011..79962040,+p@chr12:79962011..79962040
+
Mm9::chr12:8528735..8528745,+p@chr12:8528735..8528745
+
Mm9::chr13:49283322..49283330,-p@chr13:49283322..49283330
-
Mm9::chr13:49283366..49283380,-p@chr13:49283366..49283380
-
Mm9::chr13:49283525..49283536,+p@chr13:49283525..49283536
+
Mm9::chr13:49283571..49283585,+p@chr13:49283571..49283585
+
Mm9::chr13:49283614..49283630,+p@chr13:49283614..49283630
+
Mm9::chr13:83711523..83711548,+p@chr13:83711523..83711548
+
Mm9::chr13:83711549..83711571,+p@chr13:83711549..83711571
+
Mm9::chr15:31279954..31279962,+p@chr15:31279954..31279962
+
Mm9::chr15:41444122..41444133,+p@chr15:41444122..41444133
+
Mm9::chr15:77631187..77631221,+p@chr15:77631187..77631221
+
Mm9::chr15:77631245..77631256,+p@chr15:77631245..77631256
+
Mm9::chr15:93229050..93229061,-p4@Zcrb1
Mm9::chr15:98397940..98397947,-p8@Ccnt1
Mm9::chr15:98398020..98398051,-p3@Ccnt1
Mm9::chr16:11456391..11456393,-p@chr16:11456391..11456393
-
Mm9::chr17:29518694..29518700,+p@chr17:29518694..29518700
+
Mm9::chr17:3115120..3115134,+p7@Scaf8
Mm9::chr17:3115707..3115720,-p@chr17:3115707..3115720
-
Mm9::chr17:34115682..34115684,-p1@ENSMUST00000174250
Mm9::chr17:44873311..44873322,-p13@Runx2
Mm9::chr17:46210659..46210702,-p@chr17:46210659..46210702
-
Mm9::chr17:6005539..6005550,+p@chr17:6005539..6005550
+
Mm9::chr17:88511949..88511988,+p@chr17:88511949..88511988
+
Mm9::chr18:46684671..46684706,-p@chr18:46684671..46684706
-
Mm9::chr18:65858142..65858165,-p@chr18:65858142..65858165
-
Mm9::chr19:6299726..6299748,+p@chr19:6299726..6299748
+
Mm9::chr1:130602006..130602019,+p@chr1:130602006..130602019
+
Mm9::chr1:133904057..133904080,-p@chr1:133904057..133904080
-
Mm9::chr1:163696854..163696864,-p@chr1:163696854..163696864
-
Mm9::chr1:66863459..66863496,-p@chr1:66863459..66863496
-
Mm9::chr2:102784406..102784417,+p@chr2:102784406..102784417
+
Mm9::chr2:103785312..103785350,+p@chr2:103785312..103785350
+
Mm9::chr2:116798113..116798135,+p@chr2:116798113..116798135
+
Mm9::chr2:128254063..128254087,+p@chr2:128254063..128254087
+
Mm9::chr2:151798685..151798694,-p@chr2:151798685..151798694
-
Mm9::chr2:151798696..151798710,-p@chr2:151798696..151798710
-
Mm9::chr2:151799939..151799953,-p9@Fam110a
Mm9::chr2:167200841..167200854,+p@chr2:167200841..167200854
+
Mm9::chr2:65026794..65026831,-p@chr2:65026794..65026831
-
Mm9::chr3:82859516..82859531,+p3@Plrg1
Mm9::chr3:9984225..9984242,+p@chr3:9984225..9984242
+
Mm9::chr5:110877458..110877473,-p4@Fbrsl1
Mm9::chr5:122841750..122841771,-p@chr5:122841750..122841771
-
Mm9::chr5:130647683..130647749,+p1@Rabgef1
Mm9::chr5:147644379..147644392,-p@chr5:147644379..147644392
-
Mm9::chr5:5420244..5420262,-p@chr5:5420244..5420262
-
Mm9::chr5:87233407..87233418,+p8@Ythdc1
Mm9::chr6:149142423..149142427,+p@chr6:149142423..149142427
+
Mm9::chr6:42299691..42299716,-p@chr6:42299691..42299716
-
Mm9::chr7:106198452..106198493,-p@chr7:106198452..106198493
-
Mm9::chr7:148127357..148127360,-p@chr7:148127357..148127360
-
Mm9::chr8:86715959..86716007,-p@chr8:86715959..86716007
-
Mm9::chr8:86724759..86724774,+p@chr8:86724759..86724774
+
Mm9::chr8:86725523..86725567,-p@chr8:86725523..86725567
-
Mm9::chrX:101176568..101176577,-p4@Rlim
Mm9::chrX:71491076..71491108,-p@chrX:71491076..71491108
-


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:0010324membrane invagination0.00968472649411227
GO:0006897endocytosis0.00968472649411227
GO:0016044membrane organization and biogenesis0.0169885790271681
GO:0016070RNA metabolic process0.0239212496634755
GO:0043654recognition of apoptotic cell0.0242151975017805
GO:0016192vesicle-mediated transport0.0345675601230205
GO:0010467gene expression0.0345675601230205
GO:0003676nucleic acid binding0.0345675601230205
GO:0043283biopolymer metabolic process0.0345675601230205
GO:0003677DNA binding0.0345675601230205
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0345675601230205
GO:0043277apoptotic cell clearance0.0345675601230205
GO:0045879negative regulation of smoothened signaling pathway0.0345675601230205
GO:0040036regulation of fibroblast growth factor receptor signaling pathway0.0345675601230205
GO:0005681spliceosome0.0355754810325557
GO:0042487regulation of odontogenesis of dentine-containing teeth0.0355754810325557
GO:0017069snRNA binding0.0355754810325557
GO:0005768endosome0.041610011908597
GO:0043231intracellular membrane-bound organelle0.041610011908597
GO:0043227membrane-bound organelle0.041610011908597
GO:0008380RNA splicing0.041610011908597
GO:0042116macrophage activation0.0439517138307661
GO:0060041retina development in camera-type eye0.0453140336107808
GO:0048821erythrocyte development0.0453140336107808



