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MCL coexpression mm9:623: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000838!2.83e-22!12;CL:0000084!1.65e-20!11;CL:0000827!1.65e-20!11;CL:0000542!2.55e-20!13;CL:0000051!2.55e-20!13;CL:0000791!4.73e-18!9;CL:0000789!4.73e-18!9;CL:0002420!4.73e-18!9;CL:0002419!4.73e-18!9;CL:0000790!4.73e-18!9;CL:0000988!9.11e-18!32;CL:0002032!9.11e-18!32;CL:0000037!9.11e-18!32;CL:0000566!9.11e-18!32;CL:0000837!9.11e-18!32;CL:0000624!4.50e-16!8;CL:0002242!6.29e-16!16;CL:0000738!8.25e-15!17;CL:0002087!8.25e-15!17;CL:0002031!1.52e-14!25;CL:0000893!1.83e-12!6;CL:0002489!1.83e-12!6;CL:0000898!1.83e-12!6;CL:0000809!1.83e-12!6;CL:0000810!1.83e-12!6;CL:0000895!1.83e-12!6;CL:0000808!1.83e-12!6;CL:0000894!1.83e-12!6;CL:0000806!1.83e-12!6;CL:0000807!1.83e-12!6;CL:0000805!1.83e-12!6;CL:0002425!1.83e-12!6;CL:0002436!1.83e-12!6;CL:0002427!1.83e-12!6;CL:0002428!1.83e-12!6;CL:0002429!1.83e-12!6;CL:0002433!1.83e-12!6;CL:0002431!1.83e-12!6;CL:0002432!1.83e-12!6;CL:0002320!3.02e-12!46;CL:0000134!3.02e-12!46;CL:0000219!1.15e-09!54;CL:0000034!1.88e-07!97
|ontology_enrichment_disease=DOID:0060100!5.81e-07!3;DOID:4045!5.81e-07!3
|ontology_enrichment_uberon=UBERON:0002370!4.12e-15!23;UBERON:0000974!4.12e-15!23;UBERON:0004807!4.12e-15!23;UBERON:0005058!4.12e-15!23;UBERON:0003351!4.12e-15!23;UBERON:0009113!4.12e-15!23;UBERON:0003295!4.12e-15!23;UBERON:0009722!4.12e-15!23;UBERON:0005562!4.12e-15!23;UBERON:0007690!4.12e-15!23;UBERON:0002193!6.48e-15!48;UBERON:0002405!6.48e-15!48;UBERON:0002390!1.08e-14!45;UBERON:0003061!1.08e-14!45;UBERON:0004177!1.32e-14!29;UBERON:0005057!1.32e-14!29;UBERON:0006562!2.53e-14!24;UBERON:0003408!2.53e-14!24;UBERON:0001557!2.53e-14!24;UBERON:0001042!2.53e-14!24;UBERON:0008814!2.53e-14!24;UBERON:0009145!2.53e-14!24;UBERON:0000077!5.07e-13!35;UBERON:0000065!8.51e-13!41;UBERON:0001004!2.26e-12!42;UBERON:0000072!2.60e-12!27;UBERON:0002384!3.02e-12!46;UBERON:0000063!1.16e-08!35;UBERON:0007811!2.53e-08!36;UBERON:0005911!2.54e-07!69;UBERON:0001041!4.20e-07!80
|tfbs_overrepresentation_for_novel_motifs=0.737036,0.2332,0.686572,0.303186,0.922539,0.847245,0.396495,0.0908011,0.658686,0.336879,1.67609,0.385627,0.0909495,0.407615,0.974258,0,0.587245,0.150639,0.586013,0.33293,0.215242,0.725792,0.406794,0.155356,0.701128,1.93601,0.265362,0.334131,0.191143,0.438367,0.860721,0.683831,0.14899,0.234079,0.169391,0.406983,0.142225,0.995071,0.398832,0.347926,0.466602,0.326286,0.668798,0.508662,0.153213,0.293566,0.512146,0.34807,0.337012,0.564214,0.570705,0.457464,0.419161,0.82076,0.837732,0.414119,0.200484,0.37415,0.0716833,1.0604,0.664611,0.46618,1.14744,0.560059,1.08652,0.598412,0.970969,1.3158,0.660133,1.17005,1.21364,0.313987,0.251765,0.870406,0.240236,0.483805,1.81769,0.50152,0.648171,0.218647,0.0952669,0.60374,0.464847,0.0868537,0.758319,0.580776,0.237482,0.766772,1.28512,1.47691,1.03946,0.763136,0.696137,0.16091,0.12392,0.11194,0.299765,0.698838,0.512384,0.0434558,0.438441,0.683562,0.803823,0.571268,0.57027,0.3259,0.627019,0.344504,0.222586,0.216685,0.261228,0.805555,0.626352,0.361667,1.04639,0.152197,1.04217,0.826326,1.43693,0.43155,0.875675,0.540309,1.94166,0.500675,1.09972,0.651709,0.403884,0.689622,0.969481,0.95011,0.787341,0.296885,0.940498,0.426575,1.06766,0.440587,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,0.326684,0.515065,1.80426,0.276297,0.927992,0.445509,0.209642,0.822286,0.370892,0.425729,0.901933,0.458393,0.52735,0.73227,0.752802,1.02862,0.757491,0.652135,0.25933,0.561023,0.418964,0.858861,0.384198,2.50591
}}

