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MCL coexpression mm9:508: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000838!2.58e-25!12;CL:0000791!1.61e-23!9;CL:0000789!1.61e-23!9;CL:0002420!1.61e-23!9;CL:0002419!1.61e-23!9;CL:0000790!1.61e-23!9;CL:0000542!3.45e-23!13;CL:0000051!3.45e-23!13;CL:0000084!3.88e-23!11;CL:0000827!3.88e-23!11;CL:0000624!3.27e-21!8;CL:0002242!2.10e-18!16;CL:0000738!3.47e-17!17;CL:0002087!3.47e-17!17;CL:0000893!2.06e-16!6;CL:0002489!2.06e-16!6;CL:0000898!2.06e-16!6;CL:0000809!2.06e-16!6;CL:0000810!2.06e-16!6;CL:0000895!2.06e-16!6;CL:0000808!2.06e-16!6;CL:0000894!2.06e-16!6;CL:0000806!2.06e-16!6;CL:0000807!2.06e-16!6;CL:0000805!2.06e-16!6;CL:0002425!2.06e-16!6;CL:0002436!2.06e-16!6;CL:0002427!2.06e-16!6;CL:0002428!2.06e-16!6;CL:0002429!2.06e-16!6;CL:0002433!2.06e-16!6;CL:0002431!2.06e-16!6;CL:0002432!2.06e-16!6;CL:0002031!2.37e-15!25;CL:0000988!3.53e-15!32;CL:0002032!3.53e-15!32;CL:0000037!3.53e-15!32;CL:0000566!3.53e-15!32;CL:0000837!3.53e-15!32;CL:0002320!1.48e-09!46;CL:0000134!1.48e-09!46;CL:0000219!1.15e-07!54
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002370!5.80e-40!23;UBERON:0000974!5.80e-40!23;UBERON:0004807!5.80e-40!23;UBERON:0005058!5.80e-40!23;UBERON:0003351!5.80e-40!23;UBERON:0009113!5.80e-40!23;UBERON:0003295!5.80e-40!23;UBERON:0009722!5.80e-40!23;UBERON:0005562!5.80e-40!23;UBERON:0007690!5.80e-40!23;UBERON:0006562!4.14e-38!24;UBERON:0003408!4.14e-38!24;UBERON:0001557!4.14e-38!24;UBERON:0001042!4.14e-38!24;UBERON:0008814!4.14e-38!24;UBERON:0009145!4.14e-38!24;UBERON:0004177!4.53e-34!29;UBERON:0005057!4.53e-34!29;UBERON:0000072!2.25e-33!27;UBERON:0000077!2.02e-27!35;UBERON:0002193!2.86e-25!48;UBERON:0002405!2.86e-25!48;UBERON:0002390!8.08e-25!45;UBERON:0003061!8.08e-25!45;UBERON:0000063!1.03e-24!35;UBERON:0007811!6.68e-24!36;UBERON:0000065!1.95e-20!41;UBERON:0001004!7.65e-20!42;UBERON:0000153!2.82e-19!43;UBERON:0003929!4.29e-14!55;UBERON:0002368!1.50e-12!60;UBERON:0002530!3.03e-11!65;UBERON:0000490!5.23e-11!66;UBERON:0003081!2.16e-10!87;UBERON:0005911!2.44e-10!69;UBERON:0000949!1.00e-09!72;UBERON:0002384!1.48e-09!46;UBERON:0001041!2.24e-09!80;UBERON:0000064!1.71e-08!99
|tfbs_overrepresentation_for_novel_motifs=0.224466,0.462564,0.204219,0.25808,0.391122,0.269875,0.346405,0.0669598,0.251553,0.236908,0.308886,0.336042,0.511203,0.357027,0.134875,0,0.530547,1.24126,0.470307,0.465097,0.176628,0.329508,0.937489,0.388504,0.210021,0.381085,0.781016,0.287195,0.154744,0.338204,0.275529,0.624931,0.373899,0.176308,0.135203,0.0302663,0.111136,0.332941,0.322338,0.0808072,0.121091,0.279796,0.145909,0.423138,0.314995,0.24907,0.457618,0.300372,1.25814,0.156829,0.514446,1.04423,0.584697,0.759566,0.776306,0.363247,0.163199,0.325117,0.190698,0.36147,0.606104,0.413233,0.0784106,0.504093,0.372973,0.541429,0.908031,1.25063,0.60172,1.10561,0.189925,0.246154,0.0681764,0.808562,0.181606,0.37844,0.17621,0.447339,0.590017,0.179738,0.247973,0.546623,0.411949,0.227715,0.69807,0.00290338,5.57794,0.958261,0.462057,1.41118,0.975915,0.702809,1.5387,0.401201,0.0951738,1.5019,0.233568,0.639644,0.457849,1.21972,0.358446,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.296997,0.539826,0.177945,0.218949,0.744577,1.02113,0.313258,0.982794,0.381263,0.189757,0.26114,0.53175,1.17709,0.813766,1.21719,0.382687,1.13466,1.03573,0.593478,0.353461,1.52534,0.906557,1.31219,0.726634,1.29819,0.877862,0.375176,1.0039,3.48353,0.231086,0.280962,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.280171,0.460443,1.73788,1.22575,0.124893,0.148959,0.0106906,0.761071,0.29706,0.374365,0.839715,0.405736,0.143092,0.633366,0.230865,0.96517,0.697256,0.593895,0.21719,0.50503,0.367885,0.722157,0.33468,0.0249603
}}