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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic cell5.64e-2632
hematopoietic oligopotent progenitor cell5.64e-2632
hematopoietic stem cell5.64e-2632
angioblastic mesenchymal cell5.64e-2632
hematopoietic multipotent progenitor cell5.64e-2632
lymphoid lineage restricted progenitor cell2.72e-2412
lymphocyte2.68e-2213
common lymphoid progenitor2.68e-2213
T cell1.91e-2111
pro-T cell1.91e-2111
connective tissue cell2.00e-1946
mesenchymal cell2.00e-1946
nucleate cell8.22e-1816
leukocyte1.15e-1617
nongranular leukocyte1.15e-1617
mature alpha-beta T cell3.30e-169
alpha-beta T cell3.30e-169
immature T cell3.30e-169
mature T cell3.30e-169
immature alpha-beta T cell3.30e-169
motile cell5.01e-1654
stem cell1.64e-1597
CD4-positive, alpha-beta T cell1.58e-138
hematopoietic lineage restricted progenitor cell4.29e-1325
somatic stem cell6.96e-1291
multi fate stem cell6.96e-1291
thymocyte2.06e-086
double negative thymocyte2.06e-086
naive T cell2.06e-086
double-positive, alpha-beta thymocyte2.06e-086
CD4-positive, alpha-beta thymocyte2.06e-086
naive thymus-derived CD4-positive, alpha-beta T cell2.06e-086
DN4 thymocyte2.06e-086
DN1 thymic pro-T cell2.06e-086
DN2 thymocyte2.06e-086
DN3 thymocyte2.06e-086
immature single positive thymocyte2.06e-086
early T lineage precursor2.06e-086
mature CD4 single-positive thymocyte2.06e-086
resting double-positive thymocyte2.06e-086
double-positive blast2.06e-086
CD69-positive double-positive thymocyte2.06e-086
CD69-positive, CD4-positive single-positive thymocyte2.06e-086
CD4-positive, CD8-intermediate double-positive thymocyte2.06e-086
CD24-positive, CD4 single-positive thymocyte2.06e-086
somatic cell3.11e-08118
common myeloid progenitor5.44e-0819

Uber Anatomy
Ontology termp-valuen
connective tissue2.00e-1946

Disease
Ontology termp-valuen
musculoskeletal system cancer1.10e-103
muscle cancer1.10e-103


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)
MA0003.10.382646
MA0004.10.291955
MA0006.10.367556
MA0007.10.264348
MA0009.10.482714
MA0014.10.183094
MA0017.10.0855882
MA0019.10.254769
MA0024.10.136175
MA0025.10.840394
MA0027.11.61241
MA0028.10.811934
MA0029.10.787566
MA0030.10.128331
MA0031.10.110801
MA0038.10.341749
MA0040.10.167138
MA0041.10.0241609
MA0042.10.147987
MA0043.10.623818
MA0046.10.180835
MA0048.10.0907375
MA0050.10.612884
MA0051.10.356522
MA0052.10.985598
MA0055.10.139639
MA0056.10
MA0057.10.110069
MA0058.10.640728
MA0059.10.466773
MA0060.10.0166702
MA0061.12.7916
MA0063.10
MA0066.10.323968
MA0067.10.397426
MA0068.12.08096
MA0069.10.171998
MA0070.10.498463
MA0071.10.610326
MA0072.10.161558
MA0073.11.40865
MA0074.10.110954
MA0076.10.755089
MA0077.10.45654
MA0078.10.184832
MA0081.11.80401
MA0083.11.8244
MA0084.10.676467
MA0087.10.558334
MA0088.10.0330858
MA0089.10
MA0090.10.230817
MA0091.10.158194
MA0092.10.635077
MA0093.10.431087
MA0095.10
MA0098.10
MA0100.10.023969
MA0101.11.33174
MA0103.10.190019
MA0105.10.535708
MA0106.10.427153
MA0107.12.27124
MA0108.20.990877
MA0109.10
MA0111.10.443356
MA0113.11.04309
MA0114.10.125162
MA0115.10.220288
MA0116.10.229425
MA0117.10.199875
MA0119.10.168873
MA0122.11.79376
MA0124.10.35604
MA0125.10.300895
MA0130.10
MA0131.10.909841
MA0132.10
MA0133.10
MA0135.10.24238
MA0136.12.19346
MA0139.10.671048
MA0140.10.76358
MA0141.10.0503163
MA0142.10.339483
MA0143.10.406106
MA0144.10.0294811
MA0145.10.114255
MA0146.10.383724
MA0147.10.254714
MA0148.10.32325
MA0149.10.00459441
MA0062.22.51332
MA0035.20.77919
MA0039.21.40988
MA0138.20.241368
MA0002.20.375398
MA0137.20.370774
MA0104.20.309103
MA0047.20.0371401
MA0112.20.419552
MA0065.20.823415
MA0150.13.14294
MA0151.10
MA0152.10.146996
MA0153.10.705792
MA0154.10.516824
MA0155.10.547511
MA0156.13.30852
MA0157.10.0897789
MA0158.10
MA0159.11.98864
MA0160.10.554176
MA0161.10
MA0162.10.770118
MA0163.10.0481976
MA0164.10.299399
MA0080.23.60276
MA0018.20.573973
MA0099.25.16563
MA0079.22.41527
MA0102.20.723908
MA0258.11.01576
MA0259.10.226086
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:169&oldid=3072168"