Latest revision as of 15:37, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:55973950..55973977,+p4@Rpl24
p4@Zbtb11
Mm9::chr19:53497833..53497852,-p@chr19:53497833..53497852
-
Mm9::chr2:126326367..126326411,-p6@Atp8b4
Mm9::chr4:48056512..48056524,+p@chr4:48056512..48056524
+
Mm9::chr4:8764875..8764901,+p@chr4:8764875..8764901
+
Mm9::chr4:8764972..8764983,+p@chr4:8764972..8764983
+
Mm9::chr5:32435323..32435338,-p3@Gm10463
Mm9::chr7:31941380..31941419,-p@chr7:31941380..31941419
-
Mm9::chr7:88138900..88138902,+p@chr7:88138900..88138902
+
Mm9::chr8:83538765..83538841,-p1@Usp38
Mm9::chr8:87185489..87185504,-p@chr8:87185489..87185504
-
Mm9::chr9:45753710..45753714,-p@chr9:45753710..45753714
-


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

no results for this coexpression

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
lymphoid lineage restricted progenitor cell2.83e-2212
T cell1.65e-2011
pro-T cell1.65e-2011
lymphocyte2.55e-2013
common lymphoid progenitor2.55e-2013
mature alpha-beta T cell4.73e-189
alpha-beta T cell4.73e-189
immature T cell4.73e-189
mature T cell4.73e-189
immature alpha-beta T cell4.73e-189
hematopoietic cell9.11e-1832
hematopoietic oligopotent progenitor cell9.11e-1832
hematopoietic stem cell9.11e-1832
angioblastic mesenchymal cell9.11e-1832
hematopoietic multipotent progenitor cell9.11e-1832
CD4-positive, alpha-beta T cell4.50e-168
nucleate cell6.29e-1616
leukocyte8.25e-1517
nongranular leukocyte8.25e-1517
hematopoietic lineage restricted progenitor cell1.52e-1425
thymocyte1.83e-126
double negative thymocyte1.83e-126
naive T cell1.83e-126
double-positive, alpha-beta thymocyte1.83e-126
CD4-positive, alpha-beta thymocyte1.83e-126
naive thymus-derived CD4-positive, alpha-beta T cell1.83e-126
DN4 thymocyte1.83e-126
DN1 thymic pro-T cell1.83e-126
DN2 thymocyte1.83e-126
DN3 thymocyte1.83e-126
immature single positive thymocyte1.83e-126
early T lineage precursor1.83e-126
mature CD4 single-positive thymocyte1.83e-126
resting double-positive thymocyte1.83e-126
double-positive blast1.83e-126
CD69-positive double-positive thymocyte1.83e-126
CD69-positive, CD4-positive single-positive thymocyte1.83e-126
CD4-positive, CD8-intermediate double-positive thymocyte1.83e-126
CD24-positive, CD4 single-positive thymocyte1.83e-126
connective tissue cell3.02e-1246
mesenchymal cell3.02e-1246
motile cell1.15e-0954
stem cell1.88e-0797