Latest revision as of 15:25, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:13713621..13713634,+p@chr10:13713621..13713634
+
Mm9::chr15:66633139..66633161,-p4@Sla
Mm9::chr16:78559794..78559797,-p@chr16:78559794..78559797
-
Mm9::chr17:35804606..35804622,+p@chr17:35804606..35804622
+
Mm9::chr19:10793612..10793616,-p@chr19:10793612..10793616
-
Mm9::chr19:10793908..10793920,-p@chr19:10793908..10793920
-
Mm9::chr19:29597656..29597665,-p1@A930007I19Rik
Mm9::chr19:34291685..34291717,+p5@Stambpl1
Mm9::chr1:36836791..36836797,+p@chr1:36836791..36836797
+
Mm9::chr6:41091281..41091292,+p@chr6:41091281..41091292
+
Mm9::chr6:41091296..41091306,+p@chr6:41091296..41091306
+
Mm9::chr7:148514080..148514108,-p4@Deaf1
Mm9::chr7:85864254..85864265,+p@chr7:85864254..85864265
+
Mm9::chr7:85864308..85864335,+p@chr7:85864308..85864335
+


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><br>

Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell2.58e-2512
mature alpha-beta T cell1.61e-239
alpha-beta T cell1.61e-239
immature T cell1.61e-239
mature T cell1.61e-239
immature alpha-beta T cell1.61e-239
lymphocyte3.45e-2313
common lymphoid progenitor3.45e-2313
T cell3.88e-2311
pro-T cell3.88e-2311
CD4-positive, alpha-beta T cell3.27e-218
nucleate cell2.10e-1816
leukocyte3.47e-1717
nongranular leukocyte3.47e-1717
thymocyte2.06e-166
double negative thymocyte2.06e-166
naive T cell2.06e-166
double-positive, alpha-beta thymocyte2.06e-166
CD4-positive, alpha-beta thymocyte2.06e-166
naive thymus-derived CD4-positive, alpha-beta T cell2.06e-166
DN4 thymocyte2.06e-166
DN1 thymic pro-T cell2.06e-166
DN2 thymocyte2.06e-166
DN3 thymocyte2.06e-166
immature single positive thymocyte2.06e-166
early T lineage precursor2.06e-166
mature CD4 single-positive thymocyte2.06e-166
resting double-positive thymocyte2.06e-166
double-positive blast2.06e-166
CD69-positive double-positive thymocyte2.06e-166
CD69-positive, CD4-positive single-positive thymocyte2.06e-166
CD4-positive, CD8-intermediate double-positive thymocyte2.06e-166
CD24-positive, CD4 single-positive thymocyte2.06e-166
hematopoietic lineage restricted progenitor cell2.37e-1525
hematopoietic cell3.53e-1532
hematopoietic oligopotent progenitor cell3.53e-1532
hematopoietic stem cell3.53e-1532
angioblastic mesenchymal cell3.53e-1532
hematopoietic multipotent progenitor cell3.53e-1532
connective tissue cell1.48e-0946
mesenchymal cell1.48e-0946
motile cell1.15e-0754