Uber Anatomy
Ontology termp-valuen
thymus4.12e-1523
neck4.12e-1523
respiratory system epithelium4.12e-1523
hemolymphoid system gland4.12e-1523
pharyngeal epithelium4.12e-1523
thymic region4.12e-1523
pharyngeal gland4.12e-1523
entire pharyngeal arch endoderm4.12e-1523
thymus primordium4.12e-1523
early pharyngeal endoderm4.12e-1523
hemolymphoid system6.48e-1548
immune system6.48e-1548
hematopoietic system1.08e-1445
blood island1.08e-1445
hemopoietic organ1.32e-1429
immune organ1.32e-1429
pharynx2.53e-1424
gland of gut2.53e-1424
upper respiratory tract2.53e-1424
chordate pharynx2.53e-1424
pharyngeal arch system2.53e-1424
pharyngeal region of foregut2.53e-1424
mixed endoderm/mesoderm-derived structure5.07e-1335
respiratory tract8.51e-1341
respiratory system2.26e-1242
segment of respiratory tract2.60e-1227
connective tissue3.02e-1246
organ segment1.16e-0835
craniocervical region2.53e-0836
endo-epithelium2.54e-0769
foregut4.20e-0780

Disease
Ontology termp-valuen
musculoskeletal system cancer5.81e-073
muscle cancer5.81e-073


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)
MA0003.10.829197
MA0004.10.819913
MA0006.10.496735
MA0007.10.290695
MA0009.11.68923
MA0014.11.34901
MA0017.10.546298
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.992869
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.648006
MA0043.10.802848
MA0046.10.743934
MA0048.10.0440103
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.10.10681
MA0056.10
MA0057.10.983678
MA0058.11.18867
MA0059.11.22696
MA0060.10.713464
MA0061.10.40468
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.647449
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.11.69472
MA0074.10.390075
MA0076.11.10234
MA0077.10.691048
MA0078.10.471303
MA0081.10.702944
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.24301
MA0089.10
MA0090.10.27428
MA0091.11.52754
MA0092.10.274547
MA0093.11.01857
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.240622
MA0103.10.566591
MA0105.10.226879
MA0106.10.478503
MA0107.10.555009
MA0108.20.557195
MA0109.10
MA0111.10.286331
MA0113.10.452439
MA0114.10.797973
MA0115.10.805567
MA0116.10.165534
MA0117.10.774259
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.11.05128
MA0139.10.61859
MA0140.10.379562
MA0141.10.603844
MA0142.10.604892
MA0143.10.467531
MA0144.10.807435
MA0145.10.494714
MA0146.11.9229
MA0147.10.845188
MA0148.10.317692
MA0149.10.245177
MA0062.21.31267
MA0035.20.383789
MA0039.21.12665
MA0138.20.523978
MA0002.20.627335
MA0137.20.207733
MA0104.21.1126
MA0047.20.431964
MA0112.21.15536
MA0065.20.79588
MA0150.10.290598
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.11.03999
MA0155.11.71283
MA0156.11.72768
MA0157.10.574484
MA0158.10
MA0159.10.446593
MA0160.10.85749
MA0161.10
MA0162.12.12712
MA0163.10.962545
MA0164.10.408402
MA0080.22.37215
MA0018.20.417217
MA0099.21.28797
MA0079.24.18363
MA0102.21.42135
MA0258.11.23793
MA0259.10.130633
MA0442.10
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