Uber Anatomy
Ontology termp-valuen
thymus5.80e-4023
neck5.80e-4023
respiratory system epithelium5.80e-4023
hemolymphoid system gland5.80e-4023
pharyngeal epithelium5.80e-4023
thymic region5.80e-4023
pharyngeal gland5.80e-4023
entire pharyngeal arch endoderm5.80e-4023
thymus primordium5.80e-4023
early pharyngeal endoderm5.80e-4023
pharynx4.14e-3824
gland of gut4.14e-3824
upper respiratory tract4.14e-3824
chordate pharynx4.14e-3824
pharyngeal arch system4.14e-3824
pharyngeal region of foregut4.14e-3824
hemopoietic organ4.53e-3429
immune organ4.53e-3429
segment of respiratory tract2.25e-3327
mixed endoderm/mesoderm-derived structure2.02e-2735
hemolymphoid system2.86e-2548
immune system2.86e-2548
hematopoietic system8.08e-2545
blood island8.08e-2545
organ segment1.03e-2435
craniocervical region6.68e-2436
respiratory tract1.95e-2041
respiratory system7.65e-2042
anterior region of body2.82e-1943
gut epithelium4.29e-1455
endocrine gland1.50e-1260
gland3.03e-1165
unilaminar epithelium5.23e-1166
lateral plate mesoderm2.16e-1087
endo-epithelium2.44e-1069
endocrine system1.00e-0972
connective tissue1.48e-0946
foregut2.24e-0980
organ part1.71e-0899


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)
MA0003.10.0263311
MA0004.10.258473
MA0006.10.412095
MA0007.10.689082
MA0009.10.649874
MA0014.10.0625332
MA0017.10.150118
MA0019.11.2076
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.10.138956
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.12.43453
MA0042.12.36259
MA0043.10.74191
MA0046.10.683926
MA0048.10.289404
MA0050.11.43876
MA0051.11.00935
MA0052.10.669354
MA0055.10.0652519
MA0056.10
MA0057.10.0252827
MA0058.10.183941
MA0059.10.19314
MA0060.10.0819399
MA0061.10.32765
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.10.112041
MA0069.10.669676
MA0070.10.660488
MA0071.10.788348
MA0072.10.652465
MA0073.17.69017
MA0074.10.340281
MA0076.10.163664
MA0077.10.632005
MA0078.10.418168
MA0081.10.605506
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.0649199
MA0089.10
MA0090.10.653402
MA0091.10.269175
MA0092.10.231323
MA0093.10.144649
MA0095.10
MA0098.10
MA0100.10.879972
MA0101.10.57968
MA0103.10.477056
MA0105.10.0444807
MA0106.10.425111
MA0107.10.46624
MA0108.21.25225
MA0109.10
MA0111.10.242308
MA0113.10.400008
MA0114.10.0981613
MA0115.10.744589
MA0116.10.131762
MA0117.10.713754
MA0119.10.580747
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.940193
MA0139.10.231431
MA0140.10.879752
MA0141.10.171891
MA0142.10.547747
MA0143.11.06535
MA0144.11.11784
MA0145.10.189432
MA0146.10.0854135
MA0147.10.107632
MA0148.10.271704
MA0149.10.204102
MA0062.20.39919
MA0035.21.5961
MA0039.20.584904
MA0138.20.469076
MA0002.20.87145
MA0137.20.97737
MA0104.20.257564
MA0047.20.380343
MA0112.20.189423
MA0065.20.0159336
MA0150.10.246295
MA0151.10
MA0152.10.990823
MA0153.10.792819
MA0154.10.118426
MA0155.10.423059
MA0156.10.949678
MA0157.10.518122
MA0158.10
MA0159.10.738546
MA0160.10.274172
MA0161.10
MA0162.10.108524
MA0163.10.0112325
MA0164.10.357779
MA0080.20.467794
MA0018.20.366212
MA0099.20.463355
MA0079.20.0981045
MA0102.21.35579
MA0258.10.626814
MA0259.10.101001
MA0442.10